Release Notes 59 (October 2018)

Table of Contents


The Gramene Team is pleased to announce its Release #59 with the Genome section providing access to information on 2,156,459 genes and  57 reference plant genomes. 1,860,691 protein-coding genes are organized in 96,500 gene families. The Plant Reactome -- Gramene's pathway portal -- introduces its new website http://plantreactome.gramene.org/ for improved user engagement and provides 14 new curated pathways. The gene orthology-based projection of pathways now extends to 78 species representing the plant tree of life.

Genomes Release Notes

  • New genomes
  • Removed genomes
    • The genome assembly of Cajanus cajan (pigeonpea, GCA_000340665.1) was removed from this release, pending import corrections
  • Updated genomes
  • New & Updated data
    • Around 80 pairs of plant genomes have whole genome alignments generated, bringing the total number of pairwise whole genome alignments to nearly 250. Examples include the alignment of all six legume genomes to Medicago truncatula (GCA_000219495.2).
    • Updated repeat feature annotation across all plants, including newly added repeat feature classification using REdat and REcat.
    • Updated gene trees across all plants, including the new and updated genomes.
      • In this release we used a new HMM-based method, resulting in 96,500 gene families with 1,860,691 protein-coding genes.
    • Updated ncRNA alignments and annotations across all plants including MirBase imports for twelve species.
    • Updated protein features for all (nearly 2 million) plant proteinsusing InterProScan with version 67 of InterPro.
    • Updated BioMarts for all gene and variation data.
    • Corrected attribution for many plant genomes.
    • Corrected chromosomal density plots for all plants.
  • Updated software
    • Updated genome browser, database schema, Mart and API to Ensembl v94
  • Genomes in the current release #59
  Species Assembly Gene Annotation
Unchanged Aegilops_tauschii ASM34733v1 2014-05-BGI
Amborella_trichopoda AMTR1.0 2013-10-AGD
Arabidopsis_lyrata v.1.0 2008-12-JGI
Arabidopsis_thaliana TAIR10 2016-06-Araport11
Beta_vulgaris RefBeet-1.2.2 2014-01-ENA
Brachypodium_distachyon Brachypodium_distachyon_v3.0 2018-01-ENA
Brassica_napus AST_PRJEB5043_v1 2007-07-ENA
Brassica_oleracea BOL 2014-05-CanSeq
Brassica_rapa Brapa_1.0 2012-03-IVFCAAS
Chlamydomonas_reinhardtii Chlamydomonas_reinhardtii_v5.5 1/29/18
Chondrus_crispus ASM35022v2 2013-03-ENA
Corchorus_capsularis CCACVL1_1.0 2017-02-ENA
Cucumis_sativus ASM407v2 2014-10-ENA
Cyanidioschyzon_merolae ASM9120v1 2003-05-ENA
Daucus_carota ASM162521v1 4/27/16
Dioscorea_rotundata TDr96_F1_Pseudo_Chromosome_v1.0 8/9/17
Galdieria_sulphuraria ASM34128v1 2013-02-ENA
Glycine_max Glycine_max_v2.0 2010-01-EnsemblPlants
Gossypium_raimondii Graimondii2_0 2013-01-EnsemblPlants
Helianthus_annuus HanXRQr1.0 2017-05-EnsemblPlants
Hordeum_vulgare IBSC_v2 2016-05-IBSC_1.0
Leersia_perrieri Lperr_V1.4 2013-09-OGE
Lupinus_angustifolius LupAngTanjil_v1.0 2016-11-EnsemblPlants
Manihot_esculenta Manihot_esculenta_v6 2016-06-EnsemblPlants
Medicago_truncatula MedtrA17_4.0 2015-01-IMGAG
Musa_acuminata ASM31385v1 2012-08-Cirad
Nicotiana_attenuata NIATTr2 2016-11-EnsemblPlants
Oryza_barthii O.barthii_v1 2014-05-OGE
Oryza_brachyantha Oryza_brachyantha.v1.4b 2011-05-OGE
Oryza_glaberrima Oryza_glaberrima_V1 2011-05-AGI
Oryza_glumipatula Oryza_glumaepatula_v1.5 2013-09-OGE
Oryza_indica ASM465v1 2010-07-BGI
Oryza_longistaminata O_longistaminata_v1.0 2015-05-OGE
Oryza_meridionalis Oryza_meridionalis_v1.3 2014-10-OGE
Oryza_nivara Oryza_nivara_v1.0 2013-09-OGE
Oryza_punctata Oryza_punctata_v1.2 2013-09-OGE
Oryza_rufipogon OR_W1943 2013-09-OGE
Oryza_sativa IRGSP-1.0 2013-04-IRGSP
Ostreococcus_lucimarinus ASM9206v1 2007-04-EnsemblPlants
Phaseolus_vulgaris PhaVulg1_0 2013-12-EnsemblPlants
Physcomitrella_patens Phypa_V3 1/26/18
Populus_trichocarpa Pop_tri_v3 1/26/18
Prunus_persica Prunus_persica_NCBIv2 2017-02-EnsemblPlants
Selaginella_moellendorffii v1.0 2010-07-ENA
Setaria_italica Setaria_italica_v2.0 2015-11-ENA
Solanum_lycopersicum SL2.50 2011-05-SolTub_3.0
Solanum_tuberosum SolTub_3.0 2011-05-SolTub_3.0
Sorghum_bicolor Sorghum_bicolor_NCBIv3 2009-06-EnsemblPlants
Theobroma_cacao Theobroma_cacao_20110822 2013-06-EnsemblPlants
Trifolium_pratense Trpr 2016-04-TGAC
Triticum_urartu ASM34745v1 2014-05-BGI
Vigna_angularis Vigan1.1 8/6/15
Vitis_vinifera 12X 2012-11-CRIBI
Zea_mays B73_RefGen_v4 2016-12-CSHL
     
