Gramene Release 39 - October 2013

Gramene Database:

• Genomes
• Maps and Markers
• Proteins
• Ontologies
• Genes
• QTL
• Pathways
• Diversity
• Germplasm
• Literature
• Website

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Genomes Release Notes

[ top ]

• Added complete genome reference sequence for Triticum aestivum (bread wheat).
• Updated Oryza sativa japonica to the first merged IRGSP v1.0 (MSU7) assembly.
• Updated Oryza glaberrima variation data.
• Projected O. sativa variations to the new assembly.
• Updated peptide comparative genomics.
• Updated whole genome alignments for O. sativa against all other species.
• Updated synteny data for O. sativa against all other Liliopsida genomes.
• Updated synteny data for Zea mays against Sorghum bicolor.
• Updated probe alignments projected to the new O. sativa assembly.
• Updated BioMarts.
• Updated genome browser, database schema and API to Ensembl version 73.

Genomes Core

	Species	Assembly	Gene Annotation
New
	Triticum aestivum	IWGSP1	IWGSP1
Updated
	Oryza sativa japonica	IRGSP-1.0 / MSU 7.0	IRGSP-1.0 / MSU 7.0
Unchanged
	Aegilops tauschii	ASM34733v1	GCA_000347335.1
	Arabidopsis lyrata	Araly1.0	Araly1.0
	Arabidopsis thaliana	TAIR10	TAIR10
	Brachypodium distachyon	Brachy1.0	Barchy1.2
	Brassica rapa	IVFCAASv1	bra_v1.01_SP2010_01
	Chlamydomonas reinhardtii	v3.0	2007-11-ENA
	Cyanidioschyzon merolae	2008-11-ENA	ASM9120v1
	Glycine max (soybean)	Glyma1.0	Glyma1.1
	Hordeum vulgare (barley)	030312v2	IBSC_1.0
	Medicago truncatula	MedtrA17_3.5	2011-11-EnsemblPlants
	Musa acuminata (banana)	MA1	2012-08-Cirad
	Oryza barthii	OGE.2012Jul	2012-10-CSHL
	Oryza brachyantha	OGEv1.4b	OGEv1.4
	Oryza glaberrima	AGI1.1 (May 2011)	2011-05-AGI
	Oryza sativa indica	ASM465v1	2010-07-BGI
	Oryza punctata	Mar 2013	CSHL Mar 2013
	Physcomitrella patens	ASM242v1	2011-03-Phypa1.6
	Populus trichocarpa	JGI 2.0	2010-01-JGI
	Selaginella moellendorffii	v1.0	2011-05-ENA
	Setaria italica (foxtail millet)	JGIv2.0	JGIv2.1
	Solanum lycopersicum (tomato)	SL2.40	ITAG2.3
	Solanum tuberosum (potato)	3.0	SolTub_3.0
	Sorghum bicolor	Sorbi1	2007-12-JGI
	Triticum urartu	ASM34745v1	GCA_000347455.1
	Vitis vinifera	IGGP 12x	2012-07-CRIBI
	Zea mays (corn)	B73_RefGen_v3	5b+
	Leersia perrieri (chr3s)	454.pools.2012Feb	2012-10-CSHL
	Oryza glumaepatula (chr3s)	454.pools.2012Feb	2012-04-CSHL
	Oryza granulata (chr3s)	454.pools.2012Feb	2012-10-CSHL
	Oryza longistaminata (chr3s)	OGE.2012Jul	2012-10-CSHL
	Oryza meridionalis (chr3s)	454.pools.2012Feb	2012-04-CSHL
	Oryza minuta (BB) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza minuta (CC) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza nivara (AA) chr3s	454.pools.1.1 (Jul 2010)	CSHL
	Oryza officinallis (CC) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza rufipogon (AA) chr3s	454.pools.1.1 (Jul 2010)	CSHL
	Oryza rufipogon (AA) FPC	OMAP_FPC_2006_JAN

Ensembl Variation

Updated	Oryza glaberrima
	Oryza sativa

Unchanged	Arabidopsis thaliana
	Brachypodium sylvaticum
	Hordeum vulgare
	Sorghum bicolor
	Triticum aestivum
	Vitis vinifera
	Zea mays

Functional Genomics

No updates in this release. Last update done in release 34 (October 2011).

Compara

• Gene Tree

  • The EnsemblCompara GeneTree database was updated. A total of 40,594 GeneTree families were constructed comprising 791,918 individual genes (910,023 input proteins) from 30 genomes, of which 5 are non-plant outgroups.
  • The OGE Compara tree was not updated. Last update was done in release 38 (August 2013). Note: The OGE Compara tree was pulled out from the website since they were build on the obsolete MSU6 gene model.

• Potential gene annotation artifacts

No new split gene annotations were identified for this release. Last update was done in release 38 (August 2013). For a complete list, see Gramene's FTP site. Summary statistics follow.

Split genes by species

Species	Count
Arabidopsis lyrata subsp. lyrata	172
Arabidopsis thaliana	34
Brachypodium distachyon	150
Brassica rapa subsp. pekinensis	150
Chlamydomonas reinhardtii	96
Cyanidioschyzon merolae	8
Glycine max	404
Hordeum vulgare subsp. vulgare	56
Musa acuminata	1558
Oryza barthi	1
Oryza brachyantha	334
Oryza glaberrima	436
Oryza sativa Indica Group	730
Oryza sativa Japonica Group	628
Physcomitrella patens subsp. patens	248
Populus trichocarpa	2076
Selaginella moellendorffii	172
Setaria italica	362
Solanum lycopersicum	1138
Solanum tuberosum	648
Sorghum bicolor	1036
Vitis vinifera	876
Zea mays	1160

• Synteny

  No updates in this release. Last update done in release 36b (March 2013).

• WGA

  New whole-genome barley alignments to B. distachyon and O. sativa (rice).

Protein Annotation, Go, Xref

No updates in this release. Last updated done in release 36 (December 2012).

Mart

• New Plant Gene and Plant Variation Marts

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Maps and Markers Release Notes

[ top ] No updates in this release. Last updated done in release 33 (April 2011). Gramene's comparative maps database hosts 215 map sets from genetic, physical, bin, sequence, cytogenetic, and QTL studies.

See also the detailed Map Module statistics report.

Marker breakdown by type

Marker Type Count AFLP 8,149 Breakpoint Interval 303 Centromere 57 Chromosomal Segment 10 Clone 3,549,765 Cytological Structure 8 DArT 1,158 Deletion 333 EST 18,974,596 EST Cluster 4,633,006/td> FISH Probe 37 FPC 17,479 Gene 8,916 Gene Candidate 17 Gene Family 3 Gene Prediction 354,564 Gene Primer 19 Genomic DNA 1,827,315 GSS 9,459,811 Insertion 308 ISBP 691 Lapsed Locus 4 Maize Bin 114 Microarray Probe 260,656 mRNA 953,688 Oligo 2,396,466 OVERGO 23,921 Point 332 Primer 76,036 Probed Site 5,220 Pseudogene 1 QTL 11,625 RAPD 175 Restriction Fragment 5 RFLP 18,754 SNP 2,942 SSR 24,389 STS 3,290 Telomere 20 Transposable Element 4 Undefined 1,391

Marker breakdown by species Species Count Hordeum 713,300 Zea 7,604,538 Avena 71,594 Oryza 6,739,198 Secale 15,058 Sorghum 1,513,436 Saccharum 44,2434 Triticum 1,432,375

See also the detailed Marker Module statistics report.

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Proteins Release Notes

[ top ] No updates in this release. Last update done in release 31 (May 2010).

The Gramene protein database provides a heterogeneous set of functional annotations from sources such as SWISS-PROT and TrEMBL, and which include Pfam, Prosite, and Interpro assignments. Various ontologies such as Gene Ontology (GO), Plant Ontologies (PO), Trait Ontology (TO) and Environment Ontology (EO) are used to attribute functional characteristics.

See also the detailed Protein Module statistics report.

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Ontologies Release Notes

[ top ]

Various ontologies and their associations to genes, gene models, proteins, QTL, markers and maps were updated. Below is a summary of the ontologies data.

Prefix	Term Type	Count
EO	plant_environment_ontology	500
GO	biological_process	24767
GO	cellular_component	3194
GO	molecular_function	10376
GRO	cereal_plant_growth_stage	235
GR_tax	gramene_taxonomy	58550
PO	plant_anatomy	1295
PO	plant_structure_development_stage	324
TO	plant_trait_ontology	1290

See also the detailed Ontology Module statistics report.

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Genes and Alleles Release Notes

[ top ] No updates in this release. Last update done in release 31 (May 2010).

A more detailed genes database statistics report can be found here.

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QTL Release Notes

[ top ] No updates in this release. Last update done in release 27 (April 2008).

A more detailed QTL database statistics report can be found here.

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Pathways Release Notes (version 3.6)

[ top ]

RiceCyc Summary (version 3.3) Class Count Pathways 316 Enzymatic Reactions 2,103 Transport Reactions 87 Polypeptides 47,894 Enzymes 6,040 Transporters 603 Compounds 1,543

BrachyCyc Summary (version 2.0) Class Count Pathways 327 Enzymatic Reactions 2,057 Transport Reactions 87 Polypeptides 26,633 Enzymes 7,723 Transporters 950 Compounds 1,641

MaizeCyc Summary (version 2.1) Class Count Pathways 428 Enzymatic Reactions 2,132 Transport Reactions 106 Polypeptides 39,655 Enzymes 8,887 Transporters 305 Compounds 1,453

SorghumCyc Summary (version 1.1) Class Count Pathways 302 Enzymatic Reactions 1,838 Transport Reactions 9 Polypeptides 36,347 Enzymes 10,636 Transporters 269 Compounds 1,356

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Diversity Release Notes

[ top ]

Data sets

Unchanged:

Arabidopsis, B. sylvaticum, H. vulgare, O. glaberiima, O. sativa spp, V. vinifera and Z. mays.

Software

Tassel

No updates in this release. Last update done in release 35 (June 2012). TASSEL 4.0 coming up on Gramene. Meanwhile, available from the TASSEL webpage.

SNP query

No updates in this release. Last update done in release 34 (October 2011).

Association Viewer

Explore Atwell GWAS data in our Association Viewer (beta).

Click here for database summary.

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Germplasm

[ top ] No updates in this release. Last update done in release 34 (October 2011).

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Literature

[ top ]

Analysis of the bread wheat genome using whole-genome shotgun sequencing. Brenchley R, Spannagl M, Pfeifer M, Barker GL, D'Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D, Kay S, Waite D, Trick M, Bancroft I, Gu Y, Huo N, Luo MC, Sehgal S, Gill B, Kianian S, Anderson O, Kersey P, Dvorak J, McCombie WR, Hall A, Mayer KF, Edwards KJ, Bevan MW, Hall N. (2012). Nature 491(7426):705-10.

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Website

[ top ]

Distributed Annotation System

Gramene provides a DAS server for our own markers and sequences database as well as our Ensembl databases. These can use by the Ensembl genome browser as well as outside applications with a need to display sequences annotations on our various genome assemblies. Substantial improvements to the architecture should improve performance and usability considerably.

Our DAS resources make use of FastBit for the retrieval engine. We offer DAS tracks for sixteen species. See our DAS sources.

Diversity via GDPC/TASSEL

The TASSEL program via Genomic Diversity and Phenotype Connection (GDPC) can connect to Gramene's genetic diversity databases for rice, maize, and arabidopsis for detailed analysis by the user.

Web Services

Gramene's web services page documents many ways to directly connect to and analyze our databases.

Programmatic access to Gramene is now available through the RESTful Ensembl API.

Public MySQL Server

Gramene provides direct MySQL access to our core Ensembl databases for each of our sequenced genomes as well our databases for markers, sequences, genes, QTL and ontologies. To connect, use the following: mysql -hgramenedb.gramene.org -pgramene

Gramene Release 38 - August 2013

Gramene Database:

• Genomes
• Maps and Markers
• Proteins
• Ontologies
• Genes
• QTL
• Pathways
• Diversity
• Germplasm
• Literature
• Website

---

Genomes Release Notes

[ top ]

• Added complete genome reference sequence for Triticum urartu (einkorn wheat).
• Added complete genome reference sequence for Aegilops tauschii (goatgrass).
• Updated gene split model predictions for 23 reference genomes.
• Added bread wheat genome alignments to barley.
• Updated barley variation data.
• Updated BioMarts.
• Updated genome browser, database schema and API to Ensembl version 72.
• Revised vitamin B pathways in MaizeCyc version 2.1, according to the review by Gerdes et al. 2012 (J Exp Bot.63:5379-95)
• Added 12 new rice pathways to the Plant Reactome.

Genomes Core

	Species	Assembly	Gene Annotation
New
	Triticum urartu	ASM34745v1	GCA_000347455.1
	Aegilops tauschii	ASM34733v1	GCA_000347335.1
Unchanged
	Arabidopsis lyrata	Araly1.0	Araly1.0
	Arabidopsis thaliana	TAIR10	TAIR10
	Brachypodium distachyon	Brachy1.0	Barchy1.2
	Brassica rapa	IVFCAASv1	bra_v1.01_SP2010_01
	Chlamydomonas reinhardtii	v3.0	2007-11-ENA
	Cyanidioschyzon merolae	2008-11-ENA	ASM9120v1
	Glycine max (soybean)	Glyma1.0	Glyma1.1
	Hordeum vulgare (barley)	030312v2	IBSC_1.0
	Medicago truncatula	MedtrA17_3.5	2011-11-EnsemblPlants
	Musa acuminata (banana)	MA1	2012-08-Cirad
	Oryza barthii	OGE.2012Jul	2012-10-CSHL
	Oryza brachyantha	OGEv1.4b	OGEv1.4
	Oryza glaberrima	AGI1.1 (May 2011)	2011-05-AGI
	Oryza sativa indica	ASM465v1	2010-07-BGI
	Oryza punctata	Mar 2013	CSHL Mar 2013
	Oryza sativa japonica	MSU 6.0	MSU 6.0
	Physcomitrella patens	ASM242v1	2011-03-Phypa1.6
	Populus trichocarpa	JGI 2.0	2010-01-JGI
	Selaginella moellendorffii	v1.0	2011-05-ENA
	Setaria italica (foxtail millet)	JGIv2.0	JGIv2.1
	Solanum lycopersicum (tomato)	SL2.40	ITAG2.3
	Solanum tuberosum (potato)	3.0	SolTub_3.0
	Sorghum bicolor	Sorbi1	2007-12-JGI
	Vitis vinifera	IGGP 12x	2012-07-CRIBI
	Zea mays (corn)	B73_RefGen_v3	5b+
	Leersia perrieri (chr3s)	454.pools.2012Feb	2012-10-CSHL
	Oryza glumaepatula (chr3s)	454.pools.2012Feb	2012-04-CSHL
	Oryza granulata (chr3s)	454.pools.2012Feb	2012-10-CSHL
	Oryza longistaminata (chr3s)	OGE.2012Jul	2012-10-CSHL
	Oryza meridionalis (chr3s)	454.pools.2012Feb	2012-04-CSHL
	Oryza minuta (BB) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza minuta (CC) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza nivara (AA) chr3s	454.pools.1.1 (Jul 2010)	CSHL
	Oryza officinallis (CC) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza rufipogon (AA) chr3s	454.pools.1.1 (Jul 2010)	CSHL
	Oryza rufipogon (AA) FPC	OMAP_FPC_2006_JAN

Ensembl Variation

Updated	Hordeum vulgare

Unchanged	Arabidopsis thaliana
	Brachypodium sylvaticum
	Oryza glaberrima
	Oryza sativa
	Sorghum bicolor
	Triticum aestivum
	Vitis vinifera
	Zea mays

Functional Genomics

No updates in this release. Last update done in release 34 (October 2011).

Compara

• Gene Tree

  • The EnsemblCompara GeneTree database was not updated. Last update done in release 36 (December 2012).
  • The OGE Compara tree as rebuilt with 16 OGE species + 3 outgroups (Sb, At, Bd). A total of 18,916 GeneTree families were constructed, comprising 285,714 individual genes.

• Potential gene annotation artifacts

De novo split gene annotations were identified for this release, see our FTP site. Summary statistics follow.

Split genes by species

Species	Count
Arabidopsis lyrata subsp. lyrata	172
Arabidopsis thaliana	34
Brachypodium distachyon	150
Brassica rapa subsp. pekinensis	150
Chlamydomonas reinhardtii	96
Cyanidioschyzon merolae	8
Glycine max	404
Hordeum vulgare subsp. vulgare	56
Musa acuminata	1558
Oryza barthi	1
Oryza brachyantha	334
Oryza glaberrima	436
Oryza sativa Indica Group	730
Oryza sativa Japonica Group	628
Physcomitrella patens subsp. patens	248
Populus trichocarpa	2076
Selaginella moellendorffii	172
Setaria italica	362
Solanum lycopersicum	1138
Solanum tuberosum	648
Sorghum bicolor	1036
Vitis vinifera	876
Zea mays	1160

• Synteny

  No updates in this release. Last update done in release 36b (March 2013).

