Release Notes 64 (September 2021)

Table of Contents

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).


GENOMES Release Notes 


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

  • Updated Split Genes: Updated split genes for the current release are available on FTP site.  These are putative gene annotation artifacts (also known as contiguous gene split models) and are based on the latest Ensembl Compara Gene Tree database. 
  • Brief statistics for each species is given below.


Species Name

Split genes

Actinidia chinensis var. chinensis.csv


Aegilops tauschii subsp. strangulata.csv


Arabidopsis lyrata subsp. lyrata.csv


Arabidopsis thaliana.csv


Asparagus officinalis.csv


Beta vulgaris subsp. vulgaris.csv


Brachypodium distachyon.csv


Brassica oleracea var. oleracea.csv


Brassica rapa.csv


Camelina sativa.csv


Cannabis sativa.csv


Capsicum annuum.csv


Chlamydomonas reinhardtii.csv


Citrullus lanatus.csv


Coffea canephora.csv


Cucumis sativus.csv


Daucus carota subsp. sativus.csv


Dioscorea cayenensis subsp. rotundata.csv


Eragrostis curvula.csv


Glycine max.csv


Gossypium raimondii.csv


Helianthus annuus.csv


Hordeum vulgare subsp. vulgare.csv


Ipomoea triloba.csv


Leersia perrieri.csv


Lupinus angustifolius.csv


Malus domestica.csv


Manihot esculenta.csv


Medicago truncatula.csv


Nicotiana attenuata.csv


Nymphaea colorata.csv


Olea europaea var. sylvestris.csv


Oryza barthii.csv


Oryza brachyantha.csv


Oryza glaberrima.csv


Oryza glumipatula.csv


Oryza meridionalis.csv


Oryza nivara.csv


Oryza punctata.csv


Oryza rufipogon.csv


Oryza sativa Indica Group.csv


Oryza sativa Japonica Group.csv


Panicum hallii var. hallii.csv


Panicum hallii.csv


Papaver somniferum.csv


Phaseolus vulgaris.csv


Physcomitrium patens.csv


Populus trichocarpa.csv


Prunus persica.csv


Rosa chinensis.csv


Saccharum spontaneum.csv


Sesamum indicum.csv


Setaria italica.csv


Setaria viridis.csv


Solanum lycopersicum.csv


Solanum tuberosum.csv


Sorghum bicolor.csv


Theobroma cacao.csv


Trifolium pratense.csv


Triticum aestivum.csv


Triticum dicoccoides.csv


Triticum turgidum subsp. durum.csv


Vigna angularis.csv


Vigna radiata var. radiata.csv


Vitis vinifera.csv


Zea mays.csv


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

PATHWAYS Release Notes
(Plant Reactome Version 21; Gramene r64) Summary:

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 ( 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 -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.

Recent Publications:

  1. Hufford MB, Seetharam AS, Woodhouse MR, Chougule KM, Ou S, Liu J, Ricci WA, Guo T, Olson A, Qiu Y, Coletta RD, Tittes S, Hudson AI, Marand AP, Wei S, Lu Z, Wang B, Tello-Ruiz MK, Piri RD, Wang N, Kim DK, Zeng Y, O’Connor CH, Li X, Gilbert AM, Baggs E, Krasileva KV, II JLP, Cannon EKS, Andorf CM, Manchanda N, Snodgrass SJ, Hufnagel DE, Jiang Q, Pedersen S, Syring ML, Kudrna DA, Llaca V, Fengler K, Schmitz RJ, Ross-Ibarra J, Yu J, Gent JI, Hirsch CN, Ware D, Dawe RK. (2021) De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science. 373(6555):655-662. doi: 10.1126/science.abg5289.
  2. Naithani S, D.A. Dikeman, P. Garg, N. Al-Bader, and P. Jaiswal (2021). Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily. PeerJ 9:e11052, doi:10.7717/peerj.11052
  3. Tello-Ruiz MK, Naithani S, Gupta P, Olson A, Wei S, Preece S, Jiao Y, Wang B, Chougule K, Garg P, Elser J, Kumari S, Kumar V, Contreras-Moreira B, Naamati G, George N, Cook J, Bolser D, D’Eustachio P, Stein LD, Gupta A, Xu W, Regala J, Papatheodorou I, Kersey PJ, Flicek P, Taylor C, Jaiswal P, and Ware D. (2021). Gramene 2021: Harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Research 49(D1): D1452–D1463. 10.1093/nar/gkaa979
  4. Naithani S., P. Gupta, J. Preece, P. D'Eustachio, J. Elser, J. Kiff, P. Garg, D.A. Dikeman$, A.J. Olson, S. Wei, M.K. Tello-Ruiz, J. Cook, A. Fabregat, T. Cheng, E. Bolton, A.F. Muñoz-Pomer, S. Mohammed, I. Papatheodorou, L. Stein, D. Ware, and P. Jaiswal (2020). Plant Reactome: A knowledgebase and resource for comparative pathway analysis. Nucleic Acids Res. 10.1093/nar/gkz996.
  5. Howe K.L., B. Contreras-Moreira, N. De Silva, G. Maslen, W. Akanni, J. Allen, J. Alvarez-Jarreta, M. Barba, D.M. Bolser, L. Cambell, M. Carbajo, M. Chakiachvili, M. Christensen, C. Cummins, A. Cuzick, P. Davis, S. Fexova, A. Gall, N. George, L. Gil, P. Gupta, K. E. Hammond-Kosack, E. Haskell, S. E. Hunt, P. Jaiswal, S. H. Janacek, P. J. Kersey, N. Langridge, U. Maheswari, T. Maurel, M. D. McDowall, B. Moore, M. Muffato, G. Naamati, S. Naithani, A. Olson, I. Papatheodorou, M. Patricio, M. Paulini, H. Pedro, E. Perry, J. Preece, M. Rosello, M. Russell, V. Sitnik, D. M. Staines, J. Stein, M. K. Tello-Ruiz, S. J. Trevanion, M. Urban, S. Wei, D. Ware, G. Williams, A. D. Yates, P. Flicek (2020). Ensembl Genomes 2020—enabling non-vertebrate genomic research. Nucleic Acids Res., gkz890, 10.1093/nar/gkz890
  6. Tello-Ruiz MK, Marco CF, Hsu FM, Khangura RS, Qiao P, et al. (2019) Double triage to identify poorly annotated genes in maize: The missing link in community curation. PLOS ONE 14(10): e0224086. 10.1371/journal.pone.0224086
  7. Naithani S, P. Gupta, J. Preece, P. Garg, V. Fraser, L.K. Padgitt-Cobb, M. Martin, K. Vining and P. Jaiswal (2019). Involving community in genes and pathway curation. Database, 2019:1-8, 10.1093/database/bay146


Please let us know if you have questions or suggestions.

The Gramene Team