Release Notes 52 (November 2016)

Table of Contents

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

# Website

See also legacy data in Gramene's Archive.

# Genomes Release Notes

• New data
  • The following data for the early release of B73 Zea mays RefGenV4 reference assembly are now available from Gramene's FTP site:
    • A preliminary gene ID association table for B73 Zea mays RefGenV3 and RefGenV4 (gene ID history)
    • Transposable element annotations (TEs in GFF)
    • Mitochondrial and chloroplast genome sequences (chrMt and chrPt from RefGenV3)
  • Mitochondrial and chloroplast chromosomes (from RefGenV3) were incorporated to the Zea mays (RefGenV4) genome browser
  • Added two pairs of synteny for Zea mays against Setaria italica and Brachypodium distachyon
  • Whole-genome alignment between the bread wheat (TGACv1) component genomes (restricted to homoeologues predicted in the Compara gene tree)
  • Whole-genome alignment between bread wheat and Brachypodium distachyon
  • New gene model annotation (Araport 11) for Arabidopsis thaliana
  • Plant gene expression data from Expression Atlas is now available via Gramene’s search
• Updated data
  • Updated protein features from InterPro
  • Updated peptide comparative genomics
  • Updated BioMarts
• Updted software
  • Updated to Ensembl 86 software

## Genomes Core

## Ensembl Variation

## Compara

### Gene Trees

The EnsemblCompara GeneTree database was updated. A total of 61,582 GeneTree families were constructed comprising 1,460,776 individual genes (1,619,230 input proteins) from 44 plant genomes (and 5 non-plant outgroups).

#### Putative Split Genes

Split gene predictions were not updated in this release. Last update was done in release 50 (April 2016), see summary statistics in build 50 release notes and Gramene's FTP site.

### Synteny

Added two pairs of synteny for maize: Setaria italica vs. Zea mays, and Brachypodium distachyon vs. Zea mays.

### WGA and other nucleotide alignments

• WGAs between the bread wheat's component genomes (restricted to homoeologues predicted in the Compara gene tree)
• WGAs between the updated bread wheat (Triticum aestivum TGACv1) assembly and Brachypodium distachyon

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

## Mart

New Plant Gene and Plant Variation Marts

# Pathway Release Notes

## Plant Reactome

The Plant Reactome has expanded gene homology-based pathway projections to 66 plant species. Newly projected species: Beta vulgaris, Brassica napus, Syncechocystis pcc6803, and Trifolium pratense. Notable updated Compara orthology data has been kindly provided by Ensembl for Triticum aestivum and Zea mays (v4). In addition, we have added nine newly curated pathways and revised two additional curated pathways. Please take a note of the following pathway statistics and status table for more details.

Pathway Curation

Newly curated pathways (O. sativa)

• Auxin transport
  • Intracellular auxin transport
• Response to stress
  • Response to cold temperature
• Circadian Rhythm
• Inflorescence development
  • Long day regulated expression of florigens
  • Short day regulated expression of florigens
  • Transition from vegetative to reproductive shoot apical meristem
• Tryptophan biosynthesis

Updated pathways (O. sativa)

Polar auxin transport

Pathway Projection Statistics and Status

*data from sequenced transcriptomes

^ projections currently exclude cell-cycle pathways and annotations

• Planteome Inparanoid data was kindly provided by the Planteome project
• When available the outgoing links from gene product IDs mapped to reactions are always hyperlinked to respective entries in collaborator databases/online resources

NOTE: The pathway counts for both reference and projected species include a few organizational "container" names, such as "Hormone biosyntheses" and "Metabolism". Additionally, the bulk of the projected pathways occur in the areas of metabolic and regulatory function, whereas the rice reference data set has additional pathways related to cell cycle functions. We are not currently using these additional pathways as a source for orthology projection.

## "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 can be seen 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. Programmatic access to Gramene is now available through the RESTful Ensembl API.

## Public MySQL Server

Our partner Ensembl Genomes offer 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 51_85 is set as version 32_85.

Gramene currently a legacy public, read-only MySQL server for release 40 of our databases. You can connect to the host "gramenedb.gramene.org" with the password "gramene," e.g.:

mysql -hgramenedb.gramene.org -pgramene