• WGA

  New whole-genome barley alignments to B. distachyon and O. sativa (rice).

Protein Annotation, Go, Xref

No updates in this release. Last updated done in release 36 (December 2012).

Mart

• New Plant Gene and Plant Variation Marts

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Maps and Markers Release Notes

[ top ] No updates in this release. Last updated done in release 33 (April 2011). Gramene's comparative maps database hosts 215 map sets from genetic, physical, bin, sequence, cytogenetic, and QTL studies.

See also the detailed Map Module statistics report.

Marker breakdown by type

Marker Type Count AFLP 8,149 Breakpoint Interval 303 Centromere 57 Chromosomal Segment 10 Clone 3,549,765 Cytological Structure 8 DArT 1,158 Deletion 333 EST 18,974,596 EST Cluster 4,633,006/td> FISH Probe 37 FPC 17,479 Gene 8,916 Gene Candidate 17 Gene Family 3 Gene Prediction 354,564 Gene Primer 19 Genomic DNA 1,827,315 GSS 9,459,811 Insertion 308 ISBP 691 Lapsed Locus 4 Maize Bin 114 Microarray Probe 260,656 mRNA 953,688 Oligo 2,396,466 OVERGO 23,921 Point 332 Primer 76,036 Probed Site 5,220 Pseudogene 1 QTL 11,625 RAPD 175 Restriction Fragment 5 RFLP 18,754 SNP 2,942 SSR 24,389 STS 3,290 Telomere 20 Transposable Element 4 Undefined 1,391

Marker breakdown by species Species Count Hordeum 713,300 Zea 7,604,538 Avena 71,594 Oryza 6,739,198 Secale 15,058 Sorghum 1,513,436 Saccharum 44,2434 Triticum 1,432,375

See also the detailed Marker Module statistics report.

---

Proteins Release Notes

[ top ] No updates in this release. Last update done in release 31 (May 2010).

The Gramene protein database provides a heterogeneous set of functional annotations from sources such as SWISS-PROT and TrEMBL, and which include Pfam, Prosite, and Interpro assignments. Various ontologies such as Gene Ontology (GO), Plant Ontologies (PO), Trait Ontology (TO) and Environment Ontology (EO) are used to attribute functional characteristics.

See also the detailed Protein Module statistics report.

---

Ontologies Release Notes

[ top ]

Various ontologies and their associations to genes, gene models, proteins, QTL, markers and maps were updated. Below is a summary of the ontologies data.

Prefix	Term Type	Count
EO	plant_environment_ontology	500
GO	biological_process	24767
GO	cellular_component	3194
GO	molecular_function	10376
GRO	cereal_plant_growth_stage	235
GR_tax	gramene_taxonomy	58550
PO	plant_anatomy	1295
PO	plant_structure_development_stage	324
TO	plant_trait_ontology	1290

See also the detailed Ontology Module statistics report.

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Genes and Alleles Release Notes

[ top ] No updates in this release. Last update done in release 31 (May 2010).

A more detailed genes database statistics report can be found here.

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QTL Release Notes

[ top ] No updates in this release. Last update done in release 27 (April 2008).

A more detailed QTL database statistics report can be found here.

---

Pathways Release Notes (version 3.6)

[ top ]

MaizeCyc is now updated to version 2.1. Vitamin B biosynthesis in maize has been updated according to the review by Gerdes et al. 2012 (J Exp Bot.63:5379-95). The 7 revised B vitamin pathways include multiple sub pathways allocated to different cellular compartments and transport reactions that link pathway components in the different cellular compartments. The Rice Reactome has been updated with 12 new pathways (ABA biosynthesis and signaling, Cholesterol biosynthesis I, Fatty acid activation/Acyl-CoA synthetase pathway, Glycolipd Desaturation, Lipid-A-precursor biosynthesis, Coenzyme A biosynthesis, Glutathione biosynthesis, Glutathione Redox reactions I, Glutathione Redox reactions II, NAD biosynthesis I-from aspartate, Pantothenate and CoA biosynthesis III, Pyridoxamine anabolism).

RiceCyc Summary (version 3.3) Class Count Pathways 316 Enzymatic Reactions 2,103 Transport Reactions 87 Polypeptides 47,894 Enzymes 6,040 Transporters 603 Compounds 1,543

BrachyCyc Summary (version 2.0) Class Count Pathways 327 Enzymatic Reactions 2,057 Transport Reactions 87 Polypeptides 26,633 Enzymes 7,723 Transporters 950 Compounds 1,641

MaizeCyc Summary (version 2.1) Class Count Pathways 428 Enzymatic Reactions 2,132 Transport Reactions 106 Polypeptides 39,655 Enzymes 8,887 Transporters 305 Compounds 1,453

SorghumCyc Summary (version 1.1) Class Count Pathways 302 Enzymatic Reactions 1,838 Transport Reactions 9 Polypeptides 36,347 Enzymes 10,636 Transporters 269 Compounds 1,356

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Diversity Release Notes

[ top ]

Data sets

Unchanged:

Arabidopsis, B. sylvaticum, H. vulgare, O. glaberiima, O. sativa spp, V. vinifera and Z. mays.

Software

Tassel

No updates in this release. Last update done in release 35 (June 2012). TASSEL 4.0 coming up on Gramene. Meanwhile, available from the TASSEL webpage.

SNP query<> No updates in this release. Last update done in release 34 (October 2011).

Association Viewer

Explore Atwell GWAS data in our Association Viewer (beta).

Click here for database summary.

---

Germplasm

[ top ] No updates in this release. Last update done in release 34 (October 2011).

---

Literature

[ top ]

• Ling-H-Q, Zhao-S, Liu-D, Sun-H, Zhang-C, Fan-H, Li-D, Dong-L, Tao-Y, Gao-C, Li-Y, Cui-Y, Guo-X, Zheng-S, Wang-B, Yu-K, Liang-Q, Yang-W, Lou-X, Chen-J, Feng-M, Jian-J, Luo-G, Jiang-Y, Liu-J, Wang-Z, Sha-Y, Zhang-B, Wu-H, Tang-D, Shen-Q, Xue-P, Zou-S, Wang-X, Liu-X, Wang-F, Yang-Y, An-X, Dong-Z, Zhang-K, Zhang-X, Luo-M-C, Dvorak-J, Tong-Y, Yang-H, Li-Z, Wang-D, Zhang-A, Wang-J, "Draft genome of the wheat A-genome progenitor Triticum urartu", Nature, 2013, vol. 496, pp. 87-90
• Jia-J, Zhao-S, Kong-X, Li-Y, Zhao-G, He-W, Pfeifer-M, Tao-Y, Zhang-X, Jing-R, Zhang-C, Ma-Y, Gao-L, Gao-C, Spannagl-M, Mayer-K-F, Li-D, Pan-S, Zheng-F, Hu-Q, Xia-X, Li-J, Liang-Q, Chen-J, Wicker-T, Gou-C, Kuang-H, He-G, Luo-Y, Xia-Q, Lu-P, Zou-H, Zhang-R, Xu-J, Gao-J, Middleton-C, Quan-Z, Liu-G, Yang-H, Liu-X, He-Z, Mao-L, Wang-J, Feuillet-C, Eversole-K, Keller-B, Dvorak-J, Gill-B, Ogihara-Y, Appels-R, "Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation", Nature, 2013, vol. 496, pp. 91-95
• Gerdes-S, Lerma-Ortiz-C, Frelin-O, Seaver-S-M, Henry-C-S, de-Crecy-Lagard-V, Hanson-A-D, "Plant B vitamin pathways and their compartmentation: a guide for the perplexed", J Exp Bot, 2012, vol. 63
• Foulon-V, Antonenkov-V-D, Croes-K, Waelkens-E, Mannaerts-G-P, Van-Veldhoven-P-P, Casteels-M, "Purification, molecular cloning, and expression of 2-hydroxyphytanoyl-CoA lyase, a peroxisomal thiamine pyrophosphate-dependent enzyme that catalyzes the carbon-carbon bond cleavage during alpha-oxidation of 3-methyl-branched fatty acids", Proc Natl Acad Sci U S A, 1999, vol. 96, pp. 10039-10044
• Farre-E-M, Tiessen-A, Roessner-U, Geigenberger-P, Trethewey-R-N, Willmitzer-L, "Analysis of the compartmentation of glycolytic intermediates, nucleotides, sugars, organic acids, amino acids, and sugar alcohols in potato tubers using a nonaqueous fractionation method", Plant Physiol, 2001, vol. 127, pp. 685-700
• Ottenhof-H-H, Ashurst-J-L, Whitney-H-M, Saldanha-S-A, Schmitzberger-F, Gweon-H-S, Blundell-T-L, Abell-C, Smith-A-G, "Organisation of the pantothenate (vitamin B5) biosynthesis pathway in higher plants", Plant J, 2004, vol. 37, pp. 61-72
• Goyer-A, Johnson-T-L, Olsen-L-J, Collakova-E, Shachar-Hill-Y, Rhodes-D, Hanson-A-D, "Characterization and metabolic function of a peroxisomal sarcosine and pipecolate oxidase from Arabidopsis", J Biol Chem, 2004, vol. 279, pp. 16947-16953
• Orsomando-G, de-la-Garza-R-D, Green-B-J, Peng-M, Rea-P-A, Ryan-T-J, Gregory-J-F-3rd, Hanson-A-D, "Plant gamma-glutamyl hydrolases and folate polyglutamates: characterization, compartmentation, and co-occurrence in vacuoles", J Biol Chem, 2005, vol. 280, pp. 28877-28884
• Bedhomme-M, Hoffmann-M, McCarthy-E-A, Gambonnet-B, Moran-R-G, Rebeille-F, Ravanel-S, "Folate metabolism in plants: an Arabidopsis homolog of the mammalian mitochondrial folate transporter mediates folate import into chloroplasts", J Biol Chem, 2005, vol. 280, pp. 34823-34831
• White-P-R, "VITAMIN B(1) IN THE NUTRITION OF EXCISED TOMATO ROOTS", Plant Physiol, 1937, vol. 12, pp. 803-811
• Welkie-G-W, Miller-G-W, "Iron Nutrition of Nicotiana Tabacum L. in Relation to Riboflavin, Riboflavin-5-phosphate, and Flavin Adenine Dinucleotide Content", Plant Physiol, 1960, vol. 35, pp. 516-520
• Titiz-O, Tambasco-Studart-M, Warzych-E, Apel-K, Amrhein-N, Laloi-C, Fitzpatrick-T-B, "PDX1 is essential for vitamin B6 biosynthesis, development and stress tolerance in Arabidopsis", Plant J, 2006, vol. 48, pp. 933-946
• Ajjawi-I, Rodriguez-Milla-M-A, Cushman-J, Shintani-D-K, "Thiamin pyrophosphokinase is required for thiamin cofactor activation in Arabidopsis", Plant Mol Biol, 2007, vol. 65, pp. 151-162
• Robbins-W-J, Bartley-M-A, "VITAMIN B1 AND THE GROWTH OF EXCISED TOMATO ROOTS", Science, 1937, vol. 85, pp. 246-247
• Higa-A, Miyamoto-E, ur-Rahman-L, Kitamura-Y, "Root tip-dependent, active riboflavin secretion by Hyoscyamus albus hairy roots under iron deficiency", Plant Physiol Biochem, 2008, vol. 46, pp. 452-460
• Sandoval-F-J, Zhang-Y, Roje-S, "Flavin nucleotide metabolism in plants: monofunctional enzymes synthesize fad in plastids", J Biol Chem, 2008, vol. 283, pp. 30890-30900
• Giancaspero-T-A, Locato-V, de-Pinto-M-C, De-Gara-L, Barile-M, "The occurrence of riboflavin kinase and FAD synthetase ensures FAD synthesis in tobacco mitochondria and maintenance of cellular redox status", FEBS J, 2009, vol. 276, pp. 219-231
• Raichaudhuri-A, Peng-M, Naponelli-V, Chen-S, Sanchez-Fernandez-R, Gu-H, Gregory-J-F-3rd, Hanson-A-D, Rea-P-A, "Plant Vacuolar ATP-binding Cassette Transporters That Translocate Folates and Antifolates in Vitro and Contribute to Antifolate Tolerance in Vivo", J Biol Chem, 2009, vol. 284, pp. 8449-8460
• Palmieri-F, Rieder-B, Ventrella-A, Blanco-E, Do-P-T, Nunes-Nesi-A, Trauth-A-U, Fiermonte-G, Tjaden-J, Agrimi-G, Kirchberger-S, Paradies-E, Fernie-A-R, Neuhaus-H-E, "Molecular identification and functional characterization of Arabidopsis thaliana mitochondrial and chloroplastic NAD+ carrier proteins", J Biol Chem, 2009, vol. 284, pp. 31249-31259
• Eudes-A, Kunji-E-R, Noiriel-A, Klaus-S-M, Vickers-T-J, Beverley-S-M, Gregory-J-F-3rd, Hanson-A-D, "Identification of transport-critical residues in a folate transporter from the folate-biopterin transporter (FBT) family", J Biol Chem, 2010, vol. 285, pp. 2867-2875
• Goyer-A, "Thiamine in plants: aspects of its metabolism and functions", Phytochemistry, 2010, vol. 71, pp. 1615-1624
• Akhtar-T-A, Orsomando-G, Mehrshahi-P, Lara-Nunez-A, Bennett-M-J, Gregory-J-F-3rd, Hanson-A-D, "A central role for gamma-glutamyl hydrolases in plant folate homeostasis", Plant J, 2010, vol. 64, pp. 256-266
• Hanson-A-D, Gregory-J-F-3rd, "Folate biosynthesis, turnover, and transport in plants", Annu Rev Plant Biol, 2011, vol. 62, pp. 105-125
• Palmieri-F, Pierri-C-L, De-Grassi-A, Nunes-Nesi-A, Fernie-A-R, "Evolution, structure and function of mitochondrial carriers: a review with new insights", Plant J, 2011, vol. 66, pp. 161-181
• Tanabe-Y, Maruyama-J, Yamaoka-S, Yahagi-D, Matsuo-I, Tsutsumi-N, Kitamoto-K, "Peroxisomes are involved in biotin biosynthesis in Aspergillus and Arabidopsis", J Biol Chem, 2011, vol. 286, pp. 30455-30461
• Ono-Y, Kim-D-W, Watanabe-K, Sasaki-A, Niitsu-M, Berberich-T, Kusano-T, Takahashi-Y, "Constitutively and highly expressed Oryza sativa polyamine oxidases localize in peroxisomes and catalyze polyamine back conversion", Amino acids, 2012, vol. 42, pp. 867-876
• Bernhardt-K, Wilkinson-S, Weber-A-P, Linka-N, "A peroxisomal carrier delivers NAD(+) and contributes to optimal fatty acid degradation during storage oil mobilization", Plant J, 2012, vol. 69, pp. 1-13
• Jeanguenin-L, Lara-Nunez-A, Rodionov-D-A, Osterman-A-L, Komarova-N-Y, Rentsch-D, Gregory-J-F-3rd, Hanson-A-D, "Comparative genomics and functional analysis of the NiaP family uncover nicotinate transporters from bacteria, plants, and mammals", Funct Integr Genomics, 2012, vol. 12, pp. 25-34
• Rawat-R, Sandoval-F-J, Wei-Z, Winkler-R, Roje-S, "An FMN hydrolase of the haloacid dehalogenase superfamily is active in plant chloroplasts", J Biol Chem, 2011, vol. 286, pp. 42091-42098
• Frelin-O, Agrimi-G, Laera-V-L, Castegna-A, Richardson-L-G, Mullen-R-T, Lerma-Ortiz-C, Palmieri-F, Hanson-A-D, "Identification of mitochondrial thiamin diphosphate carriers from Arabidopsis and maize", Funct Integr Genomics, 2012, vol. 12, pp. 317-326
• Li-S-L, Redei-G-P, "Thiamine mutants of the crucifer, Arabidopsis", Biochem Genet, 1969, vol. 3, pp. 163-170
• Feenstra-W-J, "Isolation of nutritional mutants in Arabidopsis thaliana", Genetica, 1964, vol. 35, pp. 259-269
• Ravanel-S, Droux-M, Douce-R, "Methionine biosynthesis in higher plants. I. Purification and characterization of cystathionine gamma-synthase from spinach chloroplasts", Arch Biochem Biophys, 1995, vol. 316, pp. 572-584
• Baldet-P, Alban-C, Axiotis-S, Douce-R, "Localization of free and bound biotin in cells from green pea leaves", Arch Biochem Biophys, 1993, vol. 303, pp. 67-73
• Neuburger-M, Rebeille-F, Jourdain-A, Nakamura-S, Douce-R, "Mitochondria are a major site for folate and thymidylate synthesis in plants", J Biol Chem, 1996, vol. 271, pp. 9466-9472
• Baldet-P, Alban-C, Douce-R, "Biotin synthesis in higher plants: purification and characterization of bioB gene product equivalent from Arabidopsis thaliana overexpressed in Escherichia coli and its subcellular localization in pea leaf cells", FEBS Lett, 1997, vol. 419, pp. 206-210

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Website

[ top ]

Distributed Annotation System

Gramene provides a DAS server for our own markers and sequences database as well as our Ensembl databases. These can use by the Ensembl genome browser as well as outside applications with a need to display sequences annotations on our various genome assemblies. Substantial improvements to the architecture should improve performance and usability considerably.

