Table of Contents

• Website
• Genome Release Notes
• Pathways Release Notes
• Infrastructure

#Website

In this release we have moved the gramene homepage to our integrated search interface. Blog content and other static pages have been moved to news.gramene.org so they can be displayed within the new interface.

See also legacy data in Gramene's Archive.

#Genomes Release Notes

• Updated genomes
  • New assembly and annotation for Hordeum vulgare (barley)
• New data
  • New automatic ncRNA feature alignments across all plants
  • New Plant Reactome downloadable data files with relationships between gene products, pathways, reactions, and external reference sources (e.g., ChEBI, Ensembl, NCBI, and UniProt)
• Updated data
  • Updated variation data for Arabidopsis thaliana, incorporating the full data set from the 1001 Genomes Project
  • Updated peptide comparative genomics including updated barley
  • Updated protein features using InterProScan with version 63 of InterPro (new sources added: CDD, MobiDB, SFLD)
  • Added links for B73 Zea mays RefGen_v4 data and annotations: gene function, TE annotation, and raw data at NCBI
  • Updated gene and variation BioMarts

Genomes

Genetic and Structural Variation

New and updated genetic variation data for Ar was incorporated to the Oryza sativa Japonica genome browser. Legacy rice SSR/RFLP markers and QTLs from Gramene's archives, as well as QTLs from the Q-TARO database were remapped to IRGSPv1 coordinates by the KeyGene coorporation.

Compara

Gene Trees

• The EnsemblCompara GeneTree database was updated to include updated barley, sorghum, corn and wheat. A total of 62,367 GeneTree families were constructed comprising 1,469,948 individual genes (1,631,582 input proteins) from 44 plant genomes (and 5 non-plant outgroups).

Putative Split Genes

• No updates in this release. Last update done in release 53 (May 2017). The latest split gene predictions are available in the Gramene's FTP site.

Synteny

• No updates in this release. Last update done in release 52 (November 2016).

WGA and other nucleotide alignments

• No updates in this release. Last update done in release 52 (November 2016).

Protein Annotation, Go, Xref Protein domain information was updated based on the latest InterProScan analysis.

Mart

• New Plant Gene and Plant Variation Marts

# Pathways

Plant Reactome has released several new data files, available for download, that articulate the relationships between gene products, pathways, and reactions, and external reference sources such as ChEBI, Ensembl, NCBI, and UniProt. Both identifiers and web links within the site are available. Visit the Download section of the Plant Reactome web site to learn more.

* Pathway Projection Statistics and Status

• Last update release 52 (November 2016). See pathway release 52 notes for a table of pathway projection counts, data source and methods.

* "Cyc" Pathways

• BioCyc-based pathway databases on Pathway Tools ver. 19.0 are available from a virtual server hosted at CyVerse. Summary tables for the Cyc pathway databases created by Gramene is available in release 46 notes.

* Ontologies Release Notes

• No updates in this release. Last update done in release 31 (May 2010). A summary of ontologies data was last provided in release 46.

# Infrastructure

Web Services: Gramene's web services page documents many ways to directly connect to and analyze our databases.

Public MySQL Server

Our partner Ensembl Genomes offers a public, read-only MySQL server with copies of the species-specific and comparative genomic databases that we use. To use this with the mysql command-line client:

$ mysql -hmysql-eg-publicsql.ebi.ac.uk -P4157 -uanonymous

Please note that the versioning scheme used at this public database differs from ours; Gramene's release 54_89 is set as version 36_89 at Ensembl.