Table of Contents
The Gramene Knowledgebase Team is pleased to announce its Release #61 with the Genome section providing access to information on 2,264,698 genes and 61 reference plant genomes. It includes three new reference genomes: kiwifruit (Actinidia chinensis), and two ecotypes of Hall's panicgrass (Panicum hallii FIL2) and (Panicum hallii HAL2), and updates to several existing genomes. This release also includes 109 manually curated maize gene models as a GFF file to attach as a custom track in Gramene's genome browser (and will soon be also available as a permanent track). The Plant Reactome, Gramene's pathway portal hosts pathway projections for 82 species including those in the Genome section ranging from unicellular autotrophs to higher plants. Total curated reference pathways are 298. See more details on the release #61 page.
Gramene Knowledgebase is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species. The genome databases were built in direct collaboration with Ensembl Plants and the Plant Reactome database was produced in collaboration with the Reactome project. Core funding for the project is provided by the National Science Foundation, USA.
Name |
Assembly |
Accession |
---|---|---|
Actinidia chinensis Red5 |
Red5_PS1_1.69.0 |
GCA_003024255.1 |
Aegilops tauschii |
Aet_v4.0 |
GCA_002575655.1 |
Amborella trichopoda |
AMTR1.0 |
GCA_000471905.1 |
Arabidopsis halleri |
Ahal2.2 |
GCA_900078215.1 |
Arabidopsis lyrata |
v.1.0 |
GCA_000004255.1 |
Arabidopsis thaliana |
TAIR10 |
GCA_000001735.1 |
Beta vulgaris |
RefBeet-1.2.2 |
GCA_000511025.2 |
Brachypodium distachyon |
Brachypodium_distachyon_v3.0 |
GCA_000005505.4 |
Brassica napus |
AST_PRJEB5043_v1 |
GCA_000751015.1 |
Brassica oleracea |
BOL |
GCA_000695525.1 |
Brassica rapa |
Brapa_1.0 |
GCA_000309985.1 |
Chlamydomonas reinhardtii |
Chlamydomonas_reinhardtii_v5.5 |
GCA_000002595.3 |
Chondrus crispus |
ASM35022v2 |
GCA_000350225.2 |
Corchorus capsularis |
CCACVL1_1.0 |
GCA_001974805.1 |
Cucumis sativus |
ASM407v2 |
GCA_000004075.2 |
Cyanidioschyzon merolae |
ASM9120v1 |
GCA_000091205.1 |
Daucus carota |
ASM162521v1 |
GCA_001625215.1 |
Dioscorea rotundata |
TDr96_F1_Pseudo_Chromosome_v1.0 |
GCA_002240015.2 |
Galdieria sulphuraria |
ASM34128v1 |
GCA_000341285.1 |
Glycine max |
Glycine_max_v2.1 |
GCA_000004515.4 |
Gossypium raimondii |
Graimondii2_0 |
GCA_000327365.1 |
Helianthus annuus |
HanXRQr1.0 |
GCA_002127325.1 |
Hordeum vulgare |
IBSC_v2 |
tbd |
Leersia perrieri |
Lperr_V1.4 |
GCA_000325765.3 |
Lupinus angustifolius |
LupAngTanjil_v1.0 |
GCA_001865875.1 |
Manihot esculenta |
Manihot_esculenta_v6 |
GCA_001659605.1 |
Medicago truncatula |
MedtrA17_4.0 |
GCA_000219495.2 |
Musa acuminata |
ASM31385v1 |
GCA_000313855.1 |
Nicotiana attenuata |
NIATTr2 |
GCA_001879085.1 |
Oryza barthii |
O.barthii_v1 |
GCA_000182155.2 |
Oryza brachyantha |
Oryza_brachyantha.v1.4b |
GCA_000231095.2 |
Oryza glaberrima |
Oryza_glaberrima_V1 |
GCA_000147395.1 |
Oryza glumipatula |
Oryza_glumaepatula_v1.5 |
GCA_000576495.1 |
Oryza longistaminata |
O_longistaminata_v1.0 |
GCA_000789195.1 |
Oryza meridionalis |
Oryza_meridionalis_v1.3 |
GCA_000338895.2 |
Oryza nivara |
Oryza_nivara_v1.0 |
GCA_000576065.1 |
Oryza punctata |
Oryza_punctata_v1.2 |
GCA_000573905.1 |
Oryza rufipogon |
OR_W1943 |
GCA_000817225.1 |
Oryza sativa Indica Group |
ASM465v1 |
GCA_000004655.2 |
Oryza sativa Japonica Group |
IRGSP-1.0 |
GCA_001433935.1 |
Ostreococcus lucimarinus |
ASM9206v1 |
