The Gramene Knowledgebase Team is pleased to announce its Release #64 with the Genome section providing access to information on 114 reference genomes and 123,064 gene family trees. We are adding 21 new reference genomes, including Persian wheat, sesame and new varieties of potato and barley. For the complete list, see below. With these new genomes, our comparative genomics collection has reached a total of 340 pairwise DNA alignments and 80 synteny maps. Updates were applied to maize, banana, Arabidopsis, earthmoss, white Guinea yam, and Peruvian cotton.
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 106 species including crops and model plants, lower plants and single-cell photoautotrophs. This release is a maintenance release with one new addition. The gene homology-based projections were added for the version #5 of the reference maize genome (Zea mays version v5). Maize v4 pathway projections are also available for comparison and continued access. In total, Plant Reactome is currently hosting 320 rice curated pathways and their gene-orthology based projection for 106 species.
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).
Note: A maximum of 100 genomes is included in the Compara Gene Family Trees analysis, which will change depending on data available for each release. You can find the list of included genomes in Ensembl Plant's github repository.
Compara
Gene Trees
The EnsemblCompara GeneTree database updated. A total of total of 123,064 GeneTree families were constructed comprising 2,956,404 individual genes from 90 plant genomes with 3,256,006 input proteins.
Putative Split Genes
Species Name |
Split genes |
Actinidia chinensis var. chinensis.csv |
149 |
Aegilops tauschii subsp. strangulata.csv |
169 |
Arabidopsis lyrata subsp. lyrata.csv |
87 |
Arabidopsis thaliana.csv |
35 |
Asparagus officinalis.csv |
483 |
Beta vulgaris subsp. vulgaris.csv |
49 |
Brachypodium distachyon.csv |
67 |
Brassica oleracea var. oleracea.csv |
631 |
Brassica rapa.csv |
98 |
Camelina sativa.csv |
721 |
Cannabis sativa.csv |
96 |
Capsicum annuum.csv |
614 |
Chlamydomonas reinhardtii.csv |
30 |
Citrullus lanatus.csv |
187 |
Coffea canephora.csv |
296 |
Cucumis sativus.csv |
408 |
Daucus carota subsp. sativus.csv |
227 |
Dioscorea cayenensis subsp. rotundata.csv |
528 |
Eragrostis curvula.csv |
316 |
Glycine max.csv |
220 |
Gossypium raimondii.csv |
357 |
Helianthus annuus.csv |
487 |
Hordeum vulgare subsp. vulgare.csv |
141 |
Ipomoea triloba.csv |
336 |
Leersia perrieri.csv |
75 |
Lupinus angustifolius.csv |
112 |
Malus domestica.csv |
763 |
Manihot esculenta.csv |
136 |
Medicago truncatula.csv |
182 |
Nicotiana attenuata.csv |
47 |
Nymphaea colorata.csv |
346 |
Olea europaea var. sylvestris.csv |
204 |
Oryza barthii.csv |
99 |
Oryza brachyantha.csv |
193 |
Oryza glaberrima.csv |
286 |
Oryza glumipatula.csv |
153 |
Oryza meridionalis.csv |
101 |
Oryza nivara.csv |
113 |
Oryza punctata.csv |
85 |
Oryza rufipogon.csv |
94 |
Oryza sativa Indica Group.csv |
402 |
Oryza sativa Japonica Group.csv |
399 |
Panicum hallii var. hallii.csv |
114 |
Panicum hallii.csv |
117 |
Papaver somniferum.csv |
201 |
Phaseolus vulgaris.csv |
574 |
Physcomitrium patens.csv |
35 |
Populus trichocarpa.csv |
168 |
Prunus persica.csv |
67 |
Rosa chinensis.csv |
1268 |
Saccharum spontaneum.csv |
324 |
Sesamum indicum.csv |
220 |
Setaria italica.csv |
397 |
Setaria viridis.csv |
164 |
Solanum lycopersicum.csv |
443 |
Solanum tuberosum.csv |
304 |
Sorghum bicolor.csv |
40 |
Theobroma cacao.csv |
88 |
Trifolium pratense.csv |
409 |
Triticum aestivum.csv |
414 |
Triticum dicoccoides.csv |
577 |
Triticum turgidum subsp. durum.csv |
491 |
Vigna angularis.csv |
189 |
Vigna radiata var. radiata.csv |
54 |
Vitis vinifera.csv |
384 |
Zea mays.csv |
293 |
Genomic alignments
There are 340 pairwise genomic alignments.
Synteny data
There are 80 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 64. This release is a maintenance release with one new addition. The gene homology-based projections were added for the version #5 of the reference maize genome (Zea mays version v5). We also provide the Maize v4 pathway projections for comparison and continued access. Plant Reactome now hosts 320 rice curated pathways and their gene-orthology based projection for 106 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 106 projected species hosted by Plant Reactome.
Pathway Projection Statistics
We have extended orthology-based pathway projections for version #5 of the reference maize genome (Zea mays version v5). In total, Plant Reactome now hosts pathway projections for 106 species ranging from unicellular autotrophs to higher plants.
