Release Notes 50 (April 2016)

Website

See also legacy data in the Gramene's Archive.

Genomes Release Notes

Genomes Core

  Species Assembly Gene Annotation
Unchanged
Aegilops tauschii ASM34733v1 GCA_000347335.1
Amborella trichopoda GCA_000471905.1 (AMTR1.0) 2014-01-AGD
Arabidopsis lyrata Araly1.0 Araly1.0
Arabidopsis thaliana TAIR10 TAIR10
Brachypodium distachyon Brachy1.0 Barchy1.2
Brassica oleracea GCA_000092065.1 ENA
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
Leersia perrieri GCA_000325765.3 OGE
Medicago truncatula MedtrA17_3.5 2011-11-EnsemblPlants
Musa acuminata (banana) MA1 2012-08-Cirad
Oryza barthii GCA_000182155.1 OGE Maker (Aug 2013)
Oryza brachyantha GCA_000231095.2 / OGEv1.4b OGEv1.4
Oryza glaberrima GCA_000147395.1 / AGI1.1 (May 2011) 2011-05-AGI (MIPS)
Oryza glumaepatula GCA_000576495.1 OGE Maker (Aug 2013)
Oryza longistaminata v0117-2013Aug OGE
Oryza meridionalis GCA_000338895.1 OGE Maker (Aug 2013)
Oryza nivara GCA_000576065.1 OGE Maker (Aug 2013)
Oryza punctata GCA_000573905.1 OGE Maker (Aug 2013)
Oryza rufipogon PRJEB4137 OGE
Oryza sativa japonica IRGSP-1.0 MSU 7.0
Oryza sativa indica ASM465v1 2010-07-BGI
Ostreococcus lucimarinus v2.0 GCA_000092065.1 JGI
Physcomitrella patens ASM242v1 2011-03-Phypa1.6
Prunus persica Prupe1_0 / GCA_000346465.1 Prupe1_0 / Peach v1.0
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) SL2.50 ITAG2.3
Solanum tuberosum (potato) 3.0 SolTub_3.0
Sorghum bicolor Sorbi1 2007-12-JGI
Theobroma cacao (cocoa) GCA_000403535.1 ENA
Triticum aestivum IWGSP1 IWGSP1 (MIPS)
Triticum urartu GCA_000347455.1 GCA_000347455.1 (ENA, Apr 2013)
Vitis vinifera IGGP 12x 2012-07-CRIBI
Zea mays (corn) B73_RefGen_v3 5b+

Ensembl Variation

Updated Oryza sativa japonica

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

Compara

Gene Trees

  • The EnsemblCompara GeneTree database was updated. The new database includes a total of 55,519 GeneTree families were constructed comprising 1,280,352 individual genes (1,432,395 input proteins) from 39 plant genomes (and 5 non-plant outgroups).

  • Last update to the OGE Compara tree at oge.gramene.org (build on the MSU6 genome assembly) was done in release 38 (August 2013).

Putative Split Genes

The putative gene annotation artifacts (also known as contiguous gene split models) based on the latest Ensembl Compara Gene Tree database were updated in the current release. Brief statistics for each species is given below.

Split genes by count
Species Count
Aegilops_tauschii 463
Amborella_trichopoda 654
Arabidopsis_lyrata_subsp._lyrata 102
Arabidopsis_thaliana 13
Brachypodium_distachyon 105
Brassica_oleracea_var._oleracea 624
Brassica_rapa_subsp._pekinensis 94
Chlamydomonas_reinhardtii 62
Cyanidioschyzon_merolae_strain_10D 4
Glycine_max 257
Hordeum_vulgare_subsp._vulgare 91
Leersia_perrieri 157
Medicago_truncatula 267
Musa_acuminata_subsp._malaccensis 889
Oryza_barthii 208
Oryza_brachyantha 229
Oryza_glaberrima 432
Oryza_glumipatula 242
Oryza_longistaminata 213
Oryza_meridionalis 157
Oryza_nivara 185
Oryza_punctata 160
Oryza_rufipogon 179
Oryza_sativa_Indica_Group 558
Oryza_sativa_Japonica_Group 558
Ostreococcus_lucimarinus_CCE9901 14
Physcomitrella_patens 149
Populus_trichocarpa 1100
Prunus_persica 307
Selaginella_moellendorffii 121
Setaria_italica 230
Solanum_lycopersicum 816
Solanum_tuberosum 458
Sorghum_bicolor 706
Theobroma_cacao 84
Triticum_aestivum 979
Triticum_urartu 357
Vitis_vinifera 465
Zea_mays 603

Synteny

No new synteny data was generated for this release. Last update was done in release 39 (October 2013).