New Triticum_dicoccoides WEWSeq_v.1.0 2017-05-WEWSeq
Vigna_radiata Vradiata_ver6 9/5/14
     
Updated Triticum_aestivum IWGSC 2018-04-IWGSC

 

Compara

  • Gene Trees
    A total of 96,500 GeneTree families were constructed comprising 1,860,691 individual genes (2,106,462 input proteins) from 57 plant genomes (and 5 non-plant outgroups).
  • Putative Split Genes
    Split gene predictions were updated in this release and are available from Gramene's 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. Split gene counts for each species is given as follows.
Species Split gene counts
Arabidopsis_lyrata_subsp._lyrata 69
Arabidopsis_thaliana 21
Beta_vulgaris_subsp._vulgaris 47
Brachypodium_distachyon 47
Brassica_oleracea_var._oleracea 563
Brassica_rapa_subsp._pekinensis 78
Chlamydomonas_reinhardtii 38
Cucumis_sativus 396
Daucus_carota_subsp._sativus 197
Dioscorea_rotundata 171
Glycine_max 516
Gossypium_raimondii 322
Helianthus_annuus 442
Hordeum_vulgare_subsp._vulgare 118
Leersia_perrieri 68
Lupinus_angustifolius 64
Manihot_esculenta 112
Medicago_truncatula 176
Musa_acuminata_subsp._malaccensis 591
Nicotiana_attenuata 46
Oryza_barthii 85
Oryza_brachyantha 138
Oryza_glaberrima 191
Oryza_glumipatula 140
Oryza_meridionalis 72
Oryza_nivara 92
Oryza_punctata 76
Oryza_rufipogon 68
Oryza_sativa_Indica_Group 282
Oryza_sativa_Japonica_Group 286
Ostreococcus_lucimarinus_CCE9901 8
Phaseolus_vulgaris 534
Physcomitrella_patens 36
Populus_trichocarpa 141
Prunus_persica 62
Setaria_italica 342
Solanum_lycopersicum 531
Solanum_tuberosum 246
Sorghum_bicolor 29
Theobroma_cacao 34
Trifolium_pratense 385
Triticum_aestivum 412
Triticum_dicoccoides 629
Vigna_angularis 191
Vigna_radiata_var._radiata 40
Vitis_vinifera 336
Zea_mays 152

Genomic alignments and Synteny

Here is a summary of all genomic alignments and syntenies. The new alignments correspond to LastZ comparisons between the new or updated genomes in release 58 versus reference monocot (Oryza sativa Japonica) and dicot (Arabidopsis thaliana or Vitis vinifera) genomes. A stats page for each paiwise LastZ alignment is available, see for example the one for carrot vs grape.

Protein Annotation, GO, Xref Protein domain information was updated based on the latest InterProScan analysis.

