The Gramene Knowledgebase Team is pleased to announce its Release #63 with the Genome section providing access to information on 93 reference genomes and 122,947 gene family trees. We are adding 26 new reference genomes, including pineapple, cantaloupe, watermelon, Golden apple, clementine, sweet cherry, almond, pistachio, olive tree, cannabis or marijuana, tobacco, a relative of sugar cane, five varieties of European wheat, and new varieties of barley and cocoa. With these new genomes, our comparative genomics collection has reached a total of 382 pairwise DNA alignments and 84 synteny maps. We have also added SNP variation datasets for sunflower, Golden apple, and durum wheat.
The Plant Reactome is the pathway knowledgebase of Gramene. We utilize the Reactome pathway data model to represent plant metabolic, transport and signaling pathways, developmental processes, organ differentiation, and transcriptional regulatory networks. Manual biocuration is conducted in the reference species rice (O. sativa) and pathways are then projected via gene orthology to other species including crops and model plants, lower plants and single-cell photoautotrophs. In this release, we have extended orthology-based pathway projections for 9 new species; added 13 newly curated pathways; and updated 8 pathways in the reference species Oryza sativa. In total, Plant Reactome is currently hosting 320 rice curated pathways and their gene-orthology based projection for 106 species ranging from unicellular autotrophs to higher plants.
The 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 Agricultural Research Service of the U.S. Department of Agriculture (USDA ARS 1907-21000-030-00D), and the National Science Foundation (NSF IOS-1127112).
Updated genome browser, database schema, and API to Ensembl 101 software.
NOTE: We are aware about the filter to select chromosome for a given region in sorghum being missing in the current release 63. This will be fixed in the next release 64. Meantime, users are encouraged to use the "Multiple regions (Chr:Start:End:Strand) [Max 250 advised]" filter for one or many regions. Examples of formatted entries are:
4:10000:1000000:-1
7:150000:250000:1
Here is a complete list of Genomes with every data category available for it in Gramene's genome browser.
Compara
Gene Trees
The EnsemblCompara GeneTree database updated. A total of total of 122,947 GeneTree families were constructed comprising 2,875,432 individual genes from 93 plant genomes with 3,169,866 input proteins.
Putative Split Genes
Species_id |
Split_genes |
Actinidia_chinensis_var._chinensis |
160 |
Aegilops_tauschii_subsp._strangulata |
200 |
Arabidopsis_lyrata_subsp._lyrata |
96 |
Arabidopsis_thaliana |
30 |
Arabis_alpina |
28 |
Beta_vulgaris_subsp._vulgaris |
46 |
Brachypodium_distachyon |
78 |
Brassica_oleracea_var._oleracea |
668 |
Brassica_rapa |
100 |
Camelina_sativa |
814 |
Cannabis_sativa |
88 |
Capsicum_annuum |
704 |
Chlamydomonas_reinhardtii |
38 |
Citrullus_lanatus |
222 |
Coffea_canephora |
326 |
Cucumis_sativus |
480 |
Daucus_carota_subsp._sativus |
218 |
Dioscorea_rotundata |
206 |
Eragrostis_curvula |
374 |
Glycine_max |
206 |
Gossypium_raimondii |
426 |
Helianthus_annuus |
606 |
Hordeum_vulgare_subsp._vulgare |
160 |
Ipomoea_triloba |
430 |
Leersia_perrieri |
88 |
Lupinus_angustifolius |
114 |
Malus_domestica |
872 |
Manihot_esculenta |
130 |
Medicago_truncatula |
218 |
Musa_acuminata_subsp._malaccensis |
690 |
Nicotiana_attenuata |
60 |
Nymphaea_colorata |
400 |
Olea_europaea_var_sylvestris |
176 |
Oryza_barthii |
122 |
Oryza_brachyantha |
192 |
Oryza_glaberrima |
422 |
Oryza_glumipatula |
166 |
Oryza_meridionalis |
110 |
Oryza_nivara |
118 |
Oryza_punctata |
90 |
Oryza_rufipogon |
122 |
Oryza_sativa_Indica_Group |
530 |
Oryza_sativa_Japonica_Group |
482 |
Ostreococcus_lucimarinus_CCE9901 |
10 |
Panicum_hallii_var._filipes |
114 |
Panicum_hallii_var._hallii |
122 |
Phaseolus_vulgaris |
662 |
Physcomitrella_patens |
46 |
Populus_trichocarpa |
210 |
Prunus_persica |
70 |
Rosa_chinensis |
1476 |
Saccharum_spontaneum |
352 |
Setaria_italica |
422 |
Setaria_viridis |
158 |
Solanum_lycopersicum |
482 |
Solanum_tuberosum |
316 |
Sorghum_bicolor |
34 |
Theobroma_cacao |
102 |
Trifolium_pratense |
448 |
Triticum_aestivum |
448 |
Triticum_dicoccoides |
908 |
Triticum_turgidum_subsp_durum |
552 |
Vigna_angularis |
206 |
Vigna_radiata_var._radiata |
60 |
Vitis_vinifera |
470 |
Zea_mays |
184 |
Genomic alignments
There are 382 pairwise genomic alignments.