WGA and other nucleotide alignments

No new alignments for this release. Last update was done in release 48 (November 2015).

Protein Annotation, Go, Xref

Protein domain information was updated based on the latest InterProScan analysis.

Mart

New Plant Gene and Plant Variation Marts

Pathway Release Notes

Plant Reactome

The Plant Reactome has expanded gene homology-based pathway projections to 62 plant species. Notable newly projected species: Eucalyptus grandis, Jatropha curcas, Manihot esculenta, and Mimulus guttatus. In addition, we have added six newly curated pathways. Please take a note of the following pathway statistics and status table for more details.

Newly projected species

  • Eucalyptus grandis
  • Jatropha curcas
  • Manihot esculenta
  • Mimulus guttatus

Newly curated pathways

  • O. sativa choline biosynthesis I
  • O. sativa choline biosynthesis III
  • O. sativa cardiolipin biosynthesis
  • O. sativa glycine betaine biosynthesis III (plants)
  • O. sativa suberin biosynthesis
  • O. sativa polar auxin transport

Reinstated pathway

  • O. sativa Auxin signaling

Pathway Projections

Planteome Inparanoid data was kindly provided by the Planteome project. When available, the outgoing links from gene product IDs mapped to reactions are always hyperlinked to respective entries in collaborator databases/online resources.

Projection Statistics

*data from sequenced transcriptomes
^ projections currently exclude cell-cycle pathways and annotations