Gramene Mart (BioMart)


Pathways (Plant Reactome) Release Notes

Website and coding updates

  • The Plant Reactome web site landing page has a new look and feel. It was redesigned on the Joomla Content Management System for better user experience.
  • Users can import/overlay gene-gene interaction data filtered by a confidence score (where available). This is done by enabling a threshold filter to be selected by the user in the Pathway Browser when viewing the interactor overlay. Try an example here.
  • The majority of gene-gene interaction data is hosted in Plant Reactome. A part of it is pulled remotely from EBI-Intact and BAR using the PSICQUIC webservices.
  • The latest Plant Reactome pathway data has been re-indexed and made available via Gramene search.

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 78 projected species currently hosted by Plant Reactome.

Curation of reference rice pathways

In Gramene Release 59, we have added 14 newly curated pathways and 2 "container" pathways, and updated 2 other existing pathways, resulting in a total of 280 reference rice pathways. Browse them at http://plantreactome.gramene.org/PathwayBrowser/. We are encouraging users to suggest pathway updates and critiques.

New Pathways

  • Tricin biosynthesis
  • Lycopene catabolism
  • Oryzalyde A biosynthesis
  • Abscisic acid homeostasis
  • Reactive oxygen species (ROS) homeostasis
  • Generation of superoxide radicals
  • Removal of superoxide radicals
  • Valine degradation
  • Cysteine degradation
  • Recognition of fungal and bacterial pathogens and immunity response
  • Reproductive meristem phase change
  • Flower development
  • Floral bract development
  • Seed development

Updated/renamed  pathways:

  • Secondary metabolism
  • Hormone signaling, transport, and metabolism

Pathway Projection Statistics and Status

We have extended orthology-based pathway projections for 4 new species: Daucus carota (carrot), Vigna radiata (mung bean), Vigna angularis (adzuki bean) and Triticum dicoccoides (Emmer wheat). Plant Reactome now hosts pathway projections for 78 species ranging from unicellular autotrophs to higher plants. In addition, we have revised pathways for Triticum aestivum (bread wheat), based on its recent genome update (IWGSC RefSeq v1.0).

