Table of Contents

• Genomes Release Notes
• Pathways Release Notes
• Infrastructure

The Gramene Team is pleased to announce its Release #59 with the Genome section providing access to information on 2,156,459 genes and  57 reference plant genomes. 1,860,691 protein-coding genes are organized in 96,500 gene families. The Plant Reactome -- Gramene's pathway portal -- introduces its new website http://plantreactome.gramene.org/ for improved user engagement and provides 14 new curated pathways. The gene orthology-based projection of pathways now extends to 78 species representing the plant tree of life.

Genomes Release Notes

• New genomes
  • Triticum dicoccoides (emmer wheat) | WEWSeq v.1.0 | INSDC Assembly GCA_002162155.1, Jun 2017
  • Vigna radiata (mungbean) | Vradiata_ver6 | INSDC Assembly GCA_000741045.2, Nov 2015
• Removed genomes​
  • The genome assembly of Cajanus cajan (pigeonpea, GCA_000340665.1) was removed from this release, pending import corrections
• Updated genomes
  • ​Triticum aestivum (bread wheat, GCA_900519105.1), gene build updated to v1.1
• New & Updated data
  • Around 80 pairs of plant genomes have whole genome alignments generated, bringing the total number of pairwise whole genome alignments to nearly 250. Examples include the alignment of all six legume genomes to Medicago truncatula (GCA_000219495.2).
  • Updated repeat feature annotation across all plants, including newly added repeat feature classification using REdat and REcat.
  • Updated gene trees across all plants, including the new and updated genomes.
    • In this release we used a new HMM-based method, resulting in 96,500 gene families with 1,860,691 protein-coding genes.
  • Updated ncRNA alignments and annotations across all plants including MirBase imports for twelve species.
  • Updated protein features for all (nearly 2 million) plant proteinsusing InterProScan with version 67 of InterPro.
  • Updated BioMarts for all gene and variation data.
  • Corrected attribution for many plant genomes.
  • Corrected chromosomal density plots for all plants.
• Updated software
  • Updated genome browser, database schema, Mart and API to Ensembl v94
• Genomes in the current release #59

Compara

• Gene Trees
  A total of 96,500 GeneTree families were constructed comprising 1,860,691 individual genes (2,106,462 input proteins) from 57 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. Split gene counts for each species is given as follows.

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.

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

Gramene Mart (BioMart)

• Updated Plant Gene and Variation Marts

Pathways (Plant Reactome) Release Notes version 16

Website and coding updates

• The Plant Reactome web site landing page has a new look and feel. It was redesigned on the Joomla Content Management System for better user experience.
• Users can import/overlay gene-gene interaction data filtered by a confidence score (where available). This is done by enabling a threshold filter to be selected by the user in the Pathway Browser when viewing the interactor overlay. Try an example here.
• The majority of gene-gene interaction data is hosted in Plant Reactome. A part of it is pulled remotely from EBI-Intact and BAR using the PSICQUIC webservices.
• The latest Plant Reactome pathway data has been re-indexed and made available via Gramene search.

Analytical Tools 

Currently, Plant Reactome supports researchers with the following analytical tools:

• Search for gene/protein, metabolites, pathways
• Upload and analyze gene-expression data on plant pathways
• Upload and analyze gene-gene interaction data on plant pathways
• Compare reference rice pathways with pathways from any of 78 projected species currently hosted by Plant Reactome.

Curation of reference rice pathways

In Gramene Release 59, we have added 14 newly curated pathways and 2 "container" pathways, and updated 2 other existing pathways, resulting in a total of 280 reference rice pathways. Browse them at http://plantreactome.gramene.org/PathwayBrowser/. We are encouraging users to suggest pathway updates and critiques.

New Pathways: 

• Tricin biosynthesis
• Lycopene catabolism
• Oryzalyde A biosynthesis
• Abscisic acid homeostasis
• Reactive oxygen species (ROS) homeostasis
• Generation of superoxide radicals
• Removal of superoxide radicals
• Valine degradation
• Cysteine degradation
• Recognition of fungal and bacterial pathogens and immunity response
• Reproductive meristem phase change
• Flower development
• Floral bract development
• Seed development

Pathway Projection Statistics and Status

We have extended orthology-based pathway projections for 4 new species: Daucus carota (carrot), Vigna radiata (mung bean), Vigna angularis (adzuki bean) and Triticum dicoccoides (Emmer wheat). Plant Reactome now hosts pathway projections for 78 species ranging from unicellular autotrophs to higher plants. In addition, we have revised pathways for Triticum aestivum (bread wheat), based on its recent genome update (IWGSC RefSeq v1.0).

• *Data from sequenced transcriptomes
• ^Projections currently exclude cell-cycle pathways and annotations
  Species names in bold represent new species projections
• 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 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.