Synteny data
There are 84 synteny maps.
Protein Annotation, GO, Xref Protein domain information
These were generated for the new and updated genomes.
Gramene Mart
Here, we provide a summary of Gramene Release 63 including website and coding updates, a list of new & updated pathways, information on new species, and projection statistics. Plant Reactome now hosts pathway projections for 105 plant species.
Website and coding updates
This release utilizes an updated ortho-inference process, converted to Java from Perl and revised for efficiency. The script uses the rules previously set up for ortho-inference while containing minor adjustments to facilitate changes in the underlying Reactome data schema and take advantage of new features and functionalities present in our partner Reactome site.
Analytical tools
Currently, Plant Reactome supports researchers with the following analytical tools:
- Search for gene/protein, metabolites, pathways
- Upload and analyze gene-expression data on plant pathways
- Upload and analyze gene-gene interaction data on plant pathways
- Compare reference rice pathways with pathways from any of 97 projected species hosted by Plant Reactome.
Curation of reference rice pathways
We have added 13 newly curated pathways, 8 updated pathways, and 1 "container" pathways, resulting in a total of 320 reference rice pathways. In this release, we focused on updates to rice metabolic pathways and curation of cell-cycle events.
New pathways | Updated pathways |
(under Cell Cycle) (under Root Structure Development) |
Photorespiration Cardiolipin biosynthesis Flower development Floral bracts development Primary root development UDP-L-arabinose biosynthesis and transport Vitamin E biosynthesis Ascorbate biosynthesis |
Pathway Projection Statistics
Species | Pathways | Reactions | Genes | Sequence Source |
Homology Method |
Oryza sativa | 320 | 1887 | 2170 | UniProt | Curated Reference |
Actinidia chinensis | 264 | 669 | 1626 | Ensembl Gramene | Compara |
Aegilops tauschii | 270 | 719 | 1257 | Ensembl Gramene | Compara |
Amborella trichopoda | 265 | 659 | 799 | Ensembl Gramene | Compara |
Ananas comosus | 255 | 634 | 852 | Ensembl Gramene | Compara |
Arabidopsis halleri | 266 | 670 | 1197 | Ensembl Gramene | Compara |
Arabidopsis lyrata | 265 | 669 | 1234 | Ensembl Gramene | Compara |
Arabidopsis thaliana | 266 | 677 | 1215 | Ensembl Gramene | Compara |
Arachis duranensis | 277 | 743 | 1581 | PeanutBase | Inparanoid |
Arachis ipaensis | 274 | 702 | 1532 | PeanutBase | Inparanoid |
Asparagus officinalis | 275 | 664 | 1075 | Phytozome | Inparanoid |
Beta vulgaris | 266 | 663 | 889 | Ensembl Gramene | Compara |
Brachypodium distachyon | 264 | 710 | 1163 | Ensembl Gramene | Compara |
Brassica napus | 268 | 676 | 3708 | Ensembl Gramene | Compara |
Brassica oleracea | 265 | 664 | 1885 | Ensembl Gramene | Compara |
Brassica rapa | 264 | 665 | 1862 | Ensembl Gramene | Compara |
Cajanus cajan | 273 | 702 | 1573 | LegumeInfo | Inparanoid |
Cannabis sativa | 267 | 651 | 1603 | JCVI | Inparanoid |
Cannabis sativa subsp. indica | 274 | 690 | 1100 | CCBR-UToronto | Inparanoid |
Capsella rubella | 274 | 700 | 1772 | Phytozome | Inparanoid |
Capsicum annuum | 261 | 638 | 1159 | Ensembl Gramene | Compara |
Chara braunii | 207 | 377 | 439 | Ensembl Gramene | Compara |
