Table of Contents

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

#Genomes Release Notes

• New genomes
  • Cajanus cajan (pigeon pea) GCA_000340665.1
  • Daucus carota (carrot) GCA_001625215.1
  • Vigna angularis (adzuki bean) GCA_001190045.1
  • Triticum aestivum (bread wheat) IWGSC(RefSeq v1.0 ). Current data includes:
    • The Axiom 820K SNP Array from CerealsDB.
    • EMS-induced mutations from sequenced TILLING populations (Kronos and Cadensa).
    • Assembly to assembly mapping and gene ID mapping to the previous TGAC v1 assembly and annotation.
    • Whole genome alignments to rice, brachypodium and barley.
• Updated genomes
  • Using the INSDC import pipeline, the following assemblies were updated:
    • Brachypodium distachyon (v3) GCA_000005505.4
    • Chlamydomonas reinhardtii (v5.5) GCA_000002595.3
    • Physcomitrella patens (v3) GCA_000002425.2
    • Populus trichocarpa (v3) GCA_000002775.3
    • Setaria italica (v2) GCA_000263155.2
  • The original 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

Genomes

Genetic and Structural Variation

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

Compara

Gene Trees

• A total of 71,284 GeneTree families were constructed comprising 1,783,803 individual genes (1,978,457 input proteins) from 56 plant genomes (and 5 non-plant outgroups).

Putative Split Genes

• Split gene predictions were updated in this release 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. The new alignments correspond to LastZ comparisons between the new or updated genomes in release 58 versus reference monocot (Oryza sativa Japonica) and dicot (Arabidopsis thaliana or Vitis vinifera) genomes. A stats page for each paiwise LastZ alignment is available, see for example the one for carrot vs grape. Also available from Gramene's FTP are Synteny tables (last updated in release 58).

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 58_93 is set as version 40_93 at Ensembl.