Release Notes 60 (February 2019)

Table of Contents

• Genomes Release Notes
• Pathways Release Notes
• Infrastructure Updates

The Gramene Team is pleased to announce its Release #60 with the Genome section providing access to information on 2,162,056 genes and 58 reference plant genomes. It includes new reference genome of Arabidopsis halleri and updates to several existing genomes. 1,891,391 protein-coding genes are organized in 93,194 gene families. The Plant Reactome, Gramene's pathway portal hosts pathway projections for 79 species ranging from unicellular autotrophs to higher plants. In this release, we have extended orthology-based pathway projections for 1 new species: Arabidopsis halleri, and revised pathways for Solanum lycopersicum (tomato) and Glycine max (soybean), based on their recent genome updates; added 10 new curated pathways for reference species Oryza sativa (total curated reference pathways are 293). 

Gramene is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species. The genome databases were built in direct collaboration with Ensembl Plants and the Plant Reactome database was produced in collaboration with the Reactome project.

Genomes Release Notes 

• New genomes:

Arabidopsis halleri, assembly GCA_900078215, annotation doi:10.5061/dryad.gn4hh

• Updated genomes:

1. Aegilops tauschii: updated assembly and annotation to version Aet v4.0 (GCA_002575655)
2. Solanum lycopersicum: updated assembly (GCA_000188115.3) and annotation (ITAG3.0, except unplaced genes)
3. Glycine max: updated assembly (GCA_000004515.4) and annotation (Rel. 137, Version 4, Glycine_max_v2.1)
4. Vigna radiata: updated annotation (vigra.VC1973A.gnm6.ann1.M1Qs)
5. Physcomitrella patens: updated annotation (V3.3)

• New & Updated data: 

1. Triticum aestivum: Inter-Homeologous Variants (IHVs) were added
2. Lupinus angustifolius: genes from previous release were added
3. Arabidopsis thaliana: TAIR10 is now the unique source of ncRNA annotations
4. Nicotiana attenuata: mapped microarray probes were updated
5. Zea mays: mapped microarray probes were updated
6. BioMarts for all gene and variation data
7. Updated split gene predictions from peptide comparative genomics.

• Updated software: Updated genome browser, database schema, and API to Ensembl 95 software.

List of Genomes

Genetic and Structural Variation

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

Compara

Gene Trees

The EnsemblCompara GeneTree database updated. A total of 93,194 GeneTree families were constructed comprising 1,891,391 individual genes from 58 plant genomes (and 5 non-plant outgroups).

Putative Split Genes

• Updated Split Genes: Updated split genes for the current release are available on 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.

Here is brief statistics of contiguous gene split models for each species.

Genomic alignments

Here is a summary of all genomic alignments and syntenies. New LastZ  were conducted between Arabidopsis halleri and each of Oryza sativa Japonica, Arabidopsis thaliana, Theobroma cacao and Vitis vinifera. A stats page for each paiwise LastZ alignment is available, see for example the one for A. halleri vs V. vinifera. Click here for a complete list of comparative analyses.

Protein Annotation, GO, Xref Protein domain information 

These were generated for the new and updated genomes.

Mart

• New Plant Gene and Variation Marts

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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 60_95 is set as version 42_95 at Ensembl.

• Website and coding updates: The latest Plant Reactome pathway data has been re-indexed and made available via Gramene search.

Pathways (Plant Reactome): Plant Reactome Release Summary - Version 17 (Gramene r60)

• 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 79 projected species currently hosted by Plant Reactome.
• Curation of reference rice pathways: 
  • ​We have added 10 newly curated pathways and 3 "container" pathways, and updated 2 existing pathways, resulting in a total of 293 reference rice pathways.
  • New Pathways:
• •          - Regulation of embryo development
  •          - Maternal tissue PCD
             - Cell cycle regulation
             - Aleurone layer formation
             - Regulatory network of nutrient accumulation
             - Regulation of seed size
             - Regulation of leaf development
             - HSFA7/ HSFA6B-regulatory network-induced by drought and ABA.
             - SNAC1 transcription network involved in drought and salinity tolerance
             - Arsenic uptake and detoxification

• Updated/renamed pathways:

         - Flower development
         - Thiosulfate disproportionation III (rhodanese)

• Pathway Projection Statistics: We have extended orthology-based pathway projections for 1 new species: Arabidopsis halleri. Plant Reactome now hosts pathway projections for 79 species ranging from unicellular autotrophs to higher plants. In addition, we have revised pathways for Solanum lycopersicum (tomato) and Glycine max (soybean), based on their recent genome updates (source: Ensembl Plants).

*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.

The Plant Reactome increasingly includes curated regulatory and developmental pathways, which require more reference DNA and RNA sequence elements, in addition to the traditional protein-coding elements. These sequence elements are not included in Reactome orthoinference at this time, although we are actively working to enhance the projection process to include these elements on projected pathways in future releases.

Please let us know if you have questions or suggestions.

The Gramene Team www.gramene.org