The Gramene Knowledgebase Team is pleased to announce its Release #62 with the Genome section providing access to information on 96,607 GeneTree families comprising 2,146,774 individual genes from 67 plant genomes with 2,365,624 input proteins. It includes six new reference genomes: robusta coffee (Coffea canephora), hot pepper (Capsicum annuum), global artichoke (Cynara cardunculus), eragrostis tef (Eragrostis tef), durum wheat (Triticum turgidum, tetraploid AABB), and common liverwort (Marchantia polymorpha), and one updated genome: criollo cocoa, cacao or chocolate tree (Theobroma cacao).
The Plant Reactome, Gramene's pathway portal, hosts pathway projections for 97 species ranging from unicellular autotrophs to higher plants. In this release, we have extended orthology-based pathway projections for 15 new species; added 6 newly curated pathways; and updated 11 pathways in tthe reference species Oryza sativa (resulting in a total of 306 rice pathways). In the following sections we provide detailed summary of updates in the Gramene Knowledgebase.
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 National Science Foundation, USA.
List of Genomes (Genome browser)
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 |
Capsicum annuum | ASM51225v2 | GCA_000512255.2 |
Chlamydomonas reinhardtii |
Chlamydomonas_reinhardtii_v5.5 |
GCA_000002595.3 |
Chondrus crispus |
ASM35022v2 |
GCA_000350225.2 |
Coffea canephora | AUK_PRJEB4211_v1 | GCA_900059795.1 |
Corchorus capsularis |
CCACVL1_1.0 |
GCA_001974805.1 |
Cucumis sativus |
ASM407v2 |
GCA_000004075.2 |
Cyanidioschyzon merolae |
ASM9120v1 |
GCA_000091205.1 |
Cynara cardunculus | CcrdV1 | GCA_001531365.1 |
Daucus carota |
ASM162521v1 |
GCA_001625215.1 |
Dioscorea rotundata |
TDr96_F1_Pseudo_Chromosome_v1.0 |
GCA_002240015.2 |
Eragrostis tef | ASM97063v1 | GCA_000970635.1 |
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 |
Marchantia polymorpha | Marchanta_polymorpha_v1 | GCA_003032435.1 |
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_000208745.2 |
Trifolium pratense |
Trpr |
GCA_900079335.1 |
Triticum aestivum |
IWGSC |
GCA_900519105.1 |
Triticum turgidum | Svevo.v1 | GCA_900231445 |
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
|
Compara
Gene Trees
The EnsemblCompara GeneTree database updated. A total of 96,607 GeneTree families comprising 2,146,774 individual genes from 67 plant genomes with 2,365,624 input proteins.
Putative Split Genes
Species_id | Split_gene_counts |
Actinidia_chinensis_var._chinensis | 156 |
Aegilops_tauschii_subsp._strangulata | 212 |
Arabidopsis_lyrata_subsp._lyrata | 94 |
Arabidopsis_thaliana | 38 |
Beta_vulgaris_subsp._vulgaris | 50 |
Brachypodium_distachyon | 76 |
Brassica_oleracea_var._oleracea | 678 |
Brassica_rapa | 90 |
Capsicum_annuum | 748 |
Chlamydomonas_reinhardtii | 38 |
Coffea_canephora | 322 |
Cucumis_sativus | 486 |
Daucus_carota_subsp._sativus | 218 |
Dioscorea_rotundata | 228 |
Glycine_max | 234 |
Gossypium_raimondii | 434 |
Helianthus_annuus | 636 |
Hordeum_vulgare_subsp._vulgare | 162 |
Leersia_perrieri | 98 |
Lupinus_angustifolius | 118 |
Manihot_esculenta | 132 |
Medicago_truncatula | 212 |
Musa_acuminata_subsp._malaccensis | 648 |
Nicotiana_attenuata | 58 |
Oryza_barthii | 120 |
Oryza_brachyantha | 198 |
Oryza_glaberrima | 422 |
Oryza_glumipatula | 174 |
Oryza_meridionalis | 118 |
Oryza_nivara | 106 |
Oryza_punctata | 100 |
Oryza_rufipogon | 102 |
Oryza_sativa_Indica_Group | 502 |
Oryza_sativa_Japonica_Group | 458 |
Ostreococcus_lucimarinus_CCE9901 | 12 |
Panicum_hallii_var._filipes | 130 |
Panicum_hallii_var._hallii | 126 |
Phaseolus_vulgaris | 682 |
Physcomitrella_patens | 48 |
Populus_trichocarpa | 220 |
Prunus_persica | 78 |
Setaria_italica | 418 |
Solanum_lycopersicum | 468 |
Solanum_tuberosum | 324 |
Sorghum_bicolor | 34 |
Theobroma_cacao | 22 |
Trifolium_pratense | 484 |
Triticum_aestivum | 500 |
Triticum_dicoccoides | 946 |
Triticum_turgidum_subsp_durum | 610 |
Vigna_angularis | 218 |
Vigna_radiata_var._radiata | 62 |
Vitis_vinifera | 498 |
Zea_mays | 200 |
Genomic alignments
Here is a summary of all 299 genomic alignments.