GCA_000092065.1 |
Panicum hallii FIL2 |
PHallii_v3.1 |
GCA_002211085.2 |
Panicum hallii HAL2 |
PhalliiHAL_v2.1 |
GCA_003061485.1 |
Phaseolus vulgaris |
PhaVulg1_0 |
GCA_000499845.1 |
Physcomitrella patens |
Phypa_V3 |
GCA_000002425.2 |
Populus trichocarpa |
Pop_tri_v3 |
GCA_000002775.3 |
Prunus persica |
Prunus_persica_NCBIv2 |
GCA_000346465.2 |
Selaginella moellendorffii |
v1.0 |
GCA_000143415.1 |
Setaria italica |
Setaria_italica_v2.0 |
GCA_000263155.2 |
Solanum lycopersicum |
SL3.0 |
GCA_000188115.3 |
Solanum tuberosum |
SolTub_3.0 |
GCA_000226075.1 |
Sorghum bicolor |
Sorghum_bicolor_NCBIv3 |
GCA_000003195.3 |
Theobroma cacao |
Theobroma_cacao_20110822 |
GCA_000403535.1 |
Trifolium pratense |
Trpr |
GCA_900079335.1 |
Triticum aestivum |
IWGSC |
GCA_900519105.1 |
Triticum dicoccoides |
WEWSeq_v.1.0 |
GCA_002162155.1 |
Triticum urartu |
ASM34745v1 |
GCA_000347455.1 |
Vigna angularis |
Vigan1.1 |
GCA_001190045.1 |
Vigna radiata |
Vradiata_ver6 |
GCA_000741045.2 |
Vitis vinifera |
12X |
GCA_000003745.2 |
Zea mays |
B73_RefGen_v4 |
GCA_000005005.6 |
For Triticum aestivum (Wheat) genome, 31,779 markers from the 35K Axiom SNP array were added. They were provided by CerealsDB and designed by Affymetrix. This Affymetrix product (ID 550524) contains 35,143 SNPs selected to be informative across a wide range of hexaploid wheat accessions. This 384-sample format array is a cost effective and efficient system for screening large numbers of lines. The array has been used to screen a large global collection of elite and landrace varieties including hexaploid and tetraploid accessions.
Gene Trees
The EnsemblCompara GeneTree database updated. A total of 92,708 GeneTree families were constructed comprising 1,948,793 individual genes from 61 plant genomes with 2,158,277 input proteins.
Putative Split Genes
Species_id | Splitgene_counts |
Actinidia_chinensis_var._chinensis | 142 |
Aegilops_tauschii_subsp._strangulata | 178 |
Arabidopsis_lyrata_subsp._lyrata | 89 |
Arabidopsis_thaliana | 31 |
Beta_vulgaris_subsp._vulgaris | 47 |
Brachypodium_distachyon | 62 |
Brassica_oleracea_var._oleracea | 604 |
Brassica_rapa | 96 |
Chlamydomonas_reinhardtii | 41 |
Cucumis_sativus | 418 |
Daucus_carota_subsp._sativus | 229 |
Dioscorea_rotundata | 182 |
Glycine_max | 215 |
Gossypium_raimondii | 336 |
Helianthus_annuus | 527 |
Hordeum_vulgare_subsp._vulgare | 145 |
Leersia_perrieri | 94 |
Lupinus_angustifolius | 114 |
Manihot_esculenta | 122 |
Medicago_truncatula | 189 |
Musa_acuminata_subsp._malaccensis | 623 |
Nicotiana_attenuata | 51 |
Oryza_barthii | 107 |
Oryza_brachyantha | 189 |
Oryza_glaberrima | 283 |
Oryza_glumipatula | 168 |
Oryza_meridionalis | 111 |
Oryza_nivara | 96 |
Oryza_punctata | 89 |
Oryza_rufipogon | 81 |
Oryza_sativa_Indica_Group | 392 |
Oryza_sativa_Japonica_Group | 376 |
Ostreococcus_lucimarinus_CCE9901 | 10 |
Panicum_hallii_var._filipes | 114 |
Panicum_hallii_var._hallii | 102 |
Phaseolus_vulgaris | 571 |
Physcomitrella_patens | 38 |
Populus_trichocarpa | 157 |
Prunus_persica | 71 |
Setaria_italica | 384 |
Solanum_lycopersicum | 427 |
Solanum_tuberosum | 296 |
Sorghum_bicolor | 37 |
Theobroma_cacao | 50 |
Trifolium_pratense | 437 |
Triticum_aestivum | 438 |
Triticum_dicoccoides | 642 |
Vigna_angularis | 189 |
Vigna_radiata_var._radiata | 59 |
Vitis_vinifera | 380 |
Zea_mays | 176 |
Here is a summary of all genomic alignments. New Whole Genome Alignments between
These were generated for the new and updated genomes.