  • *Data from sequenced transcriptomes
  • ^Projections currently exclude cell-cycle pathways and annotations
    Species names in bold represent new species projections
  • 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 Source Homology Method
Oryza sativa 280 1228 1607 UniProt Curated Reference
Aegilops tauschii 211 513 922 Ensembl Gramene Compara
Amborella trichopoda 219 550 660 Ensembl Gramene Compara
Arabidopsis lyrata 226 560 1042 Ensembl Gramene Compara
Arabidopsis thaliana 225 565 1016 Ensembl Gramene Compara
Arachis duranensis 233 585 982 PeanutBase Inparanoid
Arachis ipaensis 230 570 911 PeanutBase Inparanoid
Beta vulgaris 224 556 750 Ensembl Gramene Compara
Brachypodium distachyon 221 587 981 Ensembl Gramene Compara
Brassica napus 227 561 3106 Ensembl Gramene Compara
Brassica oleracea 224 550 1583 Ensembl Gramene Compara
Brassica rapa 225 557 1571 Ensembl Gramene Compara
Cajanus cajan 233 609 1315 LegumeInfo Inparanoid
Capsicum annuum 232 561 1159 PMID: 24441736 Inparanoid
Chlamydomonas reinhardtii 164 316 260 Ensembl Gramene Compara
Chondrus crispus 131 198 172 Ensembl Gramene Compara
Cicer arietinum 231 572 1416 NCBI Inparanoid
Citrus sinensis 230 569 2287 Phytozome Inparanoid
Coffea canephora 230 567 1003 PMID:25190796 Inparanoid
Corchorus capsularis 222 529 762 Ensembl Gramene Compara
Cucumis sativus 224 556 808 Ensembl Gramene Compara
Cyanidioschyzon merolae 130 186 159 Ensembl Gramene Compara
Daucus carota 224 535 1015 Ensembl Gramene Compara
Dioscorea rotundata 215 458 567 Ensembl Gramene Compara
Erythranthe guttata 206 497 664 Phytozome Inparanoid
Eucalyptus grandis 208 496 714 Phytozome Inparanoid
Fragaria vesca 230 545 964 Phytozome Inparanoid
Galdieria sulphuraria 132 226 182 Ensembl Gramene Compara
Glycine max 226 574 1909 Ensembl Gramene Compara
Gossypium raimondii 227 568 1402 Ensembl Gramene Compara
Helianthus annuus 223 547 1467 Ensembl Gramene Compara
Hordeum vulgare 224 562 983 Ensembl Gramene Compara
Jatropha curcas 206 488 539 KDRI (Kazusa) Inparanoid
Leersia perrieri 227 586 938 Ensembl Gramene Compara
Lupinus angustifolius 188 387 572 Ensembl Gramene Compara
Malus domestica 228 551 1920 PMID: 20802477 Inparanoid
Manihot esculenta 226 566 1167 Ensembl Gramene Compara
Medicago truncatula 222 556 1112 Ensembl Gramene Compara
Musa acuminata 214 532 1175 Ensembl Gramene Compara
Nicotiana attenuata 216 457 667 Ensembl Gramene Compara
Oryza australiensis * 224 523 1613 OMAP/OGE Inparanoid
Oryza barthii 228 603 997 Ensembl Gramene Compara
Oryza brachyantha 226 592 963 Ensembl Gramene Compara
Oryza glaberrima 232 600 1001 Ensembl Gramene Compara
Oryza glumaepatula 230 605 1002 Ensembl Gramene Compara
Oryza longistaminata * 225 561 855 Ensembl Gramene Compara
Oryza meridionalis 222 541 870 Ensembl Gramene Compara
Oryza meyeriana var. granulata 229 546 3306 OMAP/OGE Inparanoid
Oryza minuta * 230 565 1979 OMAP/OGE Inparanoid
Oryza nivara 227 612 1004 Ensembl Gramene Compara
Oryza officinalis * 227 556 1771 OMAP/OGE Inparanoid
Oryza punctata 226 590 1001 Ensembl Gramene Compara
Oryza rufipogon 227 610 1020 Ensembl Gramene Compara
Oryza sativa aus subgroup 180 268 345 PMID: 24578372 Inparanoid
Oryza sativa Indica Group 233 627 1083 Ensembl Gramene Compara
Ostreococcus lucimarinus 144 230 203 Ensembl Gramene Compara
Phaseolus vulgaris 226 564 1012 Ensembl Gramene Compara
Phoenix dactylifera 224 534 1037 PMID: 23917264 Inparanoid
Physcomitrella patens 202 464 958 Ensembl Gramene Compara
Picea abies 226 508 1249 Congenie Inparanoid
Pinus taeda 215 460 1187 TreeBase Inparanoid
Populus trichocarpa 225 559 1300 Ensembl Gramene Compara
Prunus persica 226 570 892 Ensembl Gramene Compara
Selaginella moellendorffii 203 470 1113 Ensembl Gramene Compara
Setaria italica 226 596 1069 Ensembl Gramene Compara
Solanum lycopersicum 223 558 1005 Ensembl Gramene Compara
Solanum tuberosum 217 528 942 Ensembl Gramene Compara
Sorghum bicolor 227 605 1043 Ensembl Gramene Compara
Synechocystis pcc6803 152 304 221 Jaiswal Inparanoid
Theobroma cacao 227 564 866 Ensembl Gramene Compara
Trifolium pratense 223 559 951 Ensembl Gramene Compara
Triticum aestivum 228 612 3469 Ensembl Gramene Compara
Triticum dicoccoides 225 593 2065 Ensembl Gramene Compara
Triticum turgidum * 228 573 2620 PMID: 23800085 Inparanoid
Triticum urartu 216 513 842 Ensembl Gramene Compara
Vigna angularis 222 548 956 Ensembl Gramene Compara
Vigna radiata 223 563 1026 Ensembl Gramene Compara
Vitis vinifera 224 563 900 Ensembl Gramene Compara
Zea mays 224 589 1312 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.

"Cyc" Pathways

BioCyc-based pathway databases on Pathway Tools ver. 19.0 are available from a virtual server hosted at CyVerse. Summary tables for the Cyc pathway databases created by Gramene is available in release 46 notes.

Ontologies Release Notes

No updates in this release. Last update done in release 31 (May 2010). A summary of ontologies data was last provided in release 46.


# Infrastructure

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 58_93 is set as version 40_93 at Ensembl.