Our DAS resources make use of FastBit for the retrieval engine. We offer DAS tracks for sixteen species. See our DAS sources.

Diversity via GDPC/TASSEL

The TASSEL program via Genomic Diversity and Phenotype Connection (GDPC) can connect to Gramene's genetic diversity databases for rice, maize, and arabidopsis for detailed analysis by the user.

Web Services

Gramene's web services page documents many ways to directly connect to and analyze our databases.

Programmatic access to Gramene is now available through the RESTful Ensembl API.

Public MySQL Server

Gramene provides direct MySQL access to our core Ensembl databases for each of our sequenced genomes as well our databases for markers, sequences, genes, QTL and ontologies. To connect, use the following: mysql -hgramenedb.gramene.org -pgramene

Gramene Release 37 - June 2013

Gramene Database:

• Genomes
• Maps and Markers
• Proteins
• Ontologies
• Genes
• QTL
• Pathways
• Diversity
• Germplasm
• Literature
• Website

---

Genomes Release Notes

[ top ]

• Added a new genome reference sequence for Medicago truncatula.
• Added complete genome reference sequence for Oryza punctata.
• Updated the Zea mays assembly and gene build to B73 RefGen_v3 (AGPv3).
• Updated the sequence for the chr3s of O. glumaepatula.
• Updated the sequence for the chr3s of O. granulata.
• Updated the sequence for the chr3s of O. meridionalis.
• Updated the sequence for the chr3s of Leersia perrieri.
• Updated gene split predictions for 23 reference genomes.
• Added new whole-genome barley alignments to Brachypodium distachyon and O. sativa (rice).
• Added new physical and genetic map data to the barley genome browser.
• Added a new RNA-Seq derived barley variation dataset.
• Removed some existing barley variations to meet higher standards of quality.
• Added new WGS and TSA alignments of Triticum aestivum (bread wheat) to barley.
• Added new UniGene wheat alignments to barley and Brachypodium.
• Added new FGENESH gene predictions for O. punctata
• Added new O. punctata EST/EST_cluster/mRNA alignments
• Added new O. punctata repeats annotation from AGI.
• Added new O. punctata nonCoding RNA gene annotations provided by AGI.
• Added new nonCoding RNA gene annotations to Oryza genomes including O. indica, O. barthii, O. brachyantha, O. glaberrima and chromosome 3 short arms of O. glumaepatula, O. granulata, O. longistaminata, O. meridionalis, O. minutabb, O. minutacc, O. nivara, O. officinalis, and O. rufipogon.
• Added new LASTZ pairwise whole-genome alignments:
  • Vitis vinifera vs Arabidopsis lyrata
  • V. vinifera vs Solanum tuberosum
  • V. vinifera vs M. truncatula
  • A. thaliana vs M. truncatula
  • Zea mays vs M. truncatula
• Updated Oryza EST/EST_cluster/mRNA alignments to updated chromosome 3 short arms of O. granulata, O. glumaepatula, O. meridionalis, and Leersia perrieri.
• Updated LASTZ DNA alignments between Zea mays and several genomes (Arabidopsis thaliana, Oryza sativa, Sorghum bicolor, and Setaria italica).
• Updated (projected) Zea mays variation data.
• Updated (remapped) Zea mays microarray probe mapping.
• Updated cross-references.
• Updated protein domain predictions.
• Updated peptide comparative genomics.
• Updated BioMarts.
• Updated genome browser, database schema and API to Ensembl version 71.
• Updated Pathway Tools to version 17 and reinstated compatible pathways DBs.
• Added 21 new rice pathways to the Plant Reactome (beta version).

Genomes Core

BAC.Sanger.1.1 (May 2011)CSHL v2.1

	Species	Assembly	Gene Annotation
New
	Medicago truncatula	MedtrA17_3.5	2011-11-EnsemblPlants
	Oryza punctata	Mar 2013	CSHL Mar 2013
Updated
	Zea mays (corn)	B73_RefGen_v3	5b+
Unchanged
	Arabidopsis lyrata	Araly1.0	Araly1.0
	Arabidopsis thaliana	TAIR10	TAIR10
	Brachypodium distachyon	Brachy1.0	Barchy1.2
	Brassica rapa	IVFCAASv1	bra_v1.01_SP2010_01
	Chlamydomonas reinhardtii	v3.0	2007-11-ENA
	Cyanidioschyzon merolae	2008-11-ENA	ASM9120v1
	Glycine max (soybean)	Glyma1.0	Glyma1.1
	Hordeum vulgare (barley)	030312v2	IBSC_1.0
	Musa acuminata (banana)	MA1	2012-08-Cirad
	Oryza barthii	OGE.2012Jul	2012-10-CSHL
	Oryza brachyantha	OGEv1.4b	OGEv1.4
	Oryza glaberrima	AGI1.1 (May 2011)	2011-05-AGI
	Oryza sativa indica	ASM465v1	2010-07-BGI
	Oryza sativa japonica	MSU 6.0	MSU 6.0
	Physcomitrella patens	ASM242v1	2011-03-Phypa1.6
	Populus trichocarpa	JGI 2.0	2010-01-JGI
	Selaginella moellendorffii	v1.0	2011-05-ENA
	Setaria italica (foxtail millet)	JGIv2.0	JGIv2.1
	Solanum lycopersicum (tomato)	SL2.40	ITAG2.3
	Solanum tuberosum (potato)	3.0	SolTub_3.0
	Sorghum bicolor	Sorbi1	2007-12-JGI
	Vitis vinifera	IGGP 12x	2012-07-CRIBI
	Leersia perrieri (chr3s)	454.pools.2012Feb	2012-10-CSHL
	Oryza barthii (AA) chr3s	454.pools.1.1 (Mar 2009)	CSHL
	Oryza brachyantha (FF) chr3s	454.pools.1.1 (Jul 2010)	CSHL
	Oryza glumaepatula (chr3s)	454.pools.2012Feb	2012-04-CSHL
	Oryza granulata (chr3s)	454.pools.2012Feb	2012-10-CSHL
	Oryza longistaminata (chr3s)	OGE.2012Jul	2012-10-CSHL
	Oryza meridionalis (chr3s)	454.pools.2012Feb	2012-04-CSHL
	Oryza minuta (BB) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza minuta (CC) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza nivara (AA) chr3s	454.pools.1.1 (Jul 2010)	CSHL
	Oryza officinallis (CC) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza rufipogon (AA) chr3s	454.pools.1.1 (Jul 2010)	CSHL
	Oryza rufipogon (AA) FPC	OMAP_FPC_2006_JAN

Ensembl Variation

Unchanged	Arabidopsis thaliana
	Brachypodium sylvaticum
	Oryza glaberrima
	Oryza sativa
	Triticum aestivum
	Vitis vinifera
	Zea mays

Functional Genomics

No updates in this release. Last update done in release 34 (October 2011).

Compara

• Gene Tree

  • The EnsemblCompara GeneTree database was not updated. Last update done in release 36 (December 2012).
  • The OGE Compara tree as rebuilt with 16 OGE species + 3 outgroups (Sb, At, Bd). A total of 18,916 GeneTree families were constructed, comprising 285,714 individual genes.
  (Sharon - please provide update on OGE trees)

• Potential gene annotation artifacts

De novo split gene annotations were identified for this release, see our FTP site. Summary statistics follow.

Split genes by species

Species	Count
Arabidopsis lyrata subsp. lyrata	172
Arabidopsis thaliana	34
Brachypodium distachyon	150
Brassica rapa subsp. pekinensis	150
Chlamydomonas reinhardtii	96
Cyanidioschyzon merolae	8
Glycine max	404
Hordeum vulgare subsp. vulgare	56
Musa acuminata	1558
Oryza barthi	1
Oryza brachyantha	334
Oryza glaberrima	436
Oryza sativa Indica Group	730
Oryza sativa Japonica Group	628
Physcomitrella patens subsp. patens	248
Populus trichocarpa	2076
Selaginella moellendorffii	172
Setaria italica	362
Solanum lycopersicum	1138
Solanum tuberosum	648
Sorghum bicolor	1036
Vitis vinifera	876
Zea mays	1160

• Synteny

  No updates in this release. Last update done in release 36b (March 2013).

• WGA

  New whole-genome barley alignments to B. distachyon and O. sativa (rice).

Protein Annotation, Go, Xref

No updates in this release. Last updated done in release 36 (December 2012).

Mart

• New Plant Gene and Plant Variation Marts

---

Maps and Markers Release Notes

[ top ] No updates in this release. Last updated done in release 33 (April 2011). Gramene's comparative maps database hosts 215 map sets from genetic, physical, bin, sequence, cytogenetic, and QTL studies.

See also the detailed Map Module statistics report.

Marker breakdown by type

Marker Type Count AFLP 8,149 Breakpoint Interval 303 Centromere 57 Chromosomal Segment 10 Clone 3,549,765 Cytological Structure 8 DArT 1,158 Deletion 333 EST 18,974,596 EST Cluster 4,633,006/td> FISH Probe 37 FPC 17,479 Gene 8,916 Gene Candidate 17 Gene Family 3 Gene Prediction 354,564 Gene Primer 19 Genomic DNA 1,827,315 GSS 9,459,811 Insertion 308 ISBP 691 Lapsed Locus 4 Maize Bin 114 Microarray Probe 260,656 mRNA 953,688 Oligo 2,396,466 OVERGO 23,921 Point 332 Primer 76,036 Probed Site 5,220 Pseudogene 1 QTL 11,625 RAPD 175 Restriction Fragment 5 RFLP 18,754 SNP 2,942 SSR 24,389 STS 3,290 Telomere 20 Transposable Element 4 Undefined 1,391

Marker breakdown by species Species Count Hordeum 713,300 Zea 7,604,538 Avena 71,594 Oryza 6,739,198 Secale 15,058 Sorghum 1,513,436 Saccharum 44,2434 Triticum 1,432,375

See also the detailed Marker Module statistics report.

---

Proteins Release Notes

[ top ] No updates in this release. Last update done in release 31 (May 2010).

The Gramene protein database provides a heterogeneous set of functional annotations from sources such as SWISS-PROT and TrEMBL, and which include Pfam, Prosite, and Interpro assignments. Various ontologies such as Gene Ontology (GO), Plant Ontologies (PO), Trait Ontology (TO) and Environment Ontology (EO) are used to attribute functional characteristics.

See also the detailed Protein Module statistics report.

---

Ontologies Release Notes

[ top ]

Various ontologies and their associations to genes, gene models, proteins, QTL, markers and maps were updated. Below is a summary of the ontologies data.

Prefix	Term Type	Count
EO	plant_environment_ontology	500
GO	biological_process	24767
GO	cellular_component	3194
GO	molecular_function	10376
GRO	cereal_plant_growth_stage	235
GR_tax	gramene_taxonomy	58550
PO	plant_anatomy	1295
PO	plant_structure_development_stage	324
TO	plant_trait_ontology	1290

See also the detailed Ontology Module statistics report.

---

Genes and Alleles Release Notes

[ top ] No updates in this release. Last update done in release 31 (May 2010).

A more detailed genes database statistics report can be found here.

---

QTL Release Notes

[ top ] No updates in this release. Last update done in release 27 (April 2008).

A more detailed QTL database statistics report can be found here.

---

Pathways Release Notes (version 3.6)

[ top ]

The Plant Reactome beta version was released in January of 2013 with 100 rice pathways. The count has now been increased to 121 pathways organized into 10 super-groups, and including 21 new pathways. The new rice pathways focus on carbohydrate biosnythesis, cofactor biosnythesis, and secondary metabolite biosnythesis.

Pathway databases are available dynamically via the Gramene's pathway server and for bulk download from Gramene's FTP site. Pathway databases maintained by their original source in Pathway Tools version 17 were reinstated.

RiceCyc Summary (version 3.3) Class Count Pathways 316 Enzymatic Reactions 2,103 Transport Reactions 87 Polypeptides 47,894 Enzymes 6,040 Transporters 603 Compounds 1,543

BrachyCyc Summary (version 2.0) Class Count Pathways 327 Enzymatic Reactions 2,057 Transport Reactions 87 Polypeptides 26,633 Enzymes 7,723 Transporters 950 Compounds 1,641

MaizeCyc Summary (version 2.0.2) Class Count Pathways 392 Enzymatic Reactions 2,110 Transport Reactions 68 Polypeptides 39,655 Enzymes 8,889 Transporters 291 Compounds 1,468

SorghumCyc Summary (version 1.1) Class Count Pathways 302 Enzymatic Reactions 1,838 Transport Reactions 9 Polypeptides 36,347 Enzymes 10,636 Transporters 269 Compounds 1,356

---

Diversity Release Notes

[ top ]

Data sets

Unchanged:

Arabidopsis, B. sylvaticum, H. vulgare, O. glaberiima, O. sativa spp, V. vinifera and Z. mays.

Software

Tassel

No updates in this release. Last update done in release 35 (June 2012). TASSEL 4.0 coming up on Gramene. Meanwhile, available from the TASSEL webpage.

SNP query

No updates in this release. Last update done in release 34 (October 2011).

Association Viewer

Explore Atwell GWAS data in our Association Viewer (beta).

Click here for database summary.

---

Germplasm

[ top ] No updates in this release. Last update done in release 34 (October 2011).

---

Literature

[ top ]

• Mayer-K-F, Martis-M, Hedley-P-E, Simkova-H, Liu-H, Morris-J-A, Steuernagel-B, Taudien-S, Roessner-S, Gundlach-H, Kubalakova-M, Suchankova-P, Murat-F, Felder-M, Nussbaumer-T, Graner-A, Salse-J, Endo-T, Sakai-H, Tanaka-T, Itoh-T, Sato-K, Platzer-M, Matsumoto-T, Scholz-U, Dolezel-J, Waugh-R, Stein-N, "Unlocking the barley genome by chromosomal and comparative genomics", Plant Cell, 2011, vol. 23, pp. 1249-1263
• Young-N-D, Debelle-F, Oldroyd-G-E, Geurts-R, Cannon-S-B, Udvardi-M-K, Benedito-V-A, Mayer-K-F, Gouzy-J, Schoof-H, Van-de-Peer-Y, Proost-S, Cook-D-R, Meyers-B-C, Spannagl-M, Cheung-F, De-Mita-S, Krishnakumar-V, Gundlach-H, Zhou-S, Mudge-J, Bharti-A-K, Murray-J-D, Naoumkina-M-A, Rosen-B, Silverstein-K-A, Tang-H, Rombauts-S, Zhao-P-X, Zhou-P, Barbe-V, Bardou-P, Bechner-M, Bellec-A, Berger-A, Berges-H, Bidwell-S, Bisseling-T, Choisne-N, Couloux-A, Denny-R, Deshpande-S, Dai-X, Doyle-J-J, Dudez-A-M, Farmer-A-D, Fouteau-S, Franken-C, Gibelin-C, Gish-J, Goldstein-S, Gonzalez-A-J, Green-P-J, Hallab-A, Hartog-M, Hua-A, Humphray-S-J, Jeong-D-H, Jing-Y, Jocker-A, Kenton-S-M, Kim-D-J, Klee-K, Lai-H, Lang-C, Lin-S, Macmil-S-L, Magdelenat-G, Matthews-L, McCorrison-J, Monaghan-E-L, Mun-J-H, Najar-F-Z, Nicholson-C, Noirot-C, O'Bleness-M, Paule-C-R, Poulain-J, Prion-F, Qin-B, Qu-C, Retzel-E-F, Riddle-C, Sallet-E, Samain-S, Samson-N, Sanders-I, Saurat-O, Scarpelli-C, Schiex-T, Segurens-B, Severin-A-J, Sherrier-D-J, Shi-R, Sims-S, Singer-S-R, Sinharoy-S, Sterck-L, Viollet-A, Wang-B-B, Wang-K, Wang-M, Wang-X, Warfsmann-J, Weissenbach-J, White-D-D, White-J-D, Wiley-G-B, Wincker-P, Xing-Y, Yang-L, Yao-Z, Ying-F, Zhai-J, Zhou-L, Zuber-A, Denarie-J, Dixon-R-A, May-G-D, Schwartz-D-C, Rogers-J, Quetier-F, Town-C-D, Roe-B-A, "The Medicago genome provides insight into the evolution of rhizobial symbioses", Nature, 2011, vol. 480, pp. 520-524

---

Website

[ top ]

Distributed Annotation System

Gramene provides a DAS server for our own markers and sequences database as well as our Ensembl databases. These can use by the Ensembl genome browser as well as outside applications with a need to display sequences annotations on our various genome assemblies. Substantial improvements to the architecture should improve performance and usability considerably.

Our DAS resources make use of FastBit for the retrieval engine. We offer DAS tracks for sixteen species. See our DAS sources.

