[Gramene-announce] Announcing Gramene knowledgebase release #62

Mon Nov 18 15:37:11 EST 2019

Dear Researchers,

The Gramene team is pleased to announce its Release #62 
<http://news.gramene.org/release-notes-62>with updates to its Genome 
portal <http://ensembl.gramene.org/genome_browser/index.html>, Pathway 
portal Plant Reactome 
<https://plantreactome.gramene.org/index.php?lang=en> and the 
infrastructure. The genome portal hosts 67 plant genomes with six new 
species and an updated chocolate tree genome. ThePlant Reactome, hosts 
pathways for 97 species. The Plant Reactome has extended orthology-based 
pathway projections for 15 new species; added six newly curated pathways 
and updated 11 pathways in the reference species /Oryza sativa 
/(resulting in a total of 306 rice pathways). In the following sections, 
we provide a summary of updates to the Gramene Knowledgebase. We also 
share four new publications highlighting major Gramene updates over the 
last two years and discuss new efforts by Gramene on community 
engagement in biocuration of plant genes and pathways.

The Gramene <http://gramene.org/>is a curated, open-source, integrated 
data resource for comparative functional genomics in crops and model 
plant species. The plant genome databases 
<http://ensembl.gramene.org/genome_browser/index.html> were co-produced 
in direct collaboration with Ensembl Plants 
<https://plants.ensembl.org/index.html>, and the Plant Reactome 
<https://plantreactome.gramene.org/index.php?lang=en>database was 
produced in collaboration with the Reactome 
<https://reactome.org/>project. The National Science Foundation, USA 
provided core funding for the project.

*Updates in the Genome Portal:*Release #62 
<http://news.gramene.org/release-notes-62> includes six new reference 
genomes and one updated genome. Overall, the Genome section providing 
access to information 96,607 Gene families comprising 2,146,774 
individual genes from 67 plant genomes with 2,365,624 input proteins.

*New genomes**:*

  * Robusta coffee (/Coffea canephora/
    <http://ensembl.gramene.org/Coffea_canephora>): assembly and
    annotation GCA_900059795.1
    <https://www.ebi.ac.uk/ena/data/view/GCA_900059795.1>.
  * Hot pepper (/Capsicum annuum/
    <http://ensembl.gramene.org/Capsicum_annuum>): assembly and
    annotation GCA_000512255.2
    <https://www.ebi.ac.uk/ena/data/view/GCA_000512255.2>.
  * Global artichoke (/Cynara cardunculus/
    <http://ensembl.gramene.org/Cynara_cardunculus>): assembly and
    annotation GCA_001531365.1
    <https://www.ebi.ac.uk/ena/data/view/GCA_001531365.1>.
  * Eragrostis tef (/Eragrostis tef/
    <http://ensembl.gramene.org/Eragrostis_tef>): assembly from ENA
    (GCA_000970635.1
    <https://www.ebi.ac.uk/ena/data/view/GCA_000970635.1>) and community
    annotation <http://130.92.252.158/tef/version1/>.
  * Durum wheat (/Triticum turgidum/
    <http://ensembl.gramene.org/Triticum_turgidum>, tetraploid AABB).
  * Common liverwort (/Marchantia polymorpha/
    <http://ensembl.gramene.org/Marchantia_polymorpha>): assembly and
    annotation GCA_003032435.1
    <https://www.ebi.ac.uk/ena/data/view/GCA_003032435.1>.

*Updated genomes**:*

  * Criollo cocoa, cacao or chocolate tree (/Theobroma cacao/
    <http://ensembl.gramene.org/Theobroma_cacao>): assembly update
    GCA_000208745.2 <https://www.ebi.ac.uk/ena/data/view/GCA_000208745.2>.

*New & Updated data: *

  * 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
    <http://ensembl.gramene.org/compara_analyses.html>.
  * New synteny data for robusta coffee (/Coffea canefora/), hot pepper
    (/Capsicum annuum/), and chocolate tree (/Theobroma cacao/); see
    summary here <http://ensembl.gramene.org/compara_analyses.html>.
  * Updated split gene predictions
    <ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/split_genes/>from
    peptide comparative genomics
    <http://ensemblgenomes.org/info/data/peptide_compara>.
  * 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/).
  * Updated metadata for wheat EMS-induced mutations.
  * KASP marker information for the TILLING population is being
    displayed on the genetic variation pages for wheat.

*Updates in the Pathway Portal (Plant Reactome): *

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 species, including single-cell 
photoautotrophs, lower plants, and higher plants.

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 
<https://plantreactome.cyverse.org/>) to facilitate training, education, 
and integration with the CyVerse platform and user community.

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 (a list of available species 
are available in the content summary 
<https://plantreactome.gramene.org/index.php?option=com_content&view=article&id=108&Itemid=360&lang=en>). 

*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.

*New Pathways:*

  * Cell Cycle G1 Phase
    <https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-9640760>
      o G1/S Transition
        <https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-9640887>
          + Assembly of pre-replication complex
            <https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-9640887><https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-9640887>
          + Activation of pre-replication complex
            <https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-9640887><https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-9640887>
          + G1/S-specific transcription
            <https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-9640887>
      o OsNAC5 transcription network involved in drought and high
        salinity tolerance
        <https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-9641042>

*Updated Pathways:*

  * Allantoin degradation
    <https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119502>
  * Aminopropanol biosynthesis
    <https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119309>
  * Ascorbate biosynthesis
    <https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119410>
  * Vitamin E biosynthesis
    <https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119287>
  * Arginine biosynthesis
    <https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119263>
  * Asparagine biosynthesis
    <https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119553>
  * Beta-alanine biosynthesis I
    <https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119567>
  * Beta-alanine biosynthesis III
    <https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119297>
  * Tyrosine degradation I
    <https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119506>
  * Ammonia assimilation cycle
    <https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119443>
  * Ureide biosynthesis
    <https://plantreactome.gramene.org/PathwayBrowser/#/R-OSA-1119407>

*Pathway Projection to other species*

We have extended orthology-based pathway projections for 15 new 
species. Plant Reactome now hosts pathway projections for 97 species 
ranging from unicellular autotrophs to higher plants (for a list of 
available species in Plant Reactome click here 
<https://plantreactome.gramene.org/index.php?option=com_content&view=article&id=108&Itemid=360&lang=en>).

*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, Gupta P, Preece J, Garg P, Fraser V, Padgitt-Cobb LK,
    Martin M, Vining K, Jaiswal P, Involving community in genes and
    pathway curation, Database, Volume 2019, 2019, bay146,
    https://doi.org/10.1093/database/bay146

Please let us know if you have any questions or suggestions.

The Gramene Team
www.gramene.org <http://www.gramene.org/>.

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