_______________________________________________________________________________________________________________________________________________________
Our partner Ensembl Genomes offers 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 61_96 is set as version 43_96 at Ensembl.
Example of recently curated rice pathway: Response to aluminum stress
*data from sequenced transcriptomes
^ projections currently exclude cell-cycle pathways and annotations
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 the collaborator databases/online resources
Species | Pathways | Reactions | Genes | Sequence Source |
Homology Method |
Oryza sativa | 298 | 1723 | 1824 | UniProt | Curated Reference |
Actinidia chinensis | 238 | 594 | 1410 | Ensembl Gramene | Compara |
Aegilops tauschii | 236 | 627 | 1123 | Ensembl Gramene | Compara |
Amborella trichopoda | 236 | 573 | 682 | Ensembl Gramene | Compara |
Arabidopsis halleri | 235 | 582 | 1021 | Ensembl Gramene | Compara |
Arabidopsis lyrata | 235 | 584 | 1053 | Ensembl Gramene | Compara |
Arabidopsis thaliana | 236 | 590 | 1059 | Ensembl Gramene | Compara |
Arachis duranensis | 245 | 624 | 1057 | PeanutBase | Inparanoid |
Arachis ipaensis | 240 | 594 | 949 | PeanutBase | Inparanoid |
Beta vulgaris | 235 | 576 | 747 | Ensembl Gramene | Compara |
Brachypodium distachyon | 231 | 619 | 1031 | Ensembl Gramene | Compara |
Brassica napus | 238 | 590 | 3209 | Ensembl Gramene | Compara |
Brassica oleracea | 236 | 581 | 1619 | Ensembl Gramene | Compara |
Brassica rapa | 235 | 578 | 1598 | Ensembl Gramene | Compara |
Cajanus cajan | 240 | 602 | 1235 | LegumeInfo | Inparanoid |
Capsicum annuum | 242 | 583 | 1214 | PMID: 24441736 | Inparanoid |
Chlamydomonas reinhardtii | 164 | 332 | 273 | Ensembl Gramene | Compara |
Chondrus crispus | 140 | 210 | 183 | Ensembl Gramene | Compara |
Cicer arietinum | 241 | 595 | 1461 | NCBI | Inparanoid |
Citrus sinensis | 240 | 594 | 2366 | Phytozome | Inparanoid |
Coffea canephora | 240 | 590 | 1050 | PMID:25190796 | Inparanoid |
Corchorus capsularis | 233 | 554 | 781 | Ensembl Gramene | Compara |
Cucumis sativus | 237 | 590 | 834 | Ensembl Gramene | Compara |
Cyanidioschyzon merolae | 142 | 216 | 169 | Ensembl Gramene | Compara |
Daucus carota | 235 | 574 | 1091 | Ensembl Gramene | Compara |
Dioscorea rotundata | 222 | 480 | 605 | Ensembl Gramene | Compara |
Erythranthe guttata | 213 | 502 | 670 | Phytozome | Inparanoid |
Eucalyptus grandis | 215 | 501 | 707 | Phytozome | Inparanoid |
Fragaria vesca | 240 | 566 | 1014 | Phytozome | Inparanoid |
Galdieria sulphuraria | 152 | 253 | 206 | Ensembl Gramene | Compara |
Glycine max | 236 | 599 | 1947 | Ensembl Gramene | Compara |
Gossypium raimondii | 238 | 602 | 1420 | Ensembl Gramene | Compara |
Helianthus annuus | 237 | 590 | 1576 | Ensembl Gramene | Compara |
Hordeum vulgare | 234 | 596 | 1043 | Ensembl Gramene | Compara |
Jatropha curcas | 213 | 493 | 534 | KDRI (Kazusa) | Inparanoid |
Leersia perrieri | 236 | 618 | 1001 | Ensembl Gramene | Compara |
Lupinus angustifolius | 237 | 597 | 1430 | Ensembl Gramene | Compara |
Malus domestica | 238 | 576 | 2009 | PMID: 20802477 | Inparanoid |
Manihot esculenta | 236 | 597 | 1180 | Ensembl Gramene | Compara |
Medicago truncatula | 236 | 587 | 1182 | Ensembl Gramene | Compara |
Musa acuminata | 227 | 566 | 1280 | Ensembl Gramene | Compara |