New whole-genome alignments between:
Synteny data
Here is a summary of all 66 synteny maps. The following synteny maps are new.
Protein Annotation, GO, Xref Protein domain information
These were generated for the new and updated genomes.
Gramene Mart
This release represents a significant expansion in the number of curated pathways, projected species, and associated inferred pathways, reactions and genes (~25% data increase). Plant Reactome now hosts pathway projections for 97 plant species. Here, we provide a summary of Gramene Release 62 including website and coding updates, a list of new & updated pathways, information on new species, and projection statistics.
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 6 newly curated pathways, 11 updated pathways, and 2 "container" pathways, resulting in a total of 306 reference rice pathways. In this release, we focused on updates to rice metabolic pathways and curation of cell-cycle events.
Below: An example of newly curated cell-cycle pathways representing G1/S transition during mitosis. Our data model represents various steps of this event within the nucleoplasm (assembly of the pre-replication complex, activation of the pre-replication complex, and G1/S-specific transcription). Clickable elements allow the user to highlight a subset of reactions. For example, in this pathway, highlighted blue lines show "Activation of the pre-replication complex in G1/S transition":
Pathway Projection Statistics
We have extended orthology-based pathway projections for 15 new species (in bold below). Plant Reactome now hosts pathway projections for 97 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 |
Genes |
Sequence |
Homology |
Oryza sativa |
306 |
1810 |
1939 |
UniProt |
Curated Reference |
Actinidia chinensis |
253 |
646 |
1575 |
Ensembl Gramene |
Compara |
Aegilops tauschii |
251 |
681 |
1231 |
Ensembl Gramene |
Compara |
Amborella trichopoda |
254 |
636 |
763 |
Ensembl Gramene |
Compara |
Arabidopsis halleri |
252 |
639 |
1157 |
Ensembl Gramene |
Compara |
Arabidopsis lyrata |
252 |
644 |
1209 |
Ensembl Gramene |
Compara |
Arabidopsis thaliana |
252 |
650 |
1203 |
Ensembl Gramene |
Compara |
Arachis duranensis |
262 |
704 |
1543 |
PeanutBase |
Inparanoid |
Arachis ipaensis |
260 |
672 |
1516 |
PeanutBase |
Inparanoid |
Asparagus officinalis |
260 |
632 |
1049 |
Phytozome |
Inparanoid |
Beta vulgaris |
249 |
630 |
848 |
Ensembl Gramene |
Compara |
Brachypodium distachyon |
248 |
676 |
1120 |
Ensembl Gramene |
Compara |
Brassica napus |
251 |
646 |
3605 |
Ensembl Gramene |
Compara |
Brassica oleracea |
252 |
641 |
1818 |
Ensembl Gramene |
Compara |
Brassica rapa |
248 |
637 |
1777 |
Ensembl Gramene |
Compara |
Cajanus cajan |
258 |
670 |
1551 |
LegumeInfo |
Inparanoid |
Cannabis sativa |
251 |
638 |
