Gramene Build 36: A Resource for Comparative Plant Genomics

Gramene (http://www.gramene.org) is a curated data resource for comparative genome analysis a wide variety of plants. The database integrates information about genomic sequence, genes, proteins, biochemical pathways, maps and markers, QTL, germplasm, and genetic and phenotypic diversity. To index and associate these different data types, Gramene makes extensive use of ontologies (controlled vocabularies) including those for plant structures and growth stages, traits and phenotypes, gene function, biological processes, cellular components, and environments. Online tutorials and help documents provide users with an overview of how to conduct a wide variety of operations on the database. All data in Gramene is publicly-available, and all code is open source.

Gramene released the 36th build in Fall, 2012. In association with Ensembl Plants, we added the following:

• Three new genomes:
  • Hordeum vulgare (barley),
  • Solanum tuberosum (potato)
  • Musa acuminata (banana)
• New EST alignments for Physcomitrella patens (moss)
• New repeats feature annotation for Selaginella moellendorffii (lycopod)
• Updated gene models for Glycine max (soybean)
• Updated peptide comparative genomics
• Many more alignments, including several between c4 species (e.g., maize, sorghum and foxtail millet) dicotyledonous species, including wine grape and potato.
• GO terms in phyologenetic gene trees.

Gramene is supported by a grant from the NSF and represents a collaborative effort between Cold Spring Harbor Laboratory, Oregon State University, Ensembl Genomes, and various national and international projects dedicated to cereal genomics and genetics research.