Chlamydomonas reinhardtii | 192 | 365 | 316 | Ensembl Gramene | Compara |
Chondrus crispus | 159 | 229 | 213 | Ensembl Gramene | Compara |
Cicer arietinum | 275 | 687 | 1298 | NCBI | Inparanoid |
Citrullus lanatus | 272 | 692 | 1172 | CuGenDB | Inparanoid |
Citrus clementina | 269 | 681 | 1058 | Ensembl Gramene | Compara |
Citrus sinensis | 270 | 700 | 2860 | Phytozome | Inparanoid |
Coffea canephora | 262 | 665 | 1005 | Ensembl Gramene | Compara |
Corchorus capsularis | 261 | 628 | 908 | Ensembl Gramene | Compara |
Corchorus olitorius | 274 | 665 | 1311 | NCBI | Inparanoid |
Cucumis sativus | 265 | 672 | 980 | Ensembl Gramene | Compara |
Cyanidioschyzon merolae | 159 | 235 | 204 | Ensembl Gramene | Compara |
Cynara cardunculus var. scolymus | 263 | 645 | 1163 | Ensembl Gramene | Compara |
Daucus carota | 264 | 644 | 1268 | Ensembl Gramene | Compara |
Dioscorea rotundata | 255 | 547 | 689 | Ensembl Gramene | Compara |
Eragrostis curvula | 267 | 697 | 1505 | Ensembl Gramene | Compara |
Eragrostis tef | 266 | 694 | 1724 | Ensembl Gramene | Compara |
Erythranthe guttata | 270 | 700 | 1515 | Phytozome | Inparanoid |
Eucalyptus grandis | 273 | 707 | 1716 | Phytozome | Inparanoid |
Fragaria vesca | 272 | 667 | 1338 | Phytozome | Inparanoid |
Galdieria sulphuraria | 173 | 290 | 246 | Galdieria sulphuraria | Compara |
Glycine max | 267 | 682 | 2250 | Glycine max | Compara |
Gossypium raimondii | 267 | 690 | 1643 | Gossypium raimondii | Compara |
Helianthus annuus | 261 | 657 | 1706 | Helianthus annuus | Compara |
Hordeum vulgare | 265 | 677 | 1169 | Hordeum vulgare | Compara |
Humulus lupulus haplotig | 249 | 478 | 720 | Hendrix | Inparanoid |
Humulus lupulus primary | 267 | 680 | 2236 | Hendrix | Inparanoid |
Ipomoea triloba | 263 | 661 | 1333 | Ensembl Gramene | Compara |
Jatropha curcas | 269 | 663 | 1233 | KDRI (Kazusa) | Inparanoid |
Leersia perrieri | 267 | 697 | 1133 | Leersia perrieri | Compara |
Lupinus angustifolius | 265 | 670 | 1631 | Lupinus angustifolius | Compara |
Malus domestica | 262 | 660 | 1610 | PMID: 20802477 | Inparanoid |
Manihot esculenta | 266 | 678 | 1381 | Ensembl Gramene | Compara |
Marchantia polymorpha | 249 | 575 | 695 | Ensembl Gramene | Compara |
Medicago truncatula | 264 | 669 | 1330 | Ensembl Gramene | Compara |
Musa acuminata | 256 | 630 | 1433 | Ensembl Gramene | Compara |
Nelumbo nucifera | 273 | 689 | 1397 | iPlant Collaborative | Inparanoid |
Nicotiana attenuata | 253 | 536 | 815 | Ensembl Gramene | Compara |
Olea europaea var. sylvestris | 256 | 627 | 1435 | Ensembl Gramene | Compara |
Oryza australiensis * | 268 | 651 | 2247 | OMAP/OGE | Inparanoid |
Oryza barthii | 269 | 737 | 1198 | Ensembl Gramene | Compara |
Oryza brachyantha | 266 | 715 | 1151 | Ensembl Gramene | Compara |
Oryza glaberrima | 271 | 721 | 1185 | Ensembl Gramene | Compara |
Oryza glumaepatula | 270 | 740 | 1201 | Ensembl Gramene | Compara |
Oryza granulata | 267 | 657 | 4182 | OMAP/OGE | Inparanoid |
Oryza indica | 271 | 756 | 1298 | Ensembl Gramene | Compara |
Oryza longistaminata * | 267 | 684 | 1033 | Ensembl Gramene | Compara |
Oryza meridionalis | 261 | 651 | 1026 | Ensembl Gramene | Compara |
Oryza minuta * | 271 | 680 | 2712 | OMAP/OGE | Inparanoid |
Oryza nivara | 267 | 743 | 1198 | Ensembl Gramene | Compara |
Oryza officinalis * | 274 | 686 | 2357 | OMAP/OGE | Inparanoid |