Diversity via GDPC/TASSEL

The TASSEL program via Genomic Diversity and Phenotype Connection (GDPC) can connect to Gramene's genetic diversity databases for rice, maize, and arabidopsis for detailed analysis by the user.

Web Services

Gramene's web services page documents many ways to directly connect to and analyze our databases.

Programmatic access to Gramene is now available through the RESTful Ensembl API.

Public MySQL Server

Gramene provides direct MySQL access to our core Ensembl databases for each of our sequenced genomes as well our databases for markers, sequences, genes, QTL and ontologies. To connect, use the following: mysql -hgramenedb.gramene.org -pgramene

Gramene Release 36b - March 2013

Gramene Database:

• Genomes
• Maps and Markers
• Proteins
• Ontologies
• Genes
• QTL
• Pathways
• Diversity
• Germplasm
• Literature
• Website

---

Genomes Release Notes

[ top ]

• Added new sequence search service to the Triticum aestivum (bread wheat) species page.
• Added new Plant Reactome beta version featuring rice pathways.
• Added entry portal for PICARA software to support GWA studies.
• Updated 'unlocalized' chromosomes for Hordeum vulgare (barley) using arm sorted survey sequences.
• Updated stable identifiers for Vitis vinifera (grape).
• Updated RepeatMasker repeats for Solanum tuberosum (potato).
• Added gene descriptions for Musa acuminata (banana).
• Updated selenocysteine in Chlamydomonas reinhardtii (green alga) protein translations.
• Added new variation data for Hordeum vulgare (barley) from four cultivars: Barke, Bowman, Igri, Haruna Nijo, and a wild barley (H. spontaneum).
• Added new variation data for Brachypodium sylvaticum from three populations from Corvallis (Oregon, USA), Spain and Greece, mapped to Brachypodium distachyon genome (Source: Jaiswal Lab.)
• Added new EST feature alignments and transcriptomics datasets for Triticum aestivum (wheat) provided in the syntenic context of Brachypodium.
• Added new EST feature alignments and transcriptomics datasets for Solanum tuberosum (potato).
• Added new DNA-derived synteny data between Solanum tuberosum (potato) and S. lycopersicum (tomato).
• Added new whole-genome alignments for seven pairs of plant species, including alignments between Vitis vinifera (grape) and four other plant species.
• Added new whole-genome alignments for Oryza barthii (WGS), O. granulata (chr3s), O. longistaminata (chr3s), and Leersia perrieri (chr3s).
• Added new EST feature alignments for Oryza barthii (WGS), O. granulata (chr3s), O. longistaminata (chr3s), and Leersia perrieri (chr3s).
• Added new phylogenetic gene trees for Oryza barthii (WGS), O. granulata (chr3s), O. longistaminata (chr3s), and Leersia perrieri (chr3s).
• Updated BioMarts.
• Updated genome browser, database schema and API to Ensembl version 70.
• Removed mirror for pathway DBs maintained in Pathway Tools version 15.5 and higher.

Genomes Core

	Species	Assembly	Gene Annotation
Unchanged
	Arabidopsis lyrata	Araly1.0	Araly1.0
	Arabidopsis thaliana	TAIR10	TAIR10
	Brachypodium distachyon	Brachy1.0	Barchy1.2
	Brassica rapa	IVFCAASv1	bra_v1.01_SP2010_01
	Chlamydomonas reinhardtii	v3.0	2007-11-ENA
	Cyanidioschyzon merolae	2008-11-ENA	ASM9120v1
	Glycine max (soybean)	Glyma1.0	Glyma1.1
	Hordeum vulgare (barley)	030312v2	IBSC_1.0
	Musa acuminata (banana)	MA1	2012-08-Cirad
	Oryza barthii	OGE.2012Jul	2012-10-CSHL
	Oryza brachyantha	OGEv1.4b	OGEv1.4
	Oryza glaberrima	AGI1.1 (May 2011)	2011-05-AGI
	Oryza sativa indica	ASM465v1	2010-07-BGI
	Oryza sativa japonica	MSU 6.0	MSU 6.0
	Physcomitrella patens	ASM242v1	2011-03-Phypa1.6
	Populus trichocarpa	JGI 2.0	2010-01-JGI
	Selaginella moellendorffii	v1.0	2011-05-ENA
	Setaria italica (foxtail millet)	JGIv2.0	JGIv2.1
	Solanum lycopersicum (tomato)	SL2.40	ITAG2.3
	Solanum tuberosum (potato)	3.0	SolTub_3.0
	Sorghum bicolor	Sorbi1	2007-12-JGI
	Vitis vinifera	IGGP 12x	2012-07-CRIBI
	Zea mays (corn)	B73 RefGen AGPv2	5a.53
	Leersia perrieri (chr3s)	454.pools.2012Feb	2012-10-CSHL
	Oryza barthii (AA) chr3s	454.pools.1.1 (Mar 2009)	CSHL
	Oryza brachyantha (FF) chr3s	454.pools.1.1 (Jul 2010)	CSHL
	Oryza glumaepatula (chr3s)	454.pools.2012Feb	2012-04-CSHL
	Oryza granulata (chr3s)	454.pools.2012Feb	2012-10-CSHL
	Oryza longistaminata (chr3s)	OGE.2012Jul	2012-10-CSHL
	Oryza meridionalis (chr3s)	454.pools.2012Feb	2012-04-CSHL
	Oryza minuta (BB) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza minuta (CC) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza nivara (AA) chr3s	454.pools.1.1 (Jul 2010)	CSHL
	Oryza officinallis (CC) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza punctata (BB) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v2.1
	Oryza rufipogon (AA) chr3s	454.pools.1.1 (Jul 2010)	CSHL
	Oryza rufipogon (AA) FPC	OMAP_FPC_2006_JAN

Ensembl Variation

New	Brachypodium sylvaticum

Unchanged	Arabidopsis thaliana
	Oryza glaberrima
	Oryza sativa
	Triticum aestivum
	Vitis vinifera
	Zea mays

Functional Genomics

No updates in this release. Last update done in release 34 (October 2011).

Compara

• Gene Tree

  • The EnsemblCompara GeneTree database was not updated. Last update done in release 36 (December 2012).
  • The OGE Compara tree as rebuilt with 16 OGE species + 3 outgroups (Sb, At, Bd). A total of 18,916 GeneTree families were constructed, comprising 285,714 individual genes.

• Potential gene annotation artifacts

No split genes identified in this release. Last update done in release 35 (June 2012).

• Synteny

  New DNA-derived synteny data between Solanum tuberosum (potato) and Solanum lycopersicum (tomato).

• WGA

  New whole-genome alignments for Oryza barthii (WGS), O. granulata (chr3s), O. longistaminata (chr3s) and Leersia perrieri (chr3s).

Protein Annotation, Go, Xref

No updates in this release. Last updated done in release 36 (December 2012).

Mart

• New Plant Gene and Plant Variation Marts

---

Maps and Markers Release Notes

[ top ] No updates in this release. Last updated done in release 33 (April 2011). Gramene's comparative maps database hosts 215 map sets from genetic, physical, bin, sequence, cytogenetic, and QTL studies.

See also the detailed Map Module statistics report.

Marker breakdown by type

Marker Type Count AFLP 8,149 Breakpoint Interval 303 Centromere 57 Chromosomal Segment 10 Clone 3,549,765 Cytological Structure 8 DArT 1,158 Deletion 333 EST 18,974,596 EST Cluster 4,633,006/td> FISH Probe 37 FPC 17,479 Gene 8,916 Gene Candidate 17 Gene Family 3 Gene Prediction 354,564 Gene Primer 19 Genomic DNA 1,827,315 GSS 9,459,811 Insertion 308 ISBP 691 Lapsed Locus 4 Maize Bin 114 Microarray Probe 260,656 mRNA 953,688 Oligo 2,396,466 OVERGO 23,921 Point 332 Primer 76,036 Probed Site 5,220 Pseudogene 1 QTL 11,625 RAPD 175 Restriction Fragment 5 RFLP 18,754 SNP 2,942 SSR 24,389 STS 3,290 Telomere 20 Transposable Element 4 Undefined 1,391

Marker breakdown by species Species Count Hordeum 713,300 Zea 7,604,538 Avena 71,594 Oryza 6,739,198 Secale 15,058 Sorghum 1,513,436 Saccharum 44,2434 Triticum 1,432,375

See also the detailed Marker Module statistics report.

---

Proteins Release Notes

[ top ] No updates in this release. Last update done in release 31 (May 2010).

The Gramene protein database provides a heterogeneous set of functional annotations from sources such as SWISS-PROT and TrEMBL, and which include Pfam, Prosite, and Interpro assignments. Various ontologies such as Gene Ontology (GO), Plant Ontologies (PO), Trait Ontology (TO) and Environment Ontology (EO) are used to attribute functional characteristics.

See also the detailed Protein Module statistics report.

---

Ontologies Release Notes

[ top ]

Various ontologies and their associations to genes, gene models, proteins, QTL, markers and maps were updated. Below is a summary of the ontologies data.

Prefix	Term Type	Count
EO	plant_environment_ontology	500
GO	biological_process	24767
GO	cellular_component	3194
GO	molecular_function	10376
GRO	cereal_plant_growth_stage	235
GR_tax	gramene_taxonomy	58550
PO	plant_anatomy	1295
PO	plant_structure_development_stage	324
TO	plant_trait_ontology	1290

See also the detailed Ontology Module statistics report.

---

Genes and Alleles Release Notes

[ top ] No updates in this release. Last update done in release 31 (May 2010).

A more detailed genes database statistics report can be found here.

---

QTL Release Notes

[ top ] No updates in this release. Last update done in release 27 (April 2008).

A more detailed QTL database statistics report can be found here.

---

Pathways Release Notes (version 3.5)

[ top ]

Pathway databases are available dynamically via the Gramene's pathway server and for bulk download from Gramene's FTP site. Pathways databases maintained by their original source in Pathway Tools version 15.5 or higher were removed to maintain the integrity of the mirror until a software upgrade on Gramene's end is in place.

RiceCyc Summary (version 3.3) Class Count Pathways 316 Enzymatic Reactions 2,103 Transport Reactions 87 Polypeptides 47,894 Enzymes 6,040 Transporters 603 Compounds 1,543

BrachyCyc Summary (version 2.0) Class Count Pathways 327 Enzymatic Reactions 2,057 Transport Reactions 87 Polypeptides 26,633 Enzymes 7,723 Transporters 950 Compounds 1,641

MaizeCyc Summary (version 2.0.2) Class Count Pathways 392 Enzymatic Reactions 2,110 Transport Reactions 68 Polypeptides 39,655 Enzymes 8,889 Transporters 291 Compounds 1,468

SorghumCyc Summary (version 1.1) Class Count Pathways 302 Enzymatic Reactions 1,838 Transport Reactions 9 Polypeptides 36,347 Enzymes 10,636 Transporters 269 Compounds 1,356

---

Diversity Release Notes

[ top ]

Data sets

New:

Brachypodium sylvaticum. Variation data for Brachypodium sylvaticum from three populations from Corvallis (Oregon, USA), Spain and Greece, mapped to Brachypodium distachyon genome (Source: Jaiswal Lab).

Unchanged:

Arabidopsis, Oryza glaberiima, Oryza sativa spp, Vitis vinifera and Zea mays.

Software

Tassel

No updates in this release. Last update done in release 35 (June 2012). TASSEL 4.0 coming up on Gramene. Meanwhile, available from the TASSEL webpage.

SNP query

No updates in this release. Last update done in release 34 (October 2011).

Association Viewer

Explore Atwell GWAS data in our Association Viewer (beta).

Click here for database summary.

---

Germplasm

[ top ] No updates in this release. Last update done in release 34 (October 2011).

---

Literature

[ top ]

• Brown-J-W, Fincher-G-B, Zhou-R, Shi-B, Langridge-P, Madishetty-K, Svensson-J-T, Bhat-P, Moscou-M, Resnik-J, Liu-H, Frenkel-Z, Korol-A, Berges-H, Graner-A, Groth-M, Himmelbach-A, Felder-M, Lonardi-S, Duma-D, Alpert-M, Cordero-F, Beccuti-M, Ciardo-G, Ma-Y, Wanamaker-S, Cattonaro-F, Radovic-S, Wing-R, Schulte-D, Nussbaumer-T, Martis-M, Ariyadasa-R, Poursarebani-N, Poland-J, Mayer-K-F, Gundlach-H, Moisy-C, Tanskanen-J, Scalabrin-S, Zuccolo-A, Vendramin-V, Morgante-M, Schulman-A, Pfeifer-M, Spannagl-M, Hedley-P, Morris-J, Russell-J, Druka-A, Swarbreck-D, Sampath-D, Ayling-S, Febrer-M, Caccamo-M, Matsumoto-T, Tanaka-T, Wise-R-P, Close-T-J, Wannamaker-S, Muehlbauer-G-J, Steuernagel-B, Schmutzer-T, Mascher-M, Scholz-U, Taudien-S, Platzer-M, Sato-K, Marshall-D, Bayer-M, Waugh-R, Stein-N, "A physical, genetic and functional sequence assembly of the barley genome", Nature, 2012, vol. 491, pp. 711-716
• Brenchley-R, Spannagl-M, Pfeifer-M, Barker-G-L, D'Amore-R, Allen-A-M, McKenzie-N, Kramer-M, Kerhornou-A, Bolser-D, Kay-S, Waite-D, Trick-M, Bancroft-I, Gu-Y, Huo-N, Luo-M-C, Sehgal-S, Gill-B, Kianian-S, Anderson-O, Kersey-P, Dvorak-J, McCombie-W-R, Hall-A, Mayer-K-F, Edwards-K-J, Bevan-M-W, Hall-N, "Analysis of the bread wheat genome using whole-genome shotgun sequencing", Nature, 2012, vol. 491, pp. 705-710
• Fox-S, Preece-J, Kimbrel-J-A, Marchini-G-L, Sage-A, Youens-Clark-K, Cruzan-M, Jaiswal-P, "Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae)", Applications in Plant Sciences, 2013, vol. 1
• Monaco-M-K, Sen-T-Z, Dharmawardhana-P-D, Ren-L, Schaeffer-M, Naithani-S, Amarasinghe-V, Thomason-J-T, Harper-L, Gardiner-J, Cannon-E-K-S, Lawrence-C-J, Ware-D, Jaiswal-P, "Maize Metabolic Network Construction and Transcriptome Analysis", The Plant Genome, 2013, vol. 1

---

Website

[ top ]

Distributed Annotation System

Gramene provides a DAS server for our own markers and sequences database as well as our Ensembl databases. These can use by the Ensembl genome browser as well as outside applications with a need to display sequences annotations on our various genome assemblies. Substantial improvements to the architecture should improve performance and usability considerably.

Our DAS resources make use of FastBit for the retrieval engine. We offer DAS tracks for sixteen species. See our DAS sources.

Diversity via GDPC/TASSEL

The TASSEL program via Genomic Diversity and Phenotype Connection (GDPC) can connect to Gramene's genetic diversity databases for rice, maize, and arabidopsis for detailed analysis by the user.

Web Services

Gramene's web services page documents many ways to directly connect to and analyze our databases.

Programmatic access to Gramene is now available through the RESTful Ensembl API.