*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 collaborator databases/online resources
Species | Pathways | Reactions | Gene Products | Sequence Source | Homology Method |
Oryza sativa | 320 | 1887 | 2170 | Uniprot | Curated Reference |
Actinidia chinensis | 264 | 669 | 1626 | Ensembl Gramene | Compara |
Aegilops tauschii | 270 | 719 | 1258 | Ensembl Gramene | Compara |
Amborella trichopoda | 265 | 659 | 796 | Ensembl Gramene | Compara |
Ananas comosus | 255 | 634 | 851 | Ensembl Gramene | Compara |
Arabidopsis halleri | 266 | 670 | 1197 | Ensembl Gramene | Compara |
Arabidopsis lyrata | 265 | 669 | 1231 | Ensembl Gramene | Compara |
Arabidopsis thaliana | 266 | 677 | 1219 | 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 | 891 | Ensembl Gramene | Compara |
Brachypodium distachyon | 264 | 710 | 1162 | Ensembl Gramene | Compara |
Brassica napus | 268 | 676 | 3708 | Ensembl Gramene | Compara |
Brassica oleracea | 265 | 664 | 1885 | Ensembl Gramene | Compara |
Brassica rapa | 264 | 666 | 1863 | 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 | 1060 | Ensembl Gramene | Compara |
Citrus sinensis | 270 | 700 | 2860 | Phytozome | Inparanoid |
Coffea canephora | 262 | 665 | 1005 | Ensembl Gramene | Compara |
Corchorus capsularis | 261 | 628 | 906 | 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 | 1165 | 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 | Ensembl Gramene | Compara |
Glycine max | 267 | 682 | 2242 | Ensembl Gramene | Compara |
Gossypium raimondii | 267 | 690 | 1639 | Ensembl Gramene | Compara |
Helianthus annuus | 261 | 657 | 1710 | Ensembl Gramene | Compara |
Hordeum vulgare | 265 | 677 | 1167 | Ensembl Gramene | Compara |
Humulus lupulus | 249 | 478 | 720 | Hendrix | Inparanoid |
Humulus lupulus var. lupulus | 267 | 680 | 2236 | Hendrix | Inparanoid |
Ipomoea triloba | 263 | 661 | 1333 | Ensembl Gramene | Compara |
Jatropha curcas | 269 | 663 | 1233 | KDRI (Kazusa) | Inparanoid |
Leersia perrieri | 267 | 696 | 1134 | Ensembl Gramene | Compara |
Lupinus angustifolius | 265 | 670 | 1631 | Ensembl Gramene | Compara |
Malus domestica | 262 | 660 | 1610 | PMID: 20802477 | Inparanoid |
Manihot esculenta | 266 | 678 | 1384 | 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 | 817 | 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 | 1197 | Ensembl Gramene | Compara |
Oryza brachyantha | 266 | 715 | 1149 | Ensembl Gramene | Compara |
Oryza glaberrima | 271 | 722 | 1186 | Ensembl Gramene | Compara |
Oryza glumaepatula | 270 | 740 | 1201 | Ensembl Gramene | Compara |
Oryza longistaminata* | 267 | 684 | 1032 | Ensembl Gramene | Compara |
Oryza meridionalis | 261 | 650 | 1026 | Ensembl Gramene | Compara |
Oryza meyeriana var. granulata | 267 | 657 | 4182 | OMAP/OGE | Inparanoid |
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 | 1201 | Ensembl Gramene | Compara |
Oryza rufipogon | 267 | 738 | 1212 | Ensembl Gramene | Compara |
Oryza sativa aus subgroup | 206 | 310 | 377 | PMID: 24578372 | Inparanoid |
Oryza sativa Indica Group | 271 | 756 | 1294 | Ensembl Gramene | Compara |
Ostreococcus lucimarinus | 178 | 304 | 267 | Ensembl Gramene | Compara |
Panicum hallii FIL2 | 267 | 734 | 1221 | Ensembl Gramene | Compara |
Panicum hallii var. hallii HAL2 | 269 | 739 | 1257 | Ensembl Gramene | Compara |
Phaseolus vulgaris | 266 | 678 | 1223 | Ensembl Gramene | Compara |
Phoenix dactylifera | 269 | 662 | 1455 | PMID: 23917264 | Inparnoid |
Phyllostachys edulis | 273 | 661 | 1908 | NCGR | Inparanoid |
Physcomitrella patens | 247 | 576 | 1209 | Ensembl Gramene | Compara |
Picea abies | 271 | 651 | 1889 | Congenie | Inparanoid |
Pinus taeda | 267 | 643 | 2630 | TreeBase | Inparanoid |
Pistacia vera | 263 | 675 | 1264 | 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 | 266 | 673 | 2124 | Ensembl Gramene | Compara |
Salvia hispanica | 273 | 672 | 2190 | Jaiswal | Inparanoid |
Selaginella moellendorffii | 249 | 575 | 1352 | Ensembl Gramene | Compara |
Setaria italica | 269 | 723 | 1244 | Ensembl Gramene | Compara |
Solanum lycopersicum | 260 | 668 | 1126 | Ensembl Gramene | Compara |
Solanum tuberosum | 254 | 626 | 1120 | Ensembl Gramene | Compara |
Sorghum bicolor | 269 | 738 | 1250 | Ensembl Gramene | Compara |
Synechocystis sp. PCC 6803 | 150 | 268 | 216 | Jaiswal | Inparanoid |
Theobroma cacao | 267 | 687 | 1008 | Ensembl Gramene | Compara |
Trifolium pratense | 264 | 667 | 1149 | Ensembl Gramene | Compara |
Triticum aestivum | 271 | 734 | 3984 | Ensembl Gramene | Compara |
Triticum dicoccoides | 271 | 728 | 2381 | Ensembl Gramene | Compara |
Triticum turgidum* | 269 | 723 | 2403 | Ensembl Gramene | Compara |
Triticum urartu | 259 | 613 | 966 | Ensembl Gramene | Compara |
Vigna angularis | 261 | 650 | 1161 | Ensembl Gramene | Compara |
Vigna radiata | 255 | 613 | 1005 | Ensembl Gramene | Compara |
Vitis vinifera | 266 | 680 | 1074 | Ensembl Gramene | Compara |
Zea mays ver4 | 269 | 708 | 1540 | Ensembl Gramene | Compara |
Zea mays ver5 | 270 | 741 | 1617 | 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 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.
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 64_104 is set as version 51_104 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.