Table of Contents

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

#Website

In this release we have added a neighborhood conservation mode to the Homology tab in the search results. It displays up to 10 protein-coding genes flanking each gene in a gene tree. The genes are color coded based on the gene families represented in the neighborhood of the gene of interest. Each neighborhood links to the Ensembl Synteny browser for the corresponding region. We have also given users the ability to customize the gene tree node labels.

#Genomes Release Notes

• New genomes
  • New assembly and annotation for Corchorus capsularis (Jute; GCA_001974805)
• New data
  • New alignment based cross references to UniProt and RefSeq across all plants
  • New automatic ncRNA gene annotations across all plants
  • New Plant Reactome cross-references across all plants
  • New whole genome alignments between Hordeum vulgare (barley) and
    • Oryza sativa (summarized here), and
    • Brachypodium distachyon (summarized here)
• Updated data
  • Updated peptide comparative genomics including the new Jute genome
  • Updated protein features using InterProScan with version 64 of InterPro
  • Updated BioMart
• New web features
  • Pathyways link on gene pages
  • Neighborhood conservation mode to the Homology tab in the results of a query (see above Website section)
• Updated software
  • Updated genome browser, database schema, Mart and API to Ensembl 90 software

Genomes

Genetic and Structural Variation

No new and updated genetic/structural variation data since release 54.

Compara

Gene Trees

• The EnsemblCompara GeneTree database was updated to include updated barley, sorghum, corn and wheat. A total of 63,367 GeneTree families were constructed comprising 1,492,253 individual genes (1,660,942 input proteins) from 45 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 Mart

# 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 updated in 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 55_90 is set as version 37_90 at Ensembl.