The Gramene Database build 58 is out with new and updated genomes!

The Gramene Team is pleased to announce its release #58 with 2,140,348 genes and 56 reference plant genomes.  Among those, 1,783,803 protein-coding genes are organized in 71,284 gene family trees.

• New genomes -- Remember that any plant genome that is submitted to the INSDC along with AGP and gene models can be added to Gramene!
  • Cajanus cajan (pigeon pea)
  • Daucus carota (carrot)
  • Vigna angularis (adzuki bean)
  • Triticum aestivum (bread wheat) IWGSC(RefSeq v1.0 )
• Updated genomes
  • Setaria italica (v2)
  • Populus trichocarpa (v3)
  • Physcomitrella patens (v3)
  • Chlamydomonas reinhardtii (v5.5)
  • Brachypodium distachyon (v3)

Note: The original (older) versions of these genomes can still be found in the Ensembl Plants Archive site, and data from BED, GFF, GTF, WIG or VCF can be mapped to the latest assembly using the Assembly Converter tool.

• New & Updated data
  • The updated genomes include updated Whole Genome Alignments and Assembly to Assembly Mapping data
  • Updated gene trees and homologies
  • New and updated synteny maps
  • Updated split gene predictions from peptide comparative genomics
  • Updated protein features
  • Updated BioMarts
• Updated software
  • Updated genome browser, database schema, Mart and API to Ensembl 93 software

A complete description of the contents of the release is available in our release notes.  The genome databases were built in direct collaboration with Ensembl Plants and the Plant Reactome database was maintained in collaboration with the Reactome project.

Please let us know if you have questions or suggestions.

The Gramene Team