Public MySQL Server

Gramene provides direct MySQL access to our core Ensembl databases for each of our sequenced genomes as well our databases for markers, sequences, genes, QTL and ontologies. To connect, use the following: mysql -hgramenedb.gramene.org -pgramene

Gramene Release 36b - March 201

Gramene Database:

• Genomes
• Maps and Markers
• Proteins
• Ontologies
• Genes
• QTL
• Pathways
• Diversity
• Germplasm
• Literature
• Website

---

Genomes Release Notes

[ top ]

• Added new sequence search service to the Triticum aestivum (bread wheat) species page.
• Updated 'unlocalized' chromosomes for Hordeum vulgare (barley) using arm sorted survey sequences.
• Updated stable identifiers for Vitis vinifera (grape).
• Updated RepeatMasker repeats for Solanum tuberosum (potato).
• Added gene descriptions for Musa acuminata (banana).
• Updated selenocysteine in Chlamydomonas reinhardtii (green alga) protein translations.
• Added new variation data for Hordeum vulgare (barley) from four cultivars: Barke, Bowman, Igri, Haruna Nijo, and a wild barley (H. spontaneum).
• Added new alignments to several EST and transcriptomics datasets for Triticum aestivum (wheat) provided in the syntenic context of Brachypodium.
• Added new alignments to several EST and transcriptomics datasets for Solanum tuberosum (potato).
• Added new whole-genome alignments for Oryza barthii (WGS), O. granulata (chr3s), O. longistaminata (chr3s), and Leersia perrieri (chr3s).
• Added new phylogenetic gene trees for Oryza barthii (WGS), O. granulata (chr3s), O. longistaminata (chr3s), and Leersia perrieri (chr3s).
• Added new DNA-derived synteny data between Solanum tuberosum (potato) and S. lycopersicum (tomato).
• Updated BioMarts
• Updated genome browser, database schema and API to Ensembl version 70

Genomes Core

	Species	Assembly	Gene Annotation
New
	Hordeum vulgare (barley)	030312v2	IBSC_1.0
	Musa acuminata (banana)	MA1	2012-08-Cirad
	Solanum tuberosum (potato)	3.0	SolTub_3.0
	Oryza barthii (WGS)	OGE.2012Jul	2012-10-CSHL
	Leersia perrieri (chr3s)	454.pools.2012Feb	2012-10-CSHL
	Oryza granulata (chr3s)	454.pools.2012Feb	2012-10-CSHL
	Oryza longistaminata (chr3s)	OGE.2012Jul	2012-10-CSHL
Updated
	Glycine max (soybean)	Glyma1.0	Glyma1.1
	Vitis vinifera	IGGP 12x	2012-07-CRIBI
Unchanged
	Arabidopsis lyrata	Araly1.0	Araly1.0
	Arabidopsis thaliana	TAIR10	TAIR10
	Brachypodium distachyon	Brachy1.0	Barchy1.2
	Brassica rapa	IVFCAASv1	bra_v1.01_SP2010_01
	Chlamydomonas reinhardtii	v3.0	2007-11-ENA
	Cyanidioschyzon merolae	2008-11-ENA	ASM9120v1
	Oryza brachyantha	OGEv1.4b	OGEv1.4
	Oryza glaberrima	AGI1.1 (May 2011)	2011-05-AGI
	Oryza sativa indica	ASM465v1	2010-07-BGI
	Oryza sativa japonica	MSU 6.0	MSU 6.0
	Physcomitrella patens	ASM242v1	2011-03-Phypa1.6
	Populus trichocarpa	JGI 2.0	2010-01-JGI
	Selaginella moellendorffii	v1.0	2011-05-ENA
	Setaria italica (foxtail millet)	JGIv2.0	JGIv2.1
	Solanum lycopersicum (tomato)	SL2.40	ITAG2.3
	Sorghum bicolor	Sorbi1	2007-12-JGI
	Zea mays (corn)	B73 RefGen AGPv2	5a.53
	Oryza barthii (AA) chr3s	454.pools.1.1 (Mar 2009)	CSHL
	Oryza brachyantha (FF) chr3s	454.pools.1.1 (Jul 2010)	CSHL
	Oryza glumaepatula (chr3s)	454.pools.2012Feb	2012-04-CSHL
	Oryza meridionalis (chr3s)	454.pools.2012Feb	2012-04-CSHL
	Oryza minuta (BB) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza minuta (CC) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza nivara (AA) chr3s	454.pools.1.1 (Jul 2010)	CSHL
	Oryza officinallis (CC) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza punctata (BB) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v2.1
	Oryza rufipogon (AA) chr3s	454.pools.1.1 (Jul 2010)	CSHL
	Oryza rufipogon (AA) FPC	OMAP_FPC_2006_JAN

Ensembl Variation

Updated	Sorghum bicolor
	Zea mays

Unchanged	Arabidopsis thaliana
	Oryza glaberrima
	Oryza sativa
	Triticum aestivum
	Vitis vinifera

Functional Genomics

No updates in this release. Last update done in release 34 (October 2011).

Compara

• Gene Tree

  The EnsemblCompara GeneTree database was rebuilt using the core genome databases listed above excluding the OGE genomes, with the addition of Ciona savigny, Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae to provide taxonomic depth. A total of 40,931 GeneTree families were constructed, comprising 739,323 individual genes.

Potential gene annotation artifacts

No updates in this release. Last update done in release 35 (June 2012).

• Synteny

  No updates in this release. Last update done in release 34 (October 2011).

• WGA

  No new WGA in this release. Last update done in release 35 (June 2012).

Protein Annotation, Go, Xref

Protein feature annotations were updated using InterProScan on the following genomes:

• Arabidopsis lyrata
• Physcomitrella patens (moss)
• Glycine max (soybean)
• Zea mays
• Chlamydomonas reinhardtii

Mart

• New Plant Gene and Plant Variation Mart

---

Maps and Markers Release Notes

[ top ] No updates in this release. Last updated done in release 33 (April 2011). Gramene's comparative maps database hosts 215 map sets from genetic, physical, bin, sequence, cytogenetic, and QTL studies.

See also the detailed Map Module statistics report.

Marker breakdown by type

Marker Type Count AFLP 8,149 Breakpoint Interval 303 Centromere 57 Chromosomal Segment 10 Clone 3,549,765 Cytological Structure 8 DArT 1,158 Deletion 333 EST 18,974,596 EST Cluster 4,633,006/td> FISH Probe 37 FPC 17,479 Gene 8,916 Gene Candidate 17 Gene Family 3 Gene Prediction 354,564 Gene Primer 19 Genomic DNA 1,827,315 GSS 9,459,811 Insertion 308 ISBP 691 Lapsed Locus 4 Maize Bin 114 Microarray Probe 260,656 mRNA 953,688 Oligo 2,396,466 OVERGO 23,921 Point 332 Primer 76,036 Probed Site 5,220 Pseudogene 1 QTL 11,625 RAPD 175 Restriction Fragment 5 RFLP 18,754 SNP 2,942 SSR 24,389 STS 3,290 Telomere 20 Transposable Element 4 Undefined 1,391

Marker breakdown by species Species Count Hordeum 713,300 Zea 7,604,538 Avena 71,594 Oryza 6,739,198 Secale 15,058 Sorghum 1,513,436 Saccharum 44,2434 Triticum 1,432,375

See also the detailed Marker Module statistics report.

---

Proteins Release Notes

[ top ] No updates in this release. Last update done in release 31 (May 2010).

The Gramene protein database provides a heterogeneous set of functional annotations from sources such as SWISS-PROT and TrEMBL, and which include Pfam, Prosite, and Interpro assignments. Various ontologies such as Gene Ontology (GO), Plant Ontologies (PO), Trait Ontology (TO) and Environment Ontology (EO) are used to attribute functional characteristics.

See also the detailed Protein Module statistics report.

---

Ontologies Release Notes

[ top ]

Various ontologies and their associations to genes, gene models, proteins, QTL, markers and maps were updated. Below is a summary of the ontologies data.

Prefix	Term Type	Count
EO	plant_environment_ontology	500
GO	biological_process	24767
GO	cellular_component	3194
GO	molecular_function	10376
GRO	cereal_plant_growth_stage	235
GR_tax	gramene_taxonomy	58550
PO	plant_anatomy	1295
PO	plant_structure_development_stage	324
TO	plant_trait_ontology	1290

See also the detailed Ontology Module statistics report.

---

Genes and Alleles Release Notes

[ top ] No updates in this release. Last update done in release 31 (May 2010).

A more detailed genes database statistics report can be found here.

---

QTL Release Notes

[ top ] No updates in this release. Last update done in release 27 (April 2008).

A more detailed QTL database statistics report can be found here.

---

Pathways Release Notes (version 3.5)

[ top ]

Pathway databases are available dynamically via the Gramene's pathway server and those created and maintained by Gramene are also available for bulk download from Gramene's FTP site.

MaizeCyc has been updated to version 2.0.2

• New pathways:


• alpha-carotene biosynthesis [PWYBWI-0]
• delta-carotene biosynthesis [PWY-5946]
• epsilon-carotene biosynthesis [PWYBWI-4118]
• lutein biosynthesis [PWY-5947]
• carotenoid biosynthesis (from lycopene to carotene and xanthophyll)[PWYBWI-7081]

Literature references: Many from the Wurtzel Laboratory, including Wurtzel et al (2012); Bai et al (2009); etc.
• Flavonoid and flavonol biosynthesis pathway leading to anthocyanin biosynthesis and accumulation [PWYBWI-410]

Literature references: Sharma et al (2011), and The Maize Anthocyanin Pathway, a specialized Plant Biochemistry course at Penn State University.

Due to these edits a number of reactions and gene annotations were also added or updated.

RiceCyc Summary (version 3.3) Class Count Pathways 316 Enzymatic Reactions 2,103 Transport Reactions 87 Polypeptides 47,894 Enzymes 6,040 Transporters 603 Compounds 1,543

BrachyCyc Summary (version 2.0) Class Count Pathways 327 Enzymatic Reactions 2,057 Transport Reactions 87 Polypeptides 26,633 Enzymes 7,723 Transporters 950 Compounds 1,641

MaizeCyc Summary (version 2.0.2) Class Count Pathways 392 Enzymatic Reactions 2,110 Transport Reactions 68 Polypeptides 39,655 Enzymes 8,889 Transporters 291 Compounds 1,468

SorghumCyc Summary (version 1.1) Class Count Pathways 302 Enzymatic Reactions 1,838 Transport Reactions 9 Polypeptides 36,347 Enzymes 10,636 Transporters 269 Compounds 1,356

---

Diversity Release Notes

[ top ]

Data sets

New:

Sorghum bicolor. Structural variation data from EBI's Database of Genomic Variants Archive (dGVA) for Sorghum bicolor. Click here for an example.

Updated:

• Zea mays. Corrections to HapMap v2 data.

Unchanged:

• Arabidopsis, Oryza glaberiima, Oryza sativa spp, and Vitis vinifera

Software

Tassel

No updates in this release. Last update done in release 35 (June 2012).

SNP query

No updates in this release. Last update done in release 34 (October 2011). See also the TASSEL webpage.

Association Viewer

Explore Atwell GWAS data in our Association Viewer (beta).

Click here for database summary.

---

Germplasm

[ top ] No updates in this release. Last update done in release 34 (October 2011).

---

Literature

[ top ] New papers by Wurtzel et al.

---

Website

[ top ]

Distributed Annotation System

Gramene provides a DAS server for our own markers and sequences database as well as our Ensembl databases. These can use by the Ensembl genome browser as well as outside applications with a need to display sequences annotations on our various genome assemblies. Substantial improvements to the architecture should improve performance and usability considerably.

Our DAS resources make use of FastBit for the retrieval engine. We offer DAS tracks for sixteen species. See our DAS sources.

Diversity via GDPC/TASSEL

The TASSEL program via Genomic Diversity and Phenotype Connection (GDPC) can connect to Gramene's genetic diversity databases for rice, maize, and arabidopsis for detailed analysis by the user.

Web Services

Gramene's web services page documents many ways to directly connect to and analyze our databases.

Public MySQL Server

Gramene provides direct MySQL access to our core Ensembl databases for each of our sequenced genomes as well our databases for markers, sequences, genes, QTL and ontologies. To connect, use the following: mysql -hgramenedb.gramene.org -pgramene

Gramene Release 36b - February 2012

Gramene Database:

• Genomes
• Maps and Markers
• Proteins
• Ontologies
• Genes
• QTL
• Pathways
• Diversity
• Germplasm
• Literature
• Website

---

Genomes Release Notes

[ top ]

• Added new sequence search service to the Triticum aestivum (bread wheat) species page.
• Updated 'unlocalized' chromosomes for Hordeum vulgare (barley) using arm sorted survey sequences.
• Updated stable identifiers for Vitis vinifera (grape).
• Updated RepeatMasker repeats for Solanum tuberosum (potato).
• Added gene descriptions for Musa acuminata (banana).
• Updated selenocysteine in Chlamydomonas reinhardtii (green alga) protein translations.
• Added new variation data for Hordeum vulgare (barley) from four cultivars: Barke, Bowman, Igri, Haruna Nijo, and a wild barley (H. spontaneum).
• Added new alignments to several EST and transcriptomics datasets for Triticum aestivum (wheat) provided in the syntenic context of Brachypodium.
• Added new alignments to several EST and transcriptomics datasets for Solanum tuberosum (potato).
• Added new whole-genome alignments for Oryza barthii (WGS), O. granulata (chr3s), O. longistaminata (chr3s), and Leersia perrieri (chr3s).
• Added new phylogenetic gene trees for Oryza barthii (WGS), O. granulata (chr3s), O. longistaminata (chr3s), and Leersia perrieri (chr3s).
• Added new DNA-derived synteny data between Solanum tuberosum (potato) and S. lycopersicum (tomato).
• Updated BioMarts
• Updated genome browser, database schema and API to Ensembl version 70

Genomes Core

	Species	Assembly	Gene Annotation
New
	Hordeum vulgare (barley)	030312v2	IBSC_1.0
	Musa acuminata (banana)	MA1	2012-08-Cirad
	Solanum tuberosum (potato)	3.0	SolTub_3.0
	Oryza barthii (WGS)	OGE.2012Jul	2012-10-CSHL
	Leersia perrieri (chr3s)	454.pools.2012Feb	2012-10-CSHL
	Oryza granulata (chr3s)	454.pools.2012Feb	2012-10-CSHL
	Oryza longistaminata (chr3s)	OGE.2012Jul	2012-10-CSHL
Updated
	Glycine max (soybean)	Glyma1.0	Glyma1.1
	Vitis vinifera	IGGP 12x	2012-07-CRIBI
Unchanged
	Arabidopsis lyrata	Araly1.0	Araly1.0
	Arabidopsis thaliana	TAIR10	TAIR10
	Brachypodium distachyon	Brachy1.0	Barchy1.2
	Brassica rapa	IVFCAASv1	bra_v1.01_SP2010_01
	Chlamydomonas reinhardtii	v3.0	2007-11-ENA
	Cyanidioschyzon merolae	2008-11-ENA	ASM9120v1
	Oryza brachyantha	OGEv1.4b	OGEv1.4
	Oryza glaberrima	AGI1.1 (May 2011)	2011-05-AGI
	Oryza sativa indica	ASM465v1	2010-07-BGI
	Oryza sativa japonica	MSU 6.0	MSU 6.0
	Physcomitrella patens	ASM242v1	2011-03-Phypa1.6
	Populus trichocarpa	JGI 2.0	2010-01-JGI
	Selaginella moellendorffii	v1.0	2011-05-ENA
	Setaria italica (foxtail millet)	JGIv2.0	JGIv2.1
	Solanum lycopersicum (tomato)	SL2.40	ITAG2.3
	Sorghum bicolor	Sorbi1	2007-12-JGI
	Zea mays (corn)	B73 RefGen AGPv2	5a.53
	Oryza barthii (AA) chr3s	454.pools.1.1 (Mar 2009)	CSHL
	Oryza brachyantha (FF) chr3s	454.pools.1.1 (Jul 2010)	CSHL
	Oryza glumaepatula (chr3s)	454.pools.2012Feb	2012-04-CSHL
	Oryza meridionalis (chr3s)	454.pools.2012Feb	2012-04-CSHL
	Oryza minuta (BB) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza minuta (CC) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza nivara (AA) chr3s	454.pools.1.1 (Jul 2010)	CSHL
	Oryza officinallis (CC) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza punctata (BB) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v2.1
	Oryza rufipogon (AA) chr3s	454.pools.1.1 (Jul 2010)	CSHL
	Oryza rufipogon (AA) FPC	OMAP_FPC_2006_JAN

Ensembl Variation

Updated	Sorghum bicolor
	Zea mays

Unchanged	Arabidopsis thaliana
	Oryza glaberrima
	Oryza sativa
	Triticum aestivum
	Vitis vinifera

Functional Genomics

No updates in this release. Last update done in release 34 (October 2011).

Compara

• Gene Tree

  The EnsemblCompara GeneTree database was rebuilt using the core genome databases listed above excluding the OGE genomes, with the addition of Ciona savigny, Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae to provide taxonomic depth. A total of 40,931 GeneTree families were constructed, comprising 739,323 individual genes.

Potential gene annotation artifacts

No updates in this release. Last update done in release 35 (June 2012).

• Synteny

  No updates in this release. Last update done in release 34 (October 2011).

• WGA

  No new WGA in this release. Last update done in release 35 (June 2012).

Protein Annotation, Go, Xref

Protein feature annotations were updated using InterProScan on the following genomes:

• Arabidopsis lyrata
• Physcomitrella patens (moss)
• Glycine max (soybean)
• Zea mays
• Chlamydomonas reinhardtii

Mart

• New Plant Gene and Plant Variation Mart

---

Maps and Markers Release Notes

[ top ] No updates in this release. Last updated done in release 33 (April 2011). Gramene's comparative maps database hosts 215 map sets from genetic, physical, bin, sequence, cytogenetic, and QTL studies.

See also the detailed Map Module statistics report.

Marker breakdown by type

Marker Type Count AFLP 8,149 Breakpoint Interval 303 Centromere 57 Chromosomal Segment 10 Clone 3,549,765 Cytological Structure 8 DArT 1,158 Deletion 333 EST 18,974,596 EST Cluster 4,633,006/td> FISH Probe 37 FPC 17,479 Gene 8,916 Gene Candidate 17 Gene Family 3 Gene Prediction 354,564 Gene Primer 19 Genomic DNA 1,827,315 GSS 9,459,811 Insertion 308 ISBP 691 Lapsed Locus 4 Maize Bin 114 Microarray Probe 260,656 mRNA 953,688 Oligo 2,396,466 OVERGO 23,921 Point 332 Primer 76,036 Probed Site 5,220 Pseudogene 1 QTL 11,625 RAPD 175 Restriction Fragment 5 RFLP 18,754 SNP 2,942 SSR 24,389 STS 3,290 Telomere 20 Transposable Element 4 Undefined 1,391

Marker breakdown by species Species Count Hordeum 713,300 Zea 7,604,538 Avena 71,594 Oryza 6,739,198 Secale 15,058 Sorghum 1,513,436 Saccharum 44,2434 Triticum 1,432,375

See also the detailed Marker Module statistics report.

---

Proteins Release Notes

[ top ] No updates in this release. Last update done in release 31 (May 2010).

The Gramene protein database provides a heterogeneous set of functional annotations from sources such as SWISS-PROT and TrEMBL, and which include Pfam, Prosite, and Interpro assignments. Various ontologies such as Gene Ontology (GO), Plant Ontologies (PO), Trait Ontology (TO) and Environment Ontology (EO) are used to attribute functional characteristics.

See also the detailed Protein Module statistics report.

---

Ontologies Release Notes

[ top ]

Various ontologies and their associations to genes, gene models, proteins, QTL, markers and maps were updated. Below is a summary of the ontologies data.

Prefix	Term Type	Count
EO	plant_environment_ontology	500
GO	biological_process	24767
GO	cellular_component	3194
GO	molecular_function	10376
GRO	cereal_plant_growth_stage	235
GR_tax	gramene_taxonomy	58550
PO	plant_anatomy	1295
PO	plant_structure_development_stage	324
TO	plant_trait_ontology	1290

See also the detailed Ontology Module statistics report.

---

Genes and Alleles Release Notes

[ top ] No updates in this release. Last update done in release 31 (May 2010).

A more detailed genes database statistics report can be found here.

---

QTL Release Notes

[ top ] No updates in this release. Last update done in release 27 (April 2008).

A more detailed QTL database statistics report can be found here.

---

Pathways Release Notes (version 3.5)

[ top ]

Pathway databases are available dynamically via the Gramene's pathway server and those created and maintained by Gramene are also available for bulk download from Gramene's FTP site.

MaizeCyc has been updated to version 2.0.2

• New pathways:


• alpha-carotene biosynthesis [PWYBWI-0]
• delta-carotene biosynthesis [PWY-5946]
• epsilon-carotene biosynthesis [PWYBWI-4118]
• lutein biosynthesis [PWY-5947]
• carotenoid biosynthesis (from lycopene to carotene and xanthophyll)[PWYBWI-7081]

Literature references: Many from the Wurtzel Laboratory, including Wurtzel et al (2012); Bai et al (2009); etc.
• Flavonoid and flavonol biosynthesis pathway leading to anthocyanin biosynthesis and accumulation [PWYBWI-410]

Literature references: Sharma et al (2011), and The Maize Anthocyanin Pathway, a specialized Plant Biochemistry course at Penn State University.

Due to these edits a number of reactions and gene annotations were also added or updated.

RiceCyc Summary (version 3.3) Class Count Pathways 316 Enzymatic Reactions 2,103 Transport Reactions 87 Polypeptides 47,894 Enzymes 6,040 Transporters 603 Compounds 1,543

BrachyCyc Summary (version 2.0) Class Count Pathways 327 Enzymatic Reactions 2,057 Transport Reactions 87 Polypeptides 26,633 Enzymes 7,723 Transporters 950 Compounds 1,641

MaizeCyc Summary (version 2.0.2) Class Count Pathways 392 Enzymatic Reactions 2,110 Transport Reactions 68 Polypeptides 39,655 Enzymes 8,889 Transporters 291 Compounds 1,468

SorghumCyc Summary (version 1.1) Class Count Pathways 302 Enzymatic Reactions 1,838 Transport Reactions 9 Polypeptides 36,347 Enzymes 10,636 Transporters 269 Compounds 1,356

---

Diversity Release Notes

[ top ]

Data sets

New:

Sorghum bicolor. Structural variation data from EBI's Database of Genomic Variants Archive (dGVA) for Sorghum bicolor. Click here for an example.

Updated:

• Zea mays. Corrections to HapMap v2 data.

Unchanged:

• Arabidopsis, Oryza glaberiima, Oryza sativa spp, and Vitis vinifera

Software

Tassel

No updates in this release. Last update done in release 35 (June 2012).

SNP query

No updates in this release. Last update done in release 34 (October 2011). See also the TASSEL webpage.

Association Viewer

Explore Atwell GWAS data in our Association Viewer (beta).

Click here for database summary.

---

Germplasm

[ top ] No updates in this release. Last update done in release 34 (October 2011).

---

Literature

[ top ] New papers by Wurtzel et al.

---

Website

[ top ]

Distributed Annotation System

Gramene provides a DAS server for our own markers and sequences database as well as our Ensembl databases. These can use by the Ensembl genome browser as well as outside applications with a need to display sequences annotations on our various genome assemblies. Substantial improvements to the architecture should improve performance and usability considerably.

Our DAS resources make use of FastBit for the retrieval engine. We offer DAS tracks for sixteen species. See our DAS sources.

Diversity via GDPC/TASSEL

The TASSEL program via Genomic Diversity and Phenotype Connection (GDPC) can connect to Gramene's genetic diversity databases for rice, maize, and arabidopsis for detailed analysis by the user.

Web Services

Gramene's web services page documents many ways to directly connect to and analyze our databases.

Public MySQL Server

Gramene provides direct MySQL access to our core Ensembl databases for each of our sequenced genomes as well our databases for markers, sequences, genes, QTL and ontologies. To connect, use the following: mysql -hgramenedb.gramene.org -pgramene

Gramene Release 36 - December 2012

Gramene Database:

• Genomes
• Maps and Markers
• Proteins
• Ontologies
• Genes
• QTL
• Pathways
• Diversity
• Germplasm
• Literature
• Website

---

Genomes Release Notes

[ top ]

• Added new genomes for Hordeum vulgare (barley), Solanum tuberosum (potato), Musa acuminata (banana), Oryza barthii (WGS), O. granulata (chr3s), O. longistaminata (chr3s), and Leersia perrieri (chr3s)
• Updated gene models for Glycine max (soybean)
• Cleaned up non-translating genes in Vitis vinifera (grape)
• Added new capability to highlight functional annotations (GO terms) in phylogenetic trees
• Added new EST alignments for Physcomitrella patens (moss), Oryza brachyantha (an ancestral rice), Setaria italica (foxtail millet), and Solanum lycopersicum (tomato)
• Updated and improved Triticum aestivum (wheat) homoeologous SNPs and 'gene space' assembly alignments to Brachypodium distachyon (purple false brome)
• Improved Zea mays variation data
• Added structural variation data from dGVA for Sorghum bicolor
• Added new repeats feature annotations for Selaginella moellendorffii (lycopod)
• Added new repeats feature annotations for 15 OGE genomes by AGI
• Updated protein features for Arabidopsis lyrata, Physcomitrella patens (moss), Glycine max (soybean), Zea mays, and Chlamydomonas reinhardtii (green algae)
• Updated features were generated using InterProScan on the latest InterPro databases (including Pfam 26)
• Updated peptide comparative genomics data
• Updated BioMarts
• Updated genome browser, database schema and API to Ensembl version 69

Genomes Core

	Species	Assembly	Gene Annotation
New
	Hordeum vulgare (barley)	030312v2	IBSC_1.0
	Musa acuminata (banana)	MA1	2012-08-Cirad
	Solanum tuberosum (potato)	3.0	SolTub_3.0
	Oryza barthii (WGS)	OGE.2012Jul	2012-10-CSHL
	Leersia perrieri (chr3s)	454.pools.2012Feb	2012-10-CSHL
	Oryza granulata (chr3s)	454.pools.2012Feb	2012-10-CSHL
	Oryza longistaminata (chr3s)	OGE.2012Jul	2012-10-CSHL
Updated
	Glycine max (soybean)	Glyma1.0	Glyma1.1
	Vitis vinifera	IGGP 12x	2012-07-CRIBI
Unchanged
	Arabidopsis lyrata	Araly1.0	Araly1.0
	Arabidopsis thaliana	TAIR10	TAIR10
	Brachypodium distachyon	Brachy1.0	Barchy1.2
	Brassica rapa	IVFCAASv1	bra_v1.01_SP2010_01
	Chlamydomonas reinhardtii	v3.0	2007-11-ENA
	Cyanidioschyzon merolae	2008-11-ENA	ASM9120v1
	Oryza brachyantha	OGEv1.4b	OGEv1.4
	Oryza glaberrima	AGI1.1 (May 2011)	2011-05-AGI
	Oryza sativa indica	ASM465v1	2010-07-BGI
	Oryza sativa japonica	MSU 6.0	MSU 6.0
	Physcomitrella patens	ASM242v1	2011-03-Phypa1.6
	Populus trichocarpa	JGI 2.0	2010-01-JGI
	Selaginella moellendorffii	v1.0	2011-05-ENA
	Setaria italica (foxtail millet)	JGIv2.0	JGIv2.1
	Solanum lycopersicum (tomato)	SL2.40	ITAG2.3
	Sorghum bicolor	Sorbi1	2007-12-JGI
	Zea mays (corn)	B73 RefGen AGPv2	5a.53
	Oryza barthii (AA) chr3s	454.pools.1.1 (Mar 2009)	CSHL
	Oryza brachyantha (FF) chr3s	454.pools.1.1 (Jul 2010)	CSHL
	Oryza glumaepatula (chr3s)	454.pools.2012Feb	2012-04-CSHL
	Oryza meridionalis (chr3s)	454.pools.2012Feb	2012-04-CSHL
	Oryza minuta (BB) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza minuta (CC) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza nivara (AA) chr3s	454.pools.1.1 (Jul 2010)	CSHL
	Oryza officinallis (CC) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza punctata (BB) chr3s	BAC.Sanger.1.1 (May 2011)	CSHL v2.1
	Oryza rufipogon (AA) chr3s	454.pools.1.1 (Jul 2010)	CSHL
	Oryza rufipogon (AA) FPC	OMAP_FPC_2006_JAN

Ensembl Variation

Updated	Sorghum bicolor
	Zea mays

Unchanged	Arabidopsis thaliana
	Oryza glaberrima
	Oryza sativa
	Triticum aestivum
	Vitis vinifera

Functional Genomics

No updates in this release. Last update done in release 34 (October 2011).

Compara

• Gene Tree

  The EnsemblCompara GeneTree database was rebuilt using the core genome databases listed above excluding the OGE genomes, with the addition of Ciona savigny, Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae to provide taxonomic depth. A total of 40,931 GeneTree families were constructed, comprising 739,323 individual genes.

Potential gene annotation artifacts

No updates in this release. Last update done in release 35 (June 2012).

• Synteny

  No updates in this release. Last update done in release 34 (October 2011).

• WGA

  No new WGA in this release. Last update done in release 35 (June 2012).

Protein Annotation, Go, Xref

Protein feature annotations were updated using InterProScan on the following genomes:

• Arabidopsis lyrata
• Physcomitrella patens (moss)
• Glycine max (soybean)
• Zea mays
• Chlamydomonas reinhardtii

Mart

• New Plant Gene and Plant Variation Mart

---

Maps and Markers Release Notes

[ top ] No updates in this release. Last updated done in release 33 (April 2011). Gramene's comparative maps database hosts 215 map sets from genetic, physical, bin, sequence, cytogenetic, and QTL studies.

See also the detailed Map Module statistics report.

Marker breakdown by type

Marker Type Count AFLP 8,149 Breakpoint Interval 303 Centromere 57 Chromosomal Segment 10 Clone 3,549,765 Cytological Structure 8 DArT 1,158 Deletion 333 EST 18,974,596 EST Cluster 4,633,006/td> FISH Probe 37 FPC 17,479 Gene 8,916 Gene Candidate 17 Gene Family 3 Gene Prediction 354,564 Gene Primer 19 Genomic DNA 1,827,315 GSS 9,459,811 Insertion 308 ISBP 691 Lapsed Locus 4 Maize Bin 114 Microarray Probe 260,656 mRNA 953,688 Oligo 2,396,466 OVERGO 23,921 Point 332 Primer 76,036 Probed Site 5,220 Pseudogene 1 QTL 11,625 RAPD 175 Restriction Fragment 5 RFLP 18,754 SNP 2,942 SSR 24,389 STS 3,290 Telomere 20 Transposable Element 4 Undefined 1,391

Marker breakdown by species Species Count Hordeum 713,300 Zea 7,604,538 Avena 71,594 Oryza 6,739,198 Secale 15,058 Sorghum 1,513,436 Saccharum 44,2434 Triticum 1,432,375

See also the detailed Marker Module statistics report.

---

Proteins Release Notes

[ top ] No updates in this release. Last update done in release 31 (May 2010).

The Gramene protein database provides a heterogeneous set of functional annotations from sources such as SWISS-PROT and TrEMBL, and which include Pfam, Prosite, and Interpro assignments. Various ontologies such as Gene Ontology (GO), Plant Ontologies (PO), Trait Ontology (TO) and Environment Ontology (EO) are used to attribute functional characteristics.

See also the detailed Protein Module statistics report.

---

Ontologies Release Notes

[ top ]

Various ontologies and their associations to genes, gene models, proteins, QTL, markers and maps were updated. Below is a summary of the ontologies data.

Prefix	Term Type	Count
EO	plant_environment_ontology	500
GO	biological_process	24767
GO	cellular_component	3194
GO	molecular_function	10376
GRO	cereal_plant_growth_stage	235
GR_tax	gramene_taxonomy	58550
PO	plant_anatomy	1295
PO	plant_structure_development_stage	324
TO	plant_trait_ontology	1290

See also the detailed Ontology Module statistics report.

---

Genes and Alleles Release Notes

[ top ] No updates in this release. Last update done in release 31 (May 2010).

A more detailed genes database statistics report can be found here.

---

QTL Release Notes

[ top ] No updates in this release. Last update done in release 27 (April 2008).

A more detailed QTL database statistics report can be found here.

---

Pathways Release Notes (version 3.5)

[ top ]

Pathway databases are available dynamically via the Gramene's pathway server and those created and maintained by Gramene are also available for bulk download from Gramene's FTP site.

MaizeCyc has been updated to version 2.0.2

• New pathways:


• alpha-carotene biosynthesis [PWYBWI-0]
• delta-carotene biosynthesis [PWY-5946]
• epsilon-carotene biosynthesis [PWYBWI-4118]
• lutein biosynthesis [PWY-5947]
• carotenoid biosynthesis (from lycopene to carotene and xanthophyll)[PWYBWI-7081]

Literature references: Many from the Wurtzel Laboratory, including Wurtzel et al (2012); Bai et al (2009); etc.
• Flavonoid and flavonol biosynthesis pathway leading to anthocyanin biosynthesis and accumulation [PWYBWI-410]

Literature references: Sharma et al (2011), and The Maize Anthocyanin Pathway, a specialized Plant Biochemistry course at Penn State University.

Due to these edits a number of reactions and gene annotations were also added or updated.

RiceCyc Summary (version 3.3) Class Count Pathways 316 Enzymatic Reactions 2,103 Transport Reactions 87 Polypeptides 47,894 Enzymes 6,040 Transporters 603 Compounds 1,543

BrachyCyc Summary (version 2.0) Class Count Pathways 327 Enzymatic Reactions 2,057 Transport Reactions 87 Polypeptides 26,633 Enzymes 7,723 Transporters 950 Compounds 1,641

MaizeCyc Summary (version 2.0.2) Class Count Pathways 392 Enzymatic Reactions 2,110 Transport Reactions 68 Polypeptides 39,655 Enzymes 8,889 Transporters 291 Compounds 1,468

SorghumCyc Summary (version 1.1) Class Count Pathways 302 Enzymatic Reactions 1,838 Transport Reactions 9 Polypeptides 36,347 Enzymes 10,636 Transporters 269 Compounds 1,356

---

Diversity Release Notes

[ top ]

Data sets

New:

Sorghum bicolor. Structural variation data from EBI's Database of Genomic Variants Archive (dGVA) for Sorghum bicolor. Click here for an example.

Updated:

• Zea mays. Corrections to HapMap v2 data.

Unchanged:

• Arabidopsis, Oryza glaberiima, Oryza sativa spp, and Vitis vinifera

Software

Tassel

No updates in this release. Last update done in release 35 (June 2012).

SNP query

No updates in this release. Last update done in release 34 (October 2011). See also the TASSEL webpage.

Association Viewer

Explore Atwell GWAS data in our Association Viewer (beta).

Click here for database summary.

---

Germplasm

[ top ] No updates in this release. Last update done in release 34 (October 2011).

---

Literature

[ top ] New papers by Wurtzel et al.

---

Website

[ top ]

Distributed Annotation System

Gramene provides a DAS server for our own markers and sequences database as well as our Ensembl databases. These can use by the Ensembl genome browser as well as outside applications with a need to display sequences annotations on our various genome assemblies. Substantial improvements to the architecture should improve performance and usability considerably.

Our DAS resources make use of FastBit for the retrieval engine. We offer DAS tracks for sixteen species. See our DAS sources.

Diversity via GDPC/TASSEL

The TASSEL program via Genomic Diversity and Phenotype Connection (GDPC) can connect to Gramene's genetic diversity databases for rice, maize, and arabidopsis for detailed analysis by the user.

Web Services

Gramene's web services page documents many ways to directly connect to and analyze our databases.

Public MySQL Server

Gramene provides direct MySQL access to our core Ensembl databases for each of our sequenced genomes as well our databases for markers, sequences, genes, QTL and ontologies. To connect, use the following: mysql -hgramenedb.gramene.org -pgramene

Gramene Release 36 - November 2012

Gramene Database:

• Genomes
• Maps and Markers
• Proteins
• Ontologies
• Genes
• QTL
• Pathways
• Diversity
• Germplasm
• Literature
• Website

---

Genomes Release Notes

[ top ]

• Added new genomes for Hordeum vulgare (barley), Solanum tuberosum (potato), and Musa acuminata (banana).
• Updated gene models for Glycine max (soybean)
• Added new EST alignments for
  • Physcomitrella patens (moss)
  • Oryza brachyantha (an ancestral rice)
  • Setaria italica (foxtail millet)
  • Solanum lycopersicum (tomato)
• Updated and improved Triticum aestivum (wheat) homoeologous SNPs and 'gene space' assembly alignments to Brachypodium distachyon (purple false brome)
• Added new repeats feature annotation for Selaginella moellendorffii (lycopod)
• Updated protein features in Chlamydomonas reinhardtii (green algae)
• Updated peptide comparative genomics database
• Corrected Zea mays variation data
• Cleaned up non-translating genes in Vitis vinifera (grape)
• Updated BioMarts
• Updated to Ensembl schema and API Version 69

Genomes Core

	Species	Assembly	Gene Annotation
New
	Hordeum vulgare (barley)	030312v2
	Solanum tuberosum (potato)	3.0
	Musa acuminata (banana)	MA1
	Oryza barthii (WGS)
	Leersia perrieri (chr3s)
	Oryza granulata (chr3s)
	Oryza longistaminata (chr3s)
	Brassica rapa	IVFCAASv1	bra_v1.01_SP2010_01
	Oryza brachyantha (WGS)	OGEv1.4	OGEv1.4
	Solanum lycopersicum (tomato)	SL2.40	ITAG2.3
	Setaria italica (foxtail millet)	JGIv2.0	JGIv2.1
	Oryza meridionalis (chr3s)	454.pools.2012Feb	2012-04-CSHL
	Oryza glumaepatula (chr3s)	454.pools.2012Feb	2012-04-CSHL
Unchanged
	Arabidopsis thaliana	TAIR10	TAIR10
	Arabidopsis lyrata	Araly1.2	Araly1.2
	Brachypodium distachyon	Brachy1.0	Barchy1.2
	Chlamydomonas reinhardtii	ENA1	ENA1
	Glycine max (soybean)	Glyma1.0	Glyma1.0
	Oryza glaberrima whole genome	AGI1.1 (May 2011)	MIPS
	Oryza sativa indica	BGI 2005	BGI GLEAN 2008
	Oryza sativa japonica	MSU 6.0	MSU 6.0
	Physcomitrella patens	v1.1	v1.6
	Populus trichocarpa	JGI 2.0	JGI 2.0
	Selaginella moellendorffii	ENA1	ENA1
	Sorghum bicolor	Sbi1	Sbi1.4
	Vitis vinifera	IGGP 12X	V1
	Zea mays (corn)	B73 RefGen v2	v5
	Oryza barthii (AA) 3S	454.pools.1.1 (Mar 2009)	CSHL
	Oryza brachyantha (FF) 3S	454.pools.1.1 (Jul 2010)	CSHL
	Oryza minuta (BB) 3S	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza minuta (CC) 3S	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza nivara (AA) 3S	454.pools.1.1 (Jul 2010)	CSHL
	Oryza officinallis (CC) 3S	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza punctata (BB) 3S	BAC.Sanger.1.1 (May 2011)	CSHL v2.1
	Oryza rufipogon (AA) 3S	454.pools.1.1 (Jul 2010)	CSHL
	Oryza rufipogon (AA) FPC	OMAP_FPC_2006_JAN

Ensembl Variation

New	...
	...

Unchanged	Oryza sativa indica
	Oryza sativa japonica
	Arabidopsis thaliana
	Vitis vinifera

Functional Genomics

No updates in this release. Last update done in release 34 (October 2011).

Compara

• Gene Tree

  The EnsemblCompara GeneTree database was rebuilt using the core genome databases listed above excluding the OGE chromosome 3 short arm genomes, with the addition of Ciona savigny, Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae to provide taxonomic depth. From a total of 736,920 input proteins, 38,001 GeneTree families were constructed, comprising 646,588 individual genes.

Potential gene annotation artifacts

As a service to the community, we are releasing the results of screening for "putative gene annotation artifacts" on 18 plant reference genomes hosted at Gramene. The split gene models are commonly related to an annotation artifact wherein a single gene is annotated as two or more genes due to incomplete evidence, but could also result from legitimate evolutionary processes. The Compara Gene Tree method predicts a special class of within-species paralogs called "contiguous_gene_split". A contiguous_gene_split is called when the two apparently paralogous genes lie on the same strand and in close proximity (<1MB) but have no (or little) overlapping sequence. For more information on the method, please read the Ensembl documentation on Gene Orthology/Paralogy prediction. The split gene models have been updated and we are also now providing them for the new genomes (Brassica rapa, Oryza brachyantha, Setaria italica, Solanum lycopersicum.

• Synteny

  No updates in this release. Last update done in release 34 (October 2011).

• WGA

  • Upgrade the analysis pipeline to Lastz-chain-net and replaced the following analysis from old Blastz-net alignments to Lastz-net alignments
  • Oryza sativa Japonica v.s. Oryza sativa Indica
  • Oryza sativa Japonica v.s. Oryza barthii (chr3s)
  • Oryza sativa Japonica v.s. Oryza glumipatula (chr3s)
  • Oryza sativa Japonica v.s. Oryza meridionalis (chr3s)
  • Oryza sativa Japonica v.s. Oryza minutabb (chr3s)
  • Oryza sativa Japonica v.s. Oryza minutacc (chr3s)
  • Oryza sativa Japonica v.s. Oryza nivara (chr3s)
  • Oryza sativa Japonica v.s. Oryza officinalis (chr3s)
  • Oryza sativa Japonica v.s. Oryza punctata (chr3s)
  • Oryza sativa Japonica v.s. Oryza rufipogon (chr3s)
  • Added the following new pairs run by Lastz-chain-net pipeline:
    • Oryza sativa Japonica v.s. Brassica rapa
    • Oryza sativa Japonica v.s. Setaria italica (foxtail millet)
    • Oryza sativa Japonica v.s. Oryza brachyantha
    • Oryza sativa Japonica v.s. Solanum lycopersicum (tomato)
    • Oryza sativa Japonica v.s. Cyanidioschyzon merolae (red algae)
    • Arabidopsis thaliana v.s. Brassica rapa
    • Arabidopsis thaliana v.s. Setaria italica (foxtail millet)
    • Arabidopsis thaliana v.s. Oryza brachyantha
    • Arabidopsis thaliana v.s. Solanum lycopersicum (tomato)
    • Arabidopsis thaliana v.s. Cyanidioschyzon merolae (red algae)

Protein Annotation, Go, Xref

No updates in this release. Last update done in release 34b (February 2012).

Mart

• New Plant Gene and Plant Variation Mart

---

Maps and Markers Release Notes

[ top ] No updates in this release. Last updated done in release 33 (April 2011). Gramene's comparative maps database hosts 215 map sets from genetic, physical, bin, sequence, cytogenetic, and QTL studies.

See also the detailed Map Module statistics report.

Marker breakdown by type

Marker Type Count AFLP 8,149 Breakpoint Interval 303 Centromere 57 Chromosomal Segment 10 Clone 3,549,765 Cytological Structure 8 DArT 1,158 Deletion 333 EST 18,974,596 EST Cluster 4,633,006/td> FISH Probe 37 FPC 17,479 Gene 8,916 Gene Candidate 17 Gene Family 3 Gene Prediction 354,564 Gene Primer 19 Genomic DNA 1,827,315 GSS 9,459,811 Insertion 308 ISBP 691 Lapsed Locus 4 Maize Bin 114 Microarray Probe 260,656 mRNA 953,688 Oligo 2,396,466 OVERGO 23,921 Point 332 Primer 76,036 Probed Site 5,220 Pseudogene 1 QTL 11,625 RAPD 175 Restriction Fragment 5 RFLP 18,754 SNP 2,942 SSR 24,389 STS 3,290 Telomere 20 Transposable Element 4 Undefined 1,391

Marker breakdown by species Species Count Hordeum 713,300 Zea 7,604,538 Avena 71,594 Oryza 6,739,198 Secale 15,058 Sorghum 1,513,436 Saccharum 44,2434 Triticum 1,432,375

See also the detailed Marker Module statistics report.

---

Proteins Release Notes

[ top ] No updates in this release. Last update done in release 31 (May 2010).

The Gramene protein database provides a heterogeneous set of functional annotations from sources such as SWISS-PROT and TrEMBL, and which include Pfam, Prosite, and Interpro assignments. Various ontologies such as Gene Ontology (GO), Plant Ontologies (PO), Trait Ontology (TO) and Environment Ontology (EO) are used to attribute functional characteristics.

See also the detailed Protein Module statistics report.

---

Ontologies Release Notes

[ top ]

Various ontologies and their associations to genes, gene models, proteins, QTL, markers and maps were updated. Below is a summary of the ontologies data.

Ontology	Total terms	Total Terms w/Associations	Total Associations
Gene Ontology (GO)	35,728	2,396	422,611
Plant Ontology (PO)	0	0	0
Growth stage Ontology (GRO)	236	80	151,040
Trait Ontology (TO)	1,146	536	14,236
Taxonomy Ontology (GR_tax)	58,550	45,927	374,161
Environment Ontology (EO)	501	82	62,724
Gazetteer ontology (GAZ)	504,297	0	0

See also the detailed Ontology Module statistics report.

---

Genes and Alleles Release Notes

[ top ] No updates in this release. Last update done in release 31 (May 2010).

A more detailed genes database statistics report can be found here.

---

QTL Release Notes

[ top ] No updates in this release. Last update done in release 27 (April 2008).

A more detailed QTL database statistics report can be found here.

---

Pathways Release Notes (version 3.5)

[ top ]

Pathway databases are available dynamically via the Gramene's pathway server and for bulk download* via the Gramene's FTP site.

MaizeCyc has been updated to version 2.0.2

• Deleted pathways:
• Deleted reactions (orphan reactions with no gene associations and may not exist in plants):
• Deleted proteins:
• Deleted compounds:

RiceCyc Summary (version 3.3)
Class	Count
Pathways	316
Enzymatic Reactions	2,103
Transport Reactions	87
Polypeptides	47,894
Enzymes	6,040
Transporters	603
Compounds	1,543

BrachyCyc Summary (version 2.0)
Class	Count
Pathways	327
Enzymatic Reactions	2,057
Transport Reactions	87
Polypeptides	26,633
Enzymes	7,723
Transporters	950
Compounds	1,641

MaizeCyc Summary (version 2.0.2)
Class	Count
Pathways	392
Enzymatic Reactions	2,110
Transport Reactions	68
Polypeptides	39,655
Enzymes	8,899
Transporters	291
Compounds	1,468

SorghumCyc Summary (version 1.1)
Class	Count
Pathways	302
Enzymatic Reactions	1,838
Transport Reactions	9
Polypeptides	36,347
Enzymes	10,636
Transporters	269
Compounds	1,356

* Only if created and maintained by Gramene.

---

Diversity Release Notes

[ top ]

Data sets

New:

Oyza glaberrima. This variation set comprises ~1 million SNPs identified within 13 accessions of African rice O. glaberrima and eight accessions of its wild progenitor, O. barthii, which were collected from geographically distributed regions of Africa. Most lines were sequenced to 7-15X coverage using Illumina GAIIx technology. Six of the O. glaberrima lines were sequenced to >100X coverage using Illumina HiSeq2000 technology. Sequence reads were aligned to the O. glaberrima reference genome using BWA. SNPs were called using the multiple-sample method in the GATK package, applying a quality score threshold, and minimum and maximum alignment coverage as criteria filters.

Updated:

• Oryza sativa japonica. Updated to MSU7 coordinates for Rice Diversity and 1536 chip experiments.


• Zea mays HapMap v2. This variation set comprises the maize HapMap2 data, 55 million SNPs and indels identified in a collection of 103 pre-domesticated and domesticated Zea mays varieties, including a representative from the sister genus, Tripsacum dactyloides (Eastern gamagrass). Each line was sequenced to an average of 4.5X coverage using the Illumina GAIIx platform. The reads can be accessed from the SRA, with accession ID: SRA051245. Reads were mapped to the B73 reference genome using a combination of Bowtie, Novoalign and SOAP. The variations were scored by taking into account identity-by-descent blocks that are shared among the lines (Chia et al, 2012).

Unchanged:

• Arabidopsis, Oryza sativa spp, and Vitis vinifera

Software

Tassel

Introduction of Tassel 4

• Additional Web-launch TASSEL files created to allow diversity data sets to be loaded automatically
• Consistent Implementation of all data types (SNP, Haplotypes, etc.)
• Bitwise Data Structures for Speed (40 - 200 fold increase) and Memory Efficiency
• Many improvements to software architecture and design
• New QQ and Manhattan Plots
• 70% speed improvement to Cladogram Function
• Improved LD results display
• Many improvements to Progress Monitoring
• Much improved Taxa and Site Name Filtering
• Tassel on iPlant Discovery Environment and Atmosphere
• New Genotype Summary Function
• More User Friendly Alignment Viewer
• Improved Error Messages
• GLM and MLM:
• GLM interface simplified
• Compression and faster P3D implemented for MLM resulting in reduced runtime
• Matrix Algebra library wrapper written to make switching to newer, faster libraries easier
• EJML Matrix Algebra library interface implemented
• Pipeline (Command Line Interface)
• Automates complex loading/analysis pipelines
• Doesn't need Java coding to create
• Has simultaneously executing pipeline segments
• Works from web site launch, command line, and GUI
• Self-Describing Plugins
• Integrated GBS Pipeline with existing Tassel Pipeline
• Added more parameters to command line interface (i.e. LD, Site Filtering, Numerical Transform)
• Can Define Pipelines in XML

SNP query

No updates in this release. Last update done in release 34 (October 2011).

Association Viewer

Explore Atwell GWAS data in our Association Viewer (beta).

Click here for database summary.

---

Germplasm

[ top ] No updates in this release. Last update done in release 34 (October 2011).

---

Literature

[ top ] [% PROCESS 'common/macros.tmpl' %]

• [% format_reference('54920') %]
• [% format_reference('54922') %]
• [% format_reference('54924') %]
• [% format_reference('54925') %]

---

Website

[ top ]

Distributed Annotation System

Gramene provides a DAS server for our own markers and sequences database as well as our Ensembl databases. These can use by the Ensembl genome browser as well as outside applications with a need to display sequences annotations on our various genome assemblies. Substantial improvements to the architecture should improve performance and usability considerably.

Our DAS resources make use of FastBit for the retrieval engine. We offer DAS tracks for sixteen species. See our DAS sources.

Diversity via GDPC/TASSEL

The TASSEL program via Genomic Diversity and Phenotype Connection (GDPC) can connect to Gramene's genetic diversity databases for rice, maize, and arabidopsis for detailed analysis by the user.

Web Services

Gramene's web services page documents many ways to directly connect to and analyze our databases.

Public MySQL Server

Gramene provides direct MySQL access to our core Ensembl databases for each of our sequenced genomes as well our databases for markers, sequences, genes, QTL and ontologies. To connect, use the following: mysql -hgramenedb.gramene.org -pgramene

Gramene Release 35 - June 2012

Gramene Database:

• Genomes
• Maps and Markers
• Proteins
• Ontologies
• Genes
• QTL
• Pathways
• Diversity
• Germplasm
• Literature
• Website

---

Genomes Release Notes

[ top ]

• Added New genomes for Brassica rapa, Oryza brachyantha, Setaria italica, Solanum lycopersicum (tomato), Oryza meridionalis (chr3s), and Oryza glumaepatula (chr3s).
• Added variation data for Oryza glaberrima and Zea mays.
• Added oligo probes from the GeneChip Maize Genome Array. E.g., Zm.155.1.A1_a_at.
• Added wheat gene sequences alignments to Brachypodium distachyon as BAM tracks.
• Updated gene split models including predictions for Brassica rapa, Oryza brachyantha, Setaria italica, and Solanum lycopersicum.
• Updated peptide and DNA comparative genomics databases.
• Updated BioMarts.
• Updated to Ensembl schema and API Version 67

Genomes Core

	Species	Assembly	Gene Annotation
New
	Brassica rapa	IVFCAASv1	bra_v1.01_SP2010_01
	Oryza brachyantha	OGEv1.4	OGEv1.4
	Solanum lycopersicum (tomato)	SL2.40	ITAG2.3
	Setaria italica (foxtail millet)	JGIv2.0	JGIv2.1
	Oryza meridionalis (chr3s)	454.pools.2012Feb	2012-04-CSHL
	Oryza glumaepatula (chr3s)	454.pools.2012Feb	2012-04-CSHL
Unchanged
	Arabidopsis thaliana	TAIR10	TAIR10
	Arabidopsis lyrata	Araly1.2	Araly1.2
	Brachypodium distachyon	Brachy1.0	Barchy1.2
	Chlamydomonas reinhardtii	ENA1	ENA1
	Glycine max (soybean)	Glyma1.0	Glyma1.0
	Oryza glaberrima	AGI1.1 (May 2011)	MIPS
	Oryza sativa indica	BGI 2005	BGI GLEAN 2008
	Oryza sativa japonica	MSU 6.0	MSU 6.0
	Physcomitrella patens	v1.1	v1.1
	Populus trichocarpa	JGI 2.0	JGI 2.0
	Selaginella moellendorffii	ENA1	ENA1
	Sorghum bicolor	Sbi1	Sbi1.4
	Vitis vinifera	IGGP 12X	V1
	Zea mays (corn)	B73 RefGen v2	v5
	Oryza barthii (AA) 3S	454.pools.1.1 (Mar 2009)	CSHL
	Oryza brachyantha (FF) 3S	454.pools.1.1 (Jul 2010)	CSHL
	Oryza minuta (BB) 3S	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza minuta (CC) 3S	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza nivara (AA) 3S	454.pools.1.1 (Jul 2010)	CSHL
	Oryza officinallis (CC) 3S	BAC.Sanger.1.1 (May 2011)	CSHL v3.1
	Oryza punctata (BB) 3S	BAC.Sanger.1.1 (May 2011)	CSHL v2.1
	Oryza rufipogon (AA) 3S	454.pools.1.1 (Jul 2010)	CSHL
	Oryza rufipogon (AA) FPC	OMAP_FPC_2006_JAN

Ensembl Variation

New	Zea mays HapMap v2
	Oryza glaberrima

Unchanged	Oryza sativa indica
	Oryza sativa japonica
	Arabidopsis thaliana
	Vitis vinifera

Functional Genomics

New maize oligo probes mapped on maize browser, oligo probes from GeneChip Maize Genome Array. E.g., Zm.155.1.A1_a_at.

Compara

• Gene Tree

  The EnsemblCompara GeneTree database was rebuilt using the core genome databases listed above excluding the OGE chromosome 3 short arm genomes, with the addition of Ciona savigny, Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae to provide taxonomic depth. From a total of 736,920 input proteins, 38,001 GeneTree families were constructed, comprising 646,588 individual genes.

Potential gene annotation artifacts

As a service to the community, we are releasing the results of screening for "putative gene annotation artifacts" on 18 plant reference genomes hosted at Gramene. The split gene models are commonly related to an annotation artifact wherein a single gene is annotated as two or more genes due to incomplete evidence, but could also result from legitimate evolutionary processes. The Compara Gene Tree method predicts a special class of within-species paralogs called "contiguous_gene_split". A contiguous_gene_split is called when the two apparently paralogous genes lie on the same strand and in close proximity (<1MB) but have no (or little) overlapping sequence. For more information on the method, please read the Ensembl documentation on Gene Orthology/Paralogy prediction. The split gene models have been updated and we are also now providing them for the new genomes (Brassica rapa, Oryza brachyantha, Setaria italica, Solanum lycopersicum.

• Synteny

  No updates in this release. Last update done in release 34 (October 2011).

• WGA

  • Upgrade the analysis pipeline to Lastz-chain-net and replaced the following analysis from old Blastz-net alignments to Lastz-net alignments
  • Oryza sativa Japonica v.s. Oryza sativa Indica
  • Oryza sativa Japonica v.s. Oryza barthii (chr3s)
  • Oryza sativa Japonica v.s. Oryza glumaepatula (chr3s)
  • Oryza sativa Japonica v.s. Oryza meridionalis (chr3s)
  • Oryza sativa Japonica v.s. Oryza minutabb (chr3s)
  • Oryza sativa Japonica v.s. Oryza minutacc (chr3s)
  • Oryza sativa Japonica v.s. Oryza nivara (chr3s)
  • Oryza sativa Japonica v.s. Oryza officinalis (chr3s)
  • Oryza sativa Japonica v.s. Oryza punctata (chr3s)
  • Oryza sativa Japonica v.s. Oryza rufipogon (chr3s)
  • Added the following new pairs run by Lastz-chain-net pipeline:
    • Oryza sativa Japonica v.s. Brassica rapa
    • Oryza sativa Japonica v.s. Setaria italica (foxtail millet)
    • Oryza sativa Japonica v.s. Oryza brachyantha
    • Oryza sativa Japonica v.s. Solanum lycopersicum (tomato)
    • Oryza sativa Japonica v.s. Cyanidioschyzon merolae (red algae)
    • Arabidopsis thaliana v.s. Brassica rapa
    • Arabidopsis thaliana v.s. Setaria italica (foxtail millet)
    • Arabidopsis thaliana v.s. Oryza brachyantha
    • Arabidopsis thaliana v.s. Solanum lycopersicum (tomato)
    • Arabidopsis thaliana v.s. Cyanidioschyzon merolae (red algae)

Protein Annotation, Go, Xref

No updates in this release. Last update done in release 34b (February 2012).

Mart

• New Plant Gene and Plant Variation Mart

---

Maps and Markers Release Notes

[ top ] No updates in this release. Last updated done in release 33 (April 2011). Gramene's comparative maps database hosts 215 map sets from genetic, physical, bin, sequence, cytogenetic, and QTL studies.

See also the detailed Map Module statistics report.

Marker breakdown by type

Marker Type Count AFLP 8,149 Breakpoint Interval 303 Centromere 57 Chromosomal Segment 10 Clone 3,549,765 Cytological Structure 8 DArT 1,158 Deletion 333 EST 18,974,596 EST Cluster 4,633,006/td> FISH Probe 37 FPC 17,479 Gene 8,916 Gene Candidate 17 Gene Family 3 Gene Prediction 354,564 Gene Primer 19 Genomic DNA 1,827,315 GSS 9,459,811 Insertion 308 ISBP 691 Lapsed Locus 4 Maize Bin 114 Microarray Probe 260,656 mRNA 953,688 Oligo 2,396,466 OVERGO 23,921 Point 332 Primer 76,036 Probed Site 5,220 Pseudogene 1 QTL 11,625 RAPD 175 Restriction Fragment 5 RFLP 18,754 SNP 2,942 SSR 24,389 STS 3,290 Telomere 20 Transposable Element 4 Undefined 1,391

Marker breakdown by species Species Count Hordeum 713,300 Zea 7,604,538 Avena 71,594 Oryza 6,739,198 Secale 15,058 Sorghum 1,513,436 Saccharum 44,2434 Triticum 1,432,375

See also the detailed Marker Module statistics report.

---

Proteins Release Notes

[ top ] No updates in this release. Last update done in release 31 (May 2010).

The Gramene protein database provides a heterogeneous set of functional annotations from sources such as SWISS-PROT and TrEMBL, and which include Pfam, Prosite, and Interpro assignments. Various ontologies such as Gene Ontology (GO), Plant Ontologies (PO), Trait Ontology (TO) and Environment Ontology (EO) are used to attribute functional characteristics.

See also the detailed Protein Module statistics report.

---

Ontologies Release Notes

[ top ]

Various ontologies and their associations to genes, gene models, proteins, QTL, markers and maps were updated. Below is a summary of the ontologies data.

Total number of ontology terms	602,120
Total number of associations	1,217,985
Number of Environment terms	501
Number of Environment associations	82
Number of Environment terms in associations	62,724
Number of GAZ terms	504,297
Number of GAZ associations	0
Number of GAZ terms in associations	0
Number of Gene Ontology terms	35,727
Number of Gene Ontology associations	2,396
Number of Gene Ontology terms in associations	422,611
Number of Growth Stage terms	236
Number of Growth Stage associations	80
Number of Growth Stage terms in associations	151,040
Number of Plant Anatomy terms	1,273
Number of Plant Anatomy associations	240
Number of Plant Anatomy terms in associations	172,170
Number of Plant Structure Development Stage terms	316
Number of Plant Structure Development Stage associations	66
Number of Plant Structure Development Stage terms in associations	21,043
Number of Taxonomy terms	58,550
Number of Taxonomy associations	45,927
Number of Taxonomy terms in associations	374,161
Number of Trait terms	1,146
Number of Trait associations	535
Number of Trait terms in associations	14,236
Total number of Protein with GO associations	140,760
Total number of Protein with Environment ontology associations	151
Total number of Protein with Growth Stage ontology associations	193
Total number of Protein with Plant Anatomy ontology associations	222
Total number of Protein with Plant Structure Development Stage ontology associations	168
Total number of Protein with Taxonomy ontology associations	245,834
Total number of Protein with Trait ontology associations	162
Total number of Gene with GO associations	31,644
Total number of Gene with Environment ontology associations	20,469
Total number of Gene with Growth Stage ontology associations	24,327
Total number of Gene with Plant Anatomy ontology associations	26,072
Total number of Gene with Plant Structure Development Stage ontology associations	1,223
Total number of Gene with Taxonomy ontology associations	71,157
Total number of Gene with Trait ontology associations	1,226
Total number of QTL with Environment ontology associations	11,442
Total number of QTL with Growth Stage ontology associations	8,558
Total number of QTL with Plant Anatomy ontology associations	11,452
Total number of QTL with Plant Structure Development Stage ontology associations	11,470
Total number of QTL with Taxonomy ontology associations	11,624
Total number of QTL with Trait ontology associations	11,624
Total number of Marker library with Environment ontology associations	198
Total number of Marker library with Growth Stage ontology associations	351
Total number of Marker library with Plant Anatomy ontology associations	7,962
Total number of Marker species with Environment ontology associations	9
Total number of Marker species with Taxonomy ontology associations	45,546
Total number of associations with only non-IEA	1,012,398
Total number of associations with only IEA	195,441
Total number of associations both IEA and non-IEA	10,147
Total number of evidences in associations	1,242,280
IEA evidences in associations	206,029
non-IEA evidences in associations	1,036,251
Total number of literature references used as evidence in associations	1,958

See also the detailed Ontology Module statistics report.

---

Genes and Alleles Release Notes

[ top ] No updates in this release. Last update done in release 31 (May 2010).

A more detailed genes database statistics report can be found here.

---

QTL Release Notes

[ top ] No updates in this release. Last update done in release 27 (April 2008).

A more detailed QTL database statistics report can be found here.

---

Pathways Release Notes (version 3.4)

[ top ]

Pathway databases are available dynamically via the Gramene's pathway server and for bulk download* via the Gramene's FTP site.

MaizeCyc has been updated to version 2.0.1

• Deleted pathways:

Glycine degradation I <-- Strictly for anaerobic bacteria

• Deleted reactions (orphan reactions with no gene associations and may not exist in plants):

RXN-12104, RXN-9544, RXN-9546, RXN-9545, 2.7.7.1-RXN, 2.7.7.33-RXN, COBINPGUANYLYLTRANS-RXN, and RXN-9990

• Deleted proteins:

Renin

• Deleted compounds:

Aggrecan, Heparin, Thrombin, SoxZY-S-Thiocysteine, Factor-V, Facton-I, and Ecdysteroids

RiceCyc has been updated to version 3.3

• Manually curated pathways:

Trehalose; Stachyose; Delphinidin 3-O-glucoside; Pelargonidin 3-O-glucoside & Cyanidin 3-O-glucoside; Gentiodelphin; Flavonol; Pinobanksin; 6,7,4'-trihydroxyisoflavone; Maackiain; Medicarpin; Leucodelphinidin; Leucopelargonidin & Leucocyanidin; and Proanthocyanidin biosynthesis from flavonols

RiceCyc Summary (version 3.3) Class Count Pathways 316 Enzymatic Reactions 2,103 Transport Reactions 87 Polypeptides 47,894 Enzymes 6,040 Transporters 603 Compounds 1,543

BrachyCyc Summary (version 2.0) Class Count Pathways 327 Enzymatic Reactions 2,057 Transport Reactions 87 Polypeptides 26,633 Enzymes 7,723 Transporters 950 Compounds 1,641

MaizeCyc Summary (version 2.0.1) Class Count Pathways 389 Enzymatic Reactions 2,089 Transport Reactions 68 Polypeptides 39,656 Enzymes 8,900 Transporters 291 Compounds 1,462

SorghumCyc Summary (version 1.1) Class Count Pathways 302 Enzymatic Reactions 1,838 Transport Reactions 9 Polypeptides 36,347 Enzymes 10,636 Transporters 269 Compounds 1,356

* Only if created and maintained by Gramene.

---

Diversity Release Notes

[ top ]

Data sets

New:

Oyza glaberrima. This variation set comprises ~1 million SNPs identified within 13 accessions of African rice O. glaberrima and eight accessions of its wild progenitor, O. barthii, which were collected from geographically distributed regions of Africa. Most lines were sequenced to 7-15X coverage using Illumina GAIIx technology. Six of the O. glaberrima lines were sequenced to >100X coverage using Illumina HiSeq2000 technology. Sequence reads were aligned to the O. glaberrima reference genome using BWA. SNPs were called using the multiple-sample method in the GATK package, applying a quality score threshold, and minimum and maximum alignment coverage as criteria filters.

Updated:

• Oryza sativa japonica. Updated to MSU7 coordinates:
• Zhao K et al (2011). Nat Comm 2:467. Rice GWAS study. 413 diverse accessions, Rice Diversity 44K SNP array, 34 phenotypes.
• Zhao K et al (2010). PLoS One 5(5):e10780. Rice Diversity 1536 SNP array: 1311 SNPs x 395 varieties.


• Zea mays HapMap v2. This variation set comprises the maize HapMap2 data, 55 million SNPs and indels identified in a collection of 103 pre-domesticated and domesticated Zea mays varieties, including a representative from the sister genus, Tripsacum dactyloides (Eastern gamagrass). Each line was sequenced to an average of 4.5X coverage using the Illumina GAIIx platform. The reads can be accessed from the SRA, with accession ID: SRA051245. Reads were mapped to the B73 reference genome using a combination of Bowtie, Novoalign and SOAP. The variations were scored by taking into account identity-by-descent blocks that are shared among the lines (Chia et al, 2012).

Unchanged:

• Arabidopsis, Oryza sativa spp, and Vitis vinifera

Software

Tassel

Introduction of Tassel 4

• Additional Web-launch TASSEL files created to allow diversity data sets to be loaded automatically
• Consistent Implementation of all data types (SNP, Haplotypes, etc.)
• Bitwise Data Structures for Speed (40 - 200 fold increase) and Memory Efficiency
• Many improvements to software architecture and design
• New QQ and Manhattan Plots
• 70% speed improvement to Cladogram Function
• Improved LD results display
• Many improvements to Progress Monitoring
• Much improved Taxa and Site Name Filtering
• Tassel on iPlant Discovery Environment and Atmosphere
• New Genotype Summary Function
• More User Friendly Alignment Viewer
• Improved Error Messages
• GLM and MLM:
• GLM interface simplified
• Compression and faster P3D implemented for MLM resulting in reduced runtime
• Matrix Algebra library wrapper written to make switching to newer, faster libraries easier
• EJML Matrix Algebra library interface implemented
• Pipeline (Command Line Interface)
• Automates complex loading/analysis pipelines
• Doesn't need Java coding to create
• Has simultaneously executing pipeline segments
• Works from web site launch, command line, and GUI
• Self-Describing Plugins
• Integrated GBS Pipeline with existing Tassel Pipeline
• Added more parameters to command line interface (i.e. LD, Site Filtering, Numerical Transform)
• Can Define Pipelines in XML

SNP query

No updates in this release. Last update done in release 34 (October 2011).

Association Viewer

Explore Atwell GWAS data in our Association Viewer (beta).

Click here for database summary.

---

Germplasm

[ top ] No updates in this release. Last update done in release 34 (October 2011).

---

Literature

[ top ] [% PROCESS 'common/macros.tmpl' %]

• [% format_reference('54920') %]
• [% format_reference('54922') %]
• [% format_reference('54924') %]
• [% format_reference('54925') %]

---

Website

[ top ]

Distributed Annotation System

Gramene provides a DAS server for our own markers and sequences database as well as our Ensembl databases. These can use by the Ensembl genome browser as well as outside applications with a need to display sequences annotations on our various genome assemblies. Substantial improvements to the architecture should improve performance and usability considerably.

Our DAS resources make use of FastBit for the retrieval engine. We offer DAS tracks for sixteen species. See our DAS sources.

Diversity via GDPC/TASSEL

The TASSEL program via Genomic Diversity and Phenotype Connection (GDPC) can connect to Gramene's genetic diversity databases for rice, maize, and arabidopsis for detailed analysis by the user.

Web Services

Gramene's web services page documents many ways to directly connect to and analyze our databases.

Public MySQL Server

Gramene provides direct MySQL access to our core Ensembl databases for each of our sequenced genomes as well our databases for markers, sequences, genes, QTL and ontologies. To connect, use the following: mysql -hgramenedb.gramene.org -pgramene