952 |
JCVI |
Inparanoid |
Cannabis sativa subsp. Indica |
259 |
660 |
1082 |
CCBR-UToronto |
Inparanoid |
Capsella rubella |
259 |
668 |
1742 |
Phytozome |
Inparanoid |
Capsicum annuum |
249 |
602 |
1093 |
Ensembl Gramene |
Compara |
Chlamydomonas reinhardtii |
178 |
348 |
295 |
Ensembl Gramene |
Compara |
Chondrus crispus |
151 |
220 |
201 |
Ensembl Gramene |
Compara |
Cicer arietinum |
260 |
655 |
1272 |
NCBI |
Inparanoid |
Citrullus lanatus |
257 |
660 |
1155 |
CuGenDB |
Inparanoid |
Citrus sinensis |
256 |
668 |
2838 |
Phytozome |
Inparanoid |
Coffea canephora |
247 |
631 |
950 |
Ensembl Gramene |
Compara |
Corchorus capsularis |
246 |
601 |
878 |
Ensembl Gramene |
Compara |
Corchorus olitorius |
259 |
636 |
1292 |
NCBI |
Inparanoid |
Cucumis sativus |
251 |
638 |
952 |
Ensembl Gramene |
Compara |
Cyanidioschyzon merolae |
143 |
229 |
196 |
Ensembl Gramene |
Compara |
Cynara cardunculus var.scolymus |
251 |
626 |
1121 |
Ensembl Gramene |
Compara |
Daucus carota |
248 |
611 |
1193 |
Ensembl Gramene |
Compara |
Dioscorea rotundata |
240 |
518 |
655 |
Ensembl Gramene |
Compara |
Eragrostis tef |
250 |
666 |
1644 |
Ensembl Gramene |
Compara |
Erythranthe guttata |
256 |
668 |
1485 |
Phytozome |
Inparanoid |
Eucalyptus grandis |
259 |
675 |
1690 |
Phytozome |
Inparanoid |
Fragaria vesca |
258 |
640 |
1317 |
Phytozome |
Inparanoid |
Galdieria sulphuraria |
157 |
278 |
238 |
Galdieria sulphuraria |
Compara |
Glycine max |
247 |
644 |
2134 |
Glycine max |
Compara |
Gossypium raimondii |
252 |
655 |
1604 |
Gossypium raimondii |
Compara |
Helianthus annuus |
251 |
634 |
1725 |
Helianthus annuus |
Compara |
Hordeum vulgare |
250 |
645 |
1137 |
Hordeum vulgare |
Compara |
Humulus lupulus haplotig |
236 |
453 |
707 |
Hendrix Lab (OSU) |
Inparanoid |
Humulus lupulus primary |
253 |
648 |
2204 |
Hendrix Lab (OSU) |
Inparanoid |
Jatropha curcas |
255 |
633 |
1208 |
KDRI (Kazusa) |
Inparanoid |
Leersia perrieri |
252 |
661 |
1075 |
Leersia perrieri |
Compara |
Lupinus angustifolius |
251 |
642 |
1577 |
Lupinus angustifolius |
Compara |
Malus domestica |
257 |
661 |
2701 |
PMID: 20802477 |
Inparanoid |
Manihot esculenta |
252 |
647 |
1326 |
Ensembl Gramene |
Compara |
Marchantia polymorpha |
235 |
558 |
665 |
Ensembl Gramene |
Compara |
Medicago truncatula |
249 |
638 |
1281 |
Ensembl Gramene |
Compara |
Musa acuminata |
242 |
618 |
1401 |
Ensembl Gramene |
Compara |
Nelumbo nucifera |
259 |
657 |
1372 |
iPlant Collaborative |
Inparanoid |
Nicotiana attenuata |
246 |
544 |
786 |
Ensembl Gramene |
Compara |
Oryza australiensis * |
254 |
622 |
2205 |
OMAP/OGE |
Inparanoid |
Oryza barthii |
254 |
692 |
1147 |
Ensembl Gramene |
Compara |
Oryza brachyantha |
251 |
677 |
1097 |
Ensembl Gramene |
Compara |
Oryza glaberrima |
259 |
689 |
1137 |
Ensembl Gramene |
