Announcing Gramene Knowledgebase release #61 with new and updated plant genomes and pathways

Submitted by pankaj.jaiswal on Thu, 05/02/2019 - 18:15

The Gramene Knowledgebase Team is pleased to announce its Release #61 with the Genome section providing access to information on 2,264,698 genes and 61 reference plant genomes. It includes three new reference genomes: kiwifruit (Actinidia chinensis), and two ecotypes of Hall's panicgrass (Panicum hallii FIL2) and (Panicum hallii HAL2), and updates to several existing genomes. This release also includes 109 manually curated maize gene models as a GFF file to attach as a custom track in Gramene's genome browser (and will soon be also available as a permanent track). The Plant Reactome, Gramene's pathway portal hosts pathway projections for 82 species including those in the Genome section ranging from unicellular autotrophs to higher plants. Total curated reference pathways are 298. See more details on the release #61 page.

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.

  • New Plant Genomes:
  1. Kiwifruit (Actinidia chinensis): assembly and annotation GCA_003024255.1
  2. Panicum hallii FIL2: PHallii_v3.1 assembly and annotation GCA_002211085.2
  3. Panicum hallii HAL2: PhalliiHAL_v2.1 assembly and annotation GCA_003061485.1
  • Updated genomes:
  1. Oryza sativa Japonica: updated nonOrganelle gene annotation from RAP-DB version 2018-11-26 and added stable_id mappings to previous annotation.
  2. Solanum lycopersicum: added ITAG3.0 unplaced gene models (Chr0)
  • New & Updated data: 
  1. Triticum aestivum (bread wheat): added 31,779 markers from the 35K Axiom SNP array (provided by CerealsDB).
  2. Triticum dicoccoides (Emma Zavitan wheat): added polyploid view.
  3. Vigna radiata: added stable_id mappings to previous annotation.
  4. Physcomitrella patens: added stable_id mappings to previous annotation.
  5. New manually curated maize gene models (custom genome track may be set up using this GFF file).
  6. New whole-genome alignments for A. chinensis, P. hallii FIL2 and P. hallii HAL2, see WGA section.
  7. New synteny data for A. chinensis, P. hallii FIL2, P. hallii HAL2 and Sorghum bicolor, see Synteny section.
  8. BioMarts for all gene and variation data.
  9. Updated split gene predictions from peptide comparative genomics.
  • Updated software: Updated genome browser, database schema, and API to Ensembl 96 software.
  • Genetic and Structural Variation : 31,779 markers from the 35K Axiom SNP array were added to the Triticum aestivum (Wheat) genome. They were provided by CerealsDB and designed by Affymetrix.
  • Compara gene trees: The Ensembl Compara GeneTree database updated. A total of 92,708 GeneTree families were constructed comprising 1,948,793 individual protein coding genes from 61 plant genomes with 2,158,277 input proteins.
  • Identifying 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. 
  • Whole genome alignments and Synteny: Kiwifruit and two Panicum genomes were included in the whole genomic alignments and synteny data sets.
  • Plant Pathways
    • Wesbite updates: For user and data security, SSL (Secure Sockets Layer) has now been implemented on Plant Reactome. The entire site and all services are now available over https. The latest Plant Reactome pathway data has also been re-indexed and made available via Gramene search.
    • Curation of reference rice pathways: 
      • We have added 4 newly curated pathways, 2 updated pathways and 1 "container" pathway, resulting in a total of 298 reference rice pathways.
      • New Pathways:
        1. Root hair development
        2. Phytic Acid biosynthesis (lipid independent)
        3. Response to aluminum stress
        4. Root-specific gene-network of NAC10_TF induced by drought, salinity, and ABA
      • Updated pathways:
        1. HSFA7-regulatory network induced by drought and ABA
        2. SNAC1 transcription network involved in drought and salinity tolerance
      • Pathway Projection Statistics: We have extended orthology-based pathway projections for three new species: Actinidia chinensis (kiwi fruit), Panicum hallii FIL2 ("Hall's panicgrass"), and Panicum hallii var. hallii HAL2. Plant Reactome now hosts pathway projections for 82 species ranging from unicellular autotrophs to higher plants.

Please let us know if you have questions or suggestions.

The Gramene Team
www.gramene.org