Nicotiana attenuata | 232 | 507 | 703 | Ensembl Gramene | Compara |
Oryza australiensis * | 234 | 545 | 1704 | OMAP/OGE | Inparanoid |
Oryza barthii | 238 | 642 | 1057 | Ensembl Gramene | Compara |
Oryza brachyantha | 236 | 625 | 1013 | Ensembl Gramene | Compara |
Oryza glaberrima | 242 | 636 | 1051 | Ensembl Gramene | Compara |
Oryza glumaepatula | 239 | 642 | 1066 | Ensembl Gramene | Compara |
Oryza granulata | 239 | 568 | 3509 | OMAP/OGE | Inparanoid |
Oryza indica | 242 | 664 | 1157 | Ensembl Gramene | Compara |
Oryza longistaminata * | 236 | 604 | 917 | Ensembl Gramene | Compara |
Oryza meridionalis | 233 | 581 | 914 | Ensembl Gramene | Compara |
Oryza minuta * | 240 | 588 | 2092 | OMAP/OGE | Inparanoid |
Oryza nivara | 238 | 652 | 1066 | Ensembl Gramene | Compara |
Oryza officinalis * | 237 | 579 | 1882 | OMAP/OGE | Inparanoid |
Oryza punctata | 235 | 628 | 1067 | Ensembl Gramene | Compara |
Oryza rufipogon | 238 | 641 | 1076 | Ensembl Gramene | Compara |
Oryza sativa aus subgroup | 191 | 287 | 365 | PMID: 24578372 | Inparanoid |
Ostreococcus lucimarinus | 156 | 274 | 226 | Ensembl Gramene | Compara |
Panicum hallii FIL2 | 235 | 639 | 1076 | Ensembl Gramene | Compara |
Panicum hallii var. hallii HAL2 | 237 | 642 | 1109 | Ensembl Gramene | Compara |
Phaseolus vulgaris | 239 | 599 | 1065 | Ensembl Gramene | Compara |
Phoenix dactylifera | 234 | 557 | 1097 | PMID: 23917264 | Inparanoid |
Physcomitrella patens | 214 | 513 | 1060 | Ensembl Gramene | Compara |
Picea abies | 236 | 530 | 1315 | Congenie | Inparanoid |
Pinus taeda | 225 | 475 | 1308 | TreeBase | Inparanoid |
Populus trichocarpa | 236 | 596 | 1329 | Ensembl Gramene | Compara |
Prunus persica | 239 | 606 | 944 | Ensembl Gramene | Compara |
Selaginella moellendorffii | 220 | 522 | 1226 | Ensembl Gramene | Compara |
Setaria italica | 237 | 631 | 1114 | Ensembl Gramene | Compara |
Solanum lycopersicum | 235 | 583 | 968 | Ensembl Gramene | Compara |
Solanum tuberosum | 229 | 561 | 967 | Ensembl Gramene | Compara |
Sorghum bicolor | 237 | 639 | 1095 | Ensembl Gramene | Compara |
Synechocystis sp. PCC 6803 | 157 | 311 | 263 | Jaiswal | Inparanoid |
Theobroma cacao | 238 | 598 | 877 | Ensembl Gramene | Compara |
Trifolium pratense | 237 | 588 | 1006 | Ensembl Gramene | Compara |
Triticum aestivum | 238 | 642 | 3574 | Ensembl Gramene | Compara |
Triticum dicoccoides | 238 | 634 | 2123 | Ensembl Gramene | Compara |
Triticum turgidum * | 238 | 597 | 2753 | PMID: 23800085 | Inparanoid |
Triticum urartu | 229 | 544 | 864 | Ensembl Gramene | Compara |
Vigna angularis | 237 | 582 | 1003 | Ensembl Gramene | Compara |
Vigna radiata | 226 | 543 | 891 | Ensembl Gramene | Compara |
Vitis vinifera | 238 | 602 | 930 | Ensembl Gramene | Compara |
Zea mays | 235 | 621 | 1380 | Ensembl Gramene | 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.
The Plant Reactome increasingly includes curated regulatory and developmental pathways, which require more reference DNA and RNA sequence elements, in addition to the traditional protein-coding elements. These sequence elements are not included in Reactome orthoinference at this time, although we are actively working to enhance the projection process to include these elements on projected pathways in future releases.
Please let us know if you have questions or suggestions.
The Gramene Team
www.gramene.org