Table of Contents

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

#Genomes Release Notes

• New features:
  • Polyploid view for wheat has been enabled, allowing users to view alignments between all 3 wheat components simultaneously.
  • SIFT scores are now displayed on the Genes and regulation view of a gene variant. Here is a sorghum SNP.
• Updated data:
  • Added gene name synonyms for O. sativa using from database sources such as CGSNL, Oryzabase and Rap-DB.
  • Updated protein features for all (nearly 2 million) plant proteins using InterProScan with version 67 of InterPro.
  • Updated BioMarts for all gene and variation data.
  • 26 new and updated functional genomic databases (see Arabidopsis for example).
  • Tandem repeats annotated by the TRF program are no longer used to soft- and hardmask the genome sequences. This affects sequences retrieved via the API and the files on the FTP site.
• Updated software
  • Updated genome browser, database schema, Mart and API to Ensembl 92 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 last updated in release 56. A total of 67,042 GeneTree families were constructed comprising 1,703,219 individual genes (1,892,629 input proteins) from 53 plant genomes (and 5 non-plant outgroups).

Putative Split Genes

• Split gene predictions were updated in release 56 and are available from Gramene's 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.  Brief statistics for each species is given below.

Genomic alignments and Synteny

Here is a summary of all genomic alignments and syntenies. These correspond to LastZ comparisons between the 8 new genomes and each of Oryza sativa Japonica, Arabidopsis thaliana, and Vitis vinifera. A stats page for each paiwise LastZ alignment is available, see for example the one for P. vulgaris vs V. vinifera and the corresponding synteny map for chromosome 9 of the common bean vs the common grape vine. Also available from Gramene's FTP are Synteny tables.

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

Mart

• New Plant Gene and Variation Marts

# Pathways

* Pathway Projection Statistics and Status

• Last updated in release 56b (February 2018). See pathway release 56b 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 57_92 is set as version 39_92 at Ensembl.