Release Notes 61 (April 2019)

Table of Contents

• Genomes Release Notes
• Pathways Release Notes
• Infrastructure Updates

The Gramene Knowledgebase Team is pleased to announce its Release #61 with the Genome section providing access to information on 2,264,698 genes and 61 reference plant genomes. It includes three new reference genomes: kiwifruit (Actinidia chinensis), and two ecotypes of Hall's panicgrass (Panicum hallii FIL2) and (Panicum hallii HAL2), and updates to several existing genomes. This release also includes 109 manually curated maize gene models as a GFF file to attach as a custom track in Gramene's genome browser (and will soon be also available as a permanent track). The Plant Reactome, Gramene's pathway portal hosts pathway projections for 82 species including those in the Genome section ranging from unicellular autotrophs to higher plants. Total curated reference pathways are 298. See more details on the release #61 page.

Gramene Knowledgebase 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. Core funding for the project is provided by the National Science Foundation, USA.

Genomes Release Notes 

• New genomes:

1. Kiwifruit (Actinidia chinensis): assembly and annotation GCA_003024255.1
2. Panicum hallii FIL2: PHallii_v3.1 assembly and annotation GCA_002211085.2
3. Panicum hallii HAL2: PhalliiHAL_v2.1 assembly and annotation GCA_003061485.1

• Updated genomes:

1. Oryza sativa Japonica: updated nonOrganelle gene annotation from RAP-DB version 2018-11-26 and added stable_id mappings to previous annotation.
2. Solanum lycopersicum: added ITAG3.0 unplaced gene models (Chr0)

• New & Updated data: 

1. Triticum aestivum (bread wheat): added 31,779 markers from the 35K Axiom SNP array (provided by CerealsDB).
2. Triticum dicoccoides (Emma Zavitan wheat): added polyploid view.
3. Vigna radiata: added stable_id mappings to previous annotation.
4. Physcomitrella patens: added stable_id mappings to previous annotation.
5. New manually curated maize gene models (custom genome track may be set up using this GFF file).
6. New whole-genome alignments for A. chinensis, P. hallii FIL2 and P. hallii HAL2, see WGA section.
7. New synteny data for A. chinensis, P. hallii FIL2, P. hallii HAL2 and Sorghum bicolor, see Synteny section.
8. BioMarts for all gene and variation data.
9. Updated split gene predictions from peptide comparative genomics.

• Updated software: Updated genome browser, database schema, and API to Ensembl 96 software.

List of Genomes (Genome browser link)

Genetic and Structural Variation 

For Triticum aestivum (Wheat) genome, 31,779 markers from the 35K Axiom SNP array were added. They were provided by CerealsDB and designed by Affymetrix. This Affymetrix product (ID 550524) contains 35,143 SNPs selected to be informative across a wide range of hexaploid wheat accessions. This 384-sample format array is a cost effective and efficient system for screening large numbers of lines. The array has been used to screen a large global collection of elite and landrace varieties including hexaploid and tetraploid accessions.

Compara

Gene Trees

The EnsemblCompara GeneTree database updated. A total of 92,708 GeneTree families were constructed comprising 1,948,793 individual genes from 61 plant genomes with 2,158,277 input proteins.

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.

Genomic alignments

 Here is a summary of all genomic alignments. New Whole Genome Alignments between  

• Kiwifruit (Actinidia chinensis) and Arabidipsis (Arabidopsis_thaliana) / Grape (Vitis_vinifera) / Rice (Oryza sativa Japonica) / Tomato (Solanum lycopersicum)
• Panicum hallii FIL2 and Arabidipsis (Arabidopsis_thaliana) / Grape (Vitis_vinifera) / Rice (Oryza sativa Japonica) 
• Panicum hallii HAL2 and Arabidipsis (Arabidopsis_thaliana) / Grape (Vitis_vinifera) / Rice (Oryza sativa Japonica) 

Synteny data

• Kiwifruit (Actinidia chinensis) and Grape (Vitis_vinifera) / Tomato (Solanum lycopersicum)
• Panicum hallii FIL2 and Rice (Oryza sativa Japonica), example 
• Panicum hallii HAL2 and Rice (Oryza sativa Japonica), example
• Sorghum (Sorghum_bicolor) and Maize (Zea_mays), example

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 61_96 is set as version 43_96 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 18 (Gramene r61)

• Wesbite updates:
  For user and data security, SSL (Secure Sockets Layer) has now been implemented on Plant Reactome. The entire site and all