Oryza punctata | 265 | 723 | 1202 | Ensembl Gramene | Compara |
Oryza rufipogon | 267 | 739 | 1212 | Ensembl Gramene | Compara |
Oryza sativa aus kasalath | 206 | 310 | 377 | PMID: 24578372 | Inparanoid |
Ostreococcus lucimarinus | 178 | 304 | 267 | Ensembl Gramene | Compara |
Panicum hallii FIL2 | 267 | 734 | 1221 | Ensembl Gramene | Compara |
Panicum hallii var. hallii HAL2 | 269 | 739 | 1256 | Ensembl Gramene | Compara |
Phaseolus vulgaris | 266 | 678 | 1223 | Ensembl Gramene | Compara |
Phoenix dactylifera | 269 | 662 | 1455 | PMID: 23917264 | Inparanoid |
Phyllostachys edulis | 273 | 661 | 1908 | NCGR | Inparanoid |
Physcomitrella patens | 247 | 576 | 1208 | Ensembl Gramene | Compara |
Picea abies | 271 | 651 | 1889 | Congenie | Inparanoid |
Pinus taeda | 267 | 643 | 2630 | TreeBase | Inparanoid |
Pistacia vera | 263 | 675 | 1269 | Ensembl Gramene | Compara |
Populus trichocarpa | 266 | 682 | 1519 | Ensembl Gramene | Compara |
Prunus avium | 256 | 612 | 848 | Ensembl Gramene | Compara |
Prunus persica | 267 | 690 | 1052 | Ensembl Gramene | Compara |
Saccharum spontaneum | 265 | 671 | 2121 | Ensembl Gramene | Compara |
Salvia hispanica | 273 | 672 | 2190 | Jaiswal | Inparanoid |
Selaginella moellendorffii | 249 | 575 | 1352 | Ensembl Gramene | Compara |
Setaria italica | 269 | 723 | 1245 | Ensembl Gramene | Compara |
Solanum lycopersicum | 260 | 668 | 1128 | Ensembl Gramene | Compara |
Solanum tuberosum | 254 | 626 | 1120 | Ensembl Gramene | Compara |
Sorghum bicolor | 269 | 737 | 1248 | Ensembl Gramene | Compara |
Synechocystis sp. PCC 6803 | 150 | 268 | 216 | Jaiswal | Inparanoid |
Theobroma cacao | 267 | 687 | 1008 | Ensembl Gramene | Compara |
Trifolium pratense | 264 | 667 | 1147 | Ensembl Gramene | Compara |
Triticum aestivum | 271 | 734 | 3990 | Ensembl Gramene | Compara |
Triticum dicoccoides | 271 | 727 | 2380 | Ensembl Gramene | Compara |
Triticum turgidum * | 269 | 723 | 2403 | Ensembl Gramene | Compara |
Triticum urartu | 259 | 613 | 965 | Ensembl Gramene | Compara |
Vigna angularis | 261 | 650 | 1157 | Ensembl Gramene | Compara |
Vigna radiata | 255 | 613 | 1005 | Ensembl Gramene | Compara |
Vitis vinifera | 266 | 680 | 1074 | Ensembl Gramene | Compara |
Zea mays | 269 | 708 | 1540 | Ensembl Gramene | Compara |
Zoysia japonica | 271 | 669 | 1920 | KDRI (Kazusa) | Inparanoid |
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 ortho-inference at this time, although we are actively working to enhance the projection process to include these elements on projected pathways in future releases.
Plant Reactome mirror at Powered-by-CyVerse
We continue to leverage the resources made available in the Powered-by-CyVerse virtual server environment by providing the Plant Reactome database mirror (https://plantreactome.cyverse.org) to facilitate training, education, and integration with the CyVerse platform and user community.
Web Services: Gramene's web services page documents many ways to directly connect to and analyze our databases.
Public MySQL Server:
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 62_98 is set as version 45_98 at Ensembl.
Website and coding updates
The latest Plant Reactome pathway data has been re-indexed and made available via Gramene search.
Please let us know if you have questions or suggestions.
The Gramene Team
www.gramene.org.