Release notes 62 (November 2019)

Table of Contents


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.

GENOMES Release Notes 

  • New genomes:
  1. Robusta coffee (Coffea canephora): assembly and annotation GCA_900059795.1.
  2. Hot pepper (Capsicum annuum): assembly and annotation GCA_000512255.2.
  3. Global artichoke (Cynara cardunculus): assembly and annotation GCA_001531365.1.
  4. Eragrostis tef (Eragrostis tef): assembly from ENA (GCA_000970635.1) and community annotation.
  5. Durum wheat (Triticum turgidum, tetraploid AABB).
  6. Common liverwort (Marchantia polymorpha): assembly and annotation GCA_003032435.1.
  • Updated genomes:
  1. Criollo cocoa, cacao or chocolate tree (Theobroma cacao): assembly update GCA_000208745.2.
  • New & Updated data: 
  1. New whole genome alignments for robusta coffee (Coffea canefora), hot pepper (Capsicum annuum), global artichoke (Cynara cardunculus), eragrostis tef (Eragrostis tef), durum wheat (Triticum turgidum), common liverwort (Marchantia polymorpha), and chocolate tree (Theobroma cacao); see summary here.
  2. New synteny data for robusta coffee (Coffea canefora), hot pepper (Capsicum annuum), and chocolate tree (Theobroma cacao); see summary here.
  3. Updated split gene predictions from peptide comparative genomics.
  4. The Pan-taxonomic Compara set of gene trees was updated with two new plant species added (Marchantia polymorpha and Brachypodium distachyon), and one removed (Chondrus crispus).
  5. Updated metadata for wheat EMS-induced mutations.
  6. KASP marker information for the TILLING population is being displayed on the genetic variation pages for wheat.

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

  • 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_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:

  • Robusta coffee (Coffea canefora) and Arabidopsis / Grape / Rice / Tomato.
  • Hot pepper (Capsicum annuum) and Arabidopsis / Grape / Rice / Tomato.
  • Global artichoke (Cynara cardunculus) and Arabidopsis / Grape / Rice / Tomato.
  • Eragrostis tef (Eragrostis tef) and Arabidopsis / Grape / Rice.
  • Durum wheat (Triticum turgidum) and Arabidipsis / Brachypodium / Grape / Rice.
  • Common liverwort (Marchantia polymorpha) and Arabidopsis / Grape / Rice.
  • Chocolate tree (Theobroma cacao) and Arabidopsis thaliana, A. lyrata, A. halleri / Brassica napus, B. oleracea, B. rapa / Corchorus capsularis / Gossypium raimondii / Grape / Rice.

Synteny data

 Here is a summary of all 66 synteny maps. The following synteny maps are new.

  • Robusta coffee (Coffea canefora) with Grape / Tomato.
  • Hot pepper (Capsicum annuum) with Tomato.
  • Chocolate tree (Theobroma cacao) with Grape.

Protein Annotation, GO, Xref Protein domain information 

These were generated for the new and updated genomes.

Gramene Mart


PATHWAYS Release Notes
(Plant Reactome Version 19; Gramene r62) Summary:

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.

    New pathways Updated pathways
    G1 Phase
        - G1/S Transition
            - Assembly of pre-replication complex
            - Activation of pre-replication complex
            - G1/S-specific transcription
    OsNAC5 transcription network involved in drought and high salinity tolerance
    Allantoin degradation
    Aminopropanol biosynthesis
    Ascorbate biosynthesis
    Vitamin E biosynthesis
    Arginine biosynthesis
    Asparagine biosynthesis
    Beta-alanine biosynthesis I
    Beta-alanine biosynthesis III
    Tyrosine degradation I
    Ammonia assimilation cycle
    Ureide biosynthesis

    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":

    Sample curated pathway r62

    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
    Source

    Homology
    Method

    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.


    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 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.


    Recent Publications:

    1. 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 (2019). Plant Reactome: A knowledgebase and resource for comparative pathway analysis. Nucleic Acids Res. https://doi.org/10.1093/nar/gkz996.
    2. 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 (2019). Ensembl Genomes 2020—enabling non-vertebrate genomic research. Nucleic Acids Res., gkz890, https://doi.org/10.1093/nar/gkz890
    3. 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. https://doi.org/10.1371/journal.pone.0224086
    4. 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,  https://doi.org/10.1093/database/bay146

     

    Please let us know if you have questions or suggestions.

    The Gramene Team
    www.gramene.org.