See also notes for release 56b (focus on new pathways).

Table of Contents

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

#Genomes Release Notes

• New genomes
  • Cucumis sativus (cucumber, GCA_000004075.2)
  • Dioscorea rotundata (white Guinea yam, GCA_002240015.2)
  • Gossypium raimondii (cotton, GCA_000327365.1)
  • Helianthus annuus (common sunflower, GCA_002127325.1)
  • Lupinus angustifolius (blue lupin, GCA_001865875.1)
  • Manihot esculenta (cassava, GCA_001659605.1)
  • Nicotiana attenuata (coyote tobacco, GCA_001879085.1)
  • Phaseolus vulgaris (common bean, GCA_000499845.1)
• Updated genomes
  • Sorghum bicolor (sorghum, GCA_000003195.3)
  • Glycine max (soybean, GCA_000004515.3)
  • Prunus persica (peach, GCA_000346465.2)
  • Updated gene models for Oryza sativa Japonica (rice)
• New data
  • New transposable elements for Zea mays (maize) provided by Jeffrey Ross-Ibarra, Department of Plant Sciences, UC Davis
  • 26 new synteny maps and 33 new whole-genome alignments involving the new and updated genomes
• Updated data
  • Updated gene trees (see phylogenetic tree statistics) across all plants, including the 12 new and updated genomes
  • Updated split gene predictions from peptide comparative genomics
  • Updated identity based cross-references to UniProt across all plants
  • Updated alignment based cross-references to UniProt and RefSeq across all plants
  • Updated ncRNA alignments across all plants including MirBase imports for 6 species
  • Updated protein features for all (nearly 2 million) plant proteins
  • Updated Plant Reactome cross-references across all plants
  • Updated BioMarts for all gene and variation data
• Updated software
  • Updated genome browser, database schema, Mart and API to Ensembl 91 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 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 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

The current Gramene release includes 24 new synteny pairs (see 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

In build 55, Plant Reactome released several new data files, available for download. 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 56_91 is set as version 38_91 at Ensembl.