Compara |
Oryza glumaepatula |
255 |
700 |
1147 |
Ensembl Gramene |
Compara |
Oryza granulata |
253 |
628 |
4099 |
OMAP/OGE |
Inparanoid |
Oryza indica |
259 |
719 |
1253 |
Ensembl Gramene |
Compara |
Oryza longistaminata * |
250 |
649 |
993 |
Ensembl Gramene |
Compara |
Oryza meridionalis |
248 |
617 |
985 |
Ensembl Gramene |
Compara |
Oryza minuta * |
256 |
649 |
2682 |
OMAP/OGE |
Inparanoid |
Oryza nivara |
254 |
709 |
1150 |
Ensembl Gramene |
Compara |
Oryza officinalis * |
259 |
655 |
2319 |
OMAP/OGE |
Inparanoid |
Oryza punctata |
251 |
683 |
1161 |
Ensembl Gramene |
Compara |
Oryza rufipogon |
254 |
699 |
1165 |
Ensembl Gramene |
Compara |
Oryza sativa aus kasalath |
203 |
301 |
377 |
PMID: 24578372 |
Inparanoid |
Ostreococcus lucimarinus |
171 |
292 |
247 |
Ensembl Gramene |
Compara |
Panicum hallii FIL2 |
252 |
693 |
1156 |
Ensembl Gramene |
Compara |
Panicum hallii var. hallii HAL2 |
254 |
696 |
1182 |
Ensembl Gramene |
Compara |
Phaseolus vulgaris |
253 |
650 |
1185 |
Ensembl Gramene |
Compara |
Phoenix dactylifera |
252 |
630 |
1423 |
PMID: 23917264 |
Inparanoid |
Phyllostachys edulis |
256 |
629 |
1877 |
NCGR |
Inparanoid |
Physcomitrella patens |
232 |
552 |
1186 |
Ensembl Gramene |
Compara |
Picea abies |
257 |
621 |
1821 |
Congenie |
Inparanoid |
Pinus taeda |
251 |
612 |
2615 |
TreeBase |
Inparanoid |
Populus trichocarpa |
253 |
648 |
1502 |
Ensembl Gramene |
Compara |
Prunus persica |
253 |
655 |
1028 |
Ensembl Gramene |
Compara |
Salvia hispanica |
258 |
642 |
2163 |
Jaiswal Lab (OSU) |
Inparanoid |
Selaginella moellendorffii |
237 |
548 |
1304 |
Ensembl Gramene |
Compara |
Setaria italica |
253 |
680 |
1185 |
Ensembl Gramene |
Compara |
Solanum lycopersicum |
250 |
639 |
1075 |
Ensembl Gramene |
Compara |
Solanum tuberosum |
244 |
607 |
1084 |
Ensembl Gramene |
Compara |
Sorghum bicolor |
251 |
690 |
1180 |
Ensembl Gramene |
Compara |
Synechocystis sp. PCC 6803 |
146 |
265 |
212 |
Jaiswal Lab (OSU) |
Inparanoid |
Theobroma cacao |
253 |
647 |
989 |
Ensembl Gramene |
Compara |
Trifolium pratense |
253 |
644 |
1116 |
Ensembl Gramene |
Compara |
Triticum aestivum |
255 |
703 |
3982 |
Ensembl Gramene |
Compara |
Triticum dicoccoides |
254 |
694 |
2334 |
Ensembl Gramene |
Compara |
Triticum turgidum * |
252 |
695 |
2387 |
Ensembl Gramene |
Compara |
Triticum urartu |
245 |
601 |
959 |
Ensembl Gramene |
Compara |
Vigna angularis |
251 |
631 |
1128 |
Ensembl Gramene |
Compara |
Vigna radiata |
242 |
590 |
975 |
Ensembl Gramene |
Compara |
Vitis vinifera |
252 |
649 |
1028 |
Ensembl Gramene |
Compara |
Zea mays |
253 |
678 |
1466 |
Ensembl Gramene |
Compara |
Zoysia japonica |
256 |
637 |
1893 |
KDRI (Kazusa) |
Inparanoid |
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 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.