Announcing Gramene release #60: New & updated genomes, pathways and other features

Submitted by Sushma_Naithani on Fri, 02/08/2019 - 13:56

The Gramene Team is pleased to announce its Release #60 with the Genome section providing access to information on 2,162,056 genes and 58 reference plant genomes. 1,891,391 protein-coding genes are organized in 93,194 gene families. The Plant Reactome, Gramene's pathway portal, hosts pathway projections for 79 species ranging from unicellular autotrophs to higher plants. In this release, we have extended orthology-based pathway projections for one new species: Arabidopsis halleri, and revised pathways for Solanum lycopersicum (tomato) and Glycine max (soybean), based on their recent genome updates; added 10 newly curated pathways for reference species Oryza sativa (total curated reference pathways: 293).

GENOMES 

  1. Aegilops tauschii: updated assembly and annotation to version Aet v4.0 (GCA_002575655).
  2. Solanum lycopersicum: updated assembly (GCA_000188115.3) and annotation (ITAG3.0, except unplaced genes).
  3. Glycine max: updated assembly (GCA_000004515.4) and annotation (Rel. 137, Version 4, Glycine_max_v2.1).
  4. Vigna radiata: updated annotation (vigra.VC1973A.gnm6.ann1.M1Qs).
  5. Physcomitrella patens: updated annotation (V3.3).
  • New & Updated data: 
  1. Triticum aestivum: Inter-Homeologous Variants (IHVs) were added.
  2. Lupinus angustifolius: genes from previous release were added.
  3. Arabidopsis thaliana: TAIR10 is now the unique source of ncRNA annotations.
  4. Nicotiana attenuata: mapped microarray probes were updated.
  5. Zea mays: mapped microarray probes were updated.
  6. BioMarts for all gene and variation data.
  7. Updated split gene predictions from peptide comparative genomics.

PATHWAYS (Plant Reactome):

For details see: Plant Reactome Release Summary - Version 17 (Gramene r60): Here is the summary of updates made to plant pathways.

  • Website and coding updates:

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 79 projected species currently hosted by Plant Reactome.

  • Curation of reference rice pathways: 

​We have added 10 newly curated pathways and 3 "container" pathways, and updated 2 existing pathways, resulting in a total of 293 reference rice pathways.

    New Pathways:

    •          - Regulation of embryo development
    •          - Maternal tissue PCD
               - Cell cycle regulation
               - Aleurone layer formation
               - Regulatory network of nutrient accumulation
               - Regulation of seed size
               - Regulation of leaf development
               - HSFA7/ HSFA6B-regulatory network-induced by drought and ABA.
               - SNAC1 transcription network involved in drought and salinity tolerance
               - Arsenic uptake and detoxification

Regulatory Network of Nutrient Accumulation

  • Updated/renamed pathways:

         - Flower development
         - Thiosulfate disproportionation III (rhodanese)

  • Pathway Projection Statistics: We have extended orthology-based pathway projections for 1 new species: Arabidopsis halleri. Plant Reactome now hosts pathway projections for 79 species ranging from unicellular autotrophs to higher plants. In addition, we have revised pathways for Solanum lycopersicum (tomato) and Glycine max (soybean), based on their recent genome updates (source: Ensembl Plants).

 

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 orthoinference at this time, although we are actively working to enhance the projection process to include these elements on projected pathways in future releases.

 Please let us know if you have questions or suggestions.

The Gramene Team
www.gramene.org.