SpeciesPathwaysReactionsGene ProductsSequence sourceOutgoing LinkHomology method
Oryza sativa japonica222^10251173Ensembl GrameneUniprotCurated Reference
Aegilops tauschii 182 472 841 Ensembl Gramene Ensembl Gramene Ensembl Compara
Amborella trichopoda 189 499 617 Ensembl Gramene Ensembl Gramene Ensembl Compara
Arabidopsis lyrata 187 506 942 Ensembl Gramene Ensembl Gramene Ensembl Compara
Arabidopsis thaliana 187 508 944 Ensembl Gramene TAIR Ensembl Compara
Arachis duranensis 196 518 788 PeanutBase PeanutBase Planteome Inparanoid
Arachis ipaensis 194 522 801 PeanutBase PeanutBase Planteome Inparanoid
Brachypodium distachyon 186 527 873 Ensembl Gramene Ensembl Gramene Ensembl Compara
Brassica oleracea 186 497 1417 Ensembl Gramene Ensembl Gramene Ensembl Compara
Brassica rapa 186 504 1443 Ensembl Gramene Ensembl Gramene Ensembl Compara
Cajanus cajan 197 525 1009 LegumeInfo LegumeInfo Planteome Inparanoid
Capsicum annuum 198 511 1004 PMID: 24441736 N/A Planteome Inparanoid
Chlamydomonas reinhardtii 141 287 233 Ensembl Gramene Ensembl Gramene Ensembl Compara
Cicer arietinum 198 528 1192 NCBI NCBI Planteome Inparanoid
Citrus sinensis 197 528 2026 Phytozome Phytozome Planteome Inparanoid
Coffea canephora 198 530 926 PMID:25190796 N/A Planteome Inparanoid
Cyanidioschyzon merolae 116 208 158 Ensembl Gramene Ensembl Gramene Ensembl Compara
Eucalyptus grandis 190 510 825 Phytozome Phytozome Planteome Inparanoid
Fragaria vesca 198 514 888 Phytozome Phytozome Planteome Inparanoid
Glycine max 187 499 1730 Ensembl Gramene Ensembl Gramene Ensembl Compara
Gossypium raimondii 197 532 1405 Phytozome Phytozome Planteome Inparanoid
Hordeum vulgare 184 469 734 Ensembl Gramene Ensembl Gramene Ensembl Compara
Jatropha curcas 187 499 575 KDRI (Kazusa) KDRI (Kazusa) Planteome Inparanoid
Leersia perrieri 193 525 861 Ensembl Gramene Ensembl Gramene Ensembl Compara
Malus domestica 196 511 1771 PMID: 20802477 Phytozome Planteome Inparanoid
Manihot esculenta 191 510 1014 Phytozome Phytozome Planteome Inparanoid
Medicago truncatula 188 497 1064 Ensembl Gramene Ensembl Gramene Ensembl Compara
Mimulus guttatus 189 512 703 Phytozome Phytozome Planteome Inparanoid
Musa acuminata 186 490 1141 Ensembl Gramene Ensembl Gramene Ensembl Compara
Oryza australiensis * 194 494 1485 OMAP/OGE N/A Planteome Inparanoid
Oryza barthii 193 536 900 Ensembl Gramene Ensembl Gramene Ensembl Compara
Oryza brachyantha 193 528 850 Ensembl Gramene Ensembl Gramene Ensembl Compara
Oryza glaberrima 195 533 910 Ensembl Gramene Ensembl Gramene Ensembl Compara
Oryza glumaepatula 195 537 918 Ensembl Gramene Ensembl Gramene Ensembl Compara
Oryza granulata * 196 510 2565 OMAP/OGE N/A Planteome Inparanoid
Oryza kasalath 157 249 298 PMID: 24578372 N/A Planteome Inparanoid
Oryza longistaminata * 192 523 790 Ensembl Gramene Ensembl Gramene Ensembl Compara
Oryza meridionalis 186 487 789 Ensembl Gramene Ensembl Gramene Ensembl Compara
Oryza minuta * 197 516 1691 OMAP/OGE N/A Planteome Inparanoid
Oryza nivara 191 542 916 Ensembl Gramene Ensembl Gramene Ensembl Compara
Oryza officinalis * 195 524 1465 OMAP/OGE N/A Planteome Inparanoid
Oryza punctata 191 534 904 Ensembl Gramene Ensembl Gramene Ensembl Compara
Oryza rufipogon 193 544 923 Ensembl Gramene Ensembl Gramene Ensembl Compara
Oryza sativa Indica 196 555 984 Ensembl Gramene Ensembl Gramene Ensembl Compara
Ostreococcus lucimarinus 131 270 220 Ensembl Gramene Ensembl Gramene Ensembl Compara
Phaseolus vulgaris 199 534 977 Phytozome Phytozome Planteome Inparanoid
Phoenix dactylifera 191 497 922 PMID: 23917264 N/A Planteome Inparanoid
Physcomitrella patens 176 454 904 Ensembl Gramene Ensembl Gramene Ensembl Compara
Picea abies 191 477 1119 Congenie Congenie Planteome Inparanoid
Pinus taeda 181 434 1088 TreeBase N/A Planteome Inparanoid
Populus trichocarpa 188 508 1181 Ensembl Gramene Ensembl Gramene Ensembl Compara
Prunus persica 188 507 797 Ensembl Gramene Ensembl Gramene Ensembl Compara
Selaginella moellendorffii 181 472 1108 Ensembl Gramene Ensembl Gramene Ensembl Compara
Setaria italica 191 531 962 Ensembl Gramene Ensembl Gramene Ensembl Compara
Solanum lycopersicum 190 504 960 Ensembl Gramene Ensembl Gramene Ensembl Compara
Solanum tuberosum 187 486 933 Ensembl Gramene Ensembl Gramene Ensembl Compara
Sorghum bicolor 192 536 929 Ensembl Gramene Ensembl Gramene Ensembl Compara
Theobroma cacao 191 511 775 Ensembl Gramene Ensembl Gramene Ensembl Compara
Triticum aestivum 193 531 2159 Ensembl Gramene Ensembl Gramene Ensembl Compara
Triticum turgidum * 197 528 2388 PMID: 23800085 N/A Planteome Inparanoid
Triticum urartu 187 481 768 Ensembl Gramene Ensembl Gramene Ensembl Compara
Vitis vinifera 184 496 835 Ensembl Gramene Ensembl Gramene Ensembl Compara
Zea mays 191 528 1102 Ensembl Gramene MaizeGDB Ensembl Compara

NOTE: The pathway counts for both reference and projected species include a few organizational “container” names, such as “Hormone biosyntheses” and “Metabolism”. Additionally, the bulk of the projected pathways occur in the areas of metabolic and regulatory function, whereas the rice reference data set has additional pathways related to cell cycle functions. We are not currently using these additional pathways as a source for orthology projection.

"Cyc" Pathways

  • BioCyc-based pathway databases on Pathway Tools ver. 19.0 are available from a virtual server hosted at CyVerse.

    Summary tables for the Cyc pathway databases created by Gramene can be seen in release 46 notes.

Ontologies Release Notes

No updates in this release. Last update done in release 31 (May 2010). A summary of ontologies data was last provided in release 46.

Infrastructure

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

Our partner Ensembl Genomes offer a public, read-only MySQL server with copies of the species-specific and comparative genomic databases that we use. To use this with the mysql command-line client:

$ mysql -hmysql-eg-publicsql.ebi.ac.uk -P4157 -uanonymous

Please note that the versioning scheme used at this public database differs from ours; Gramene's release 50_84 is set as version 31_84.

Gramene currently a legacy public, read-only MySQL server for release 40 of our databases. You can connect to the host "gramenedb.gramene.org" with the password "gramene," e.g.:

mysql -hgramenedb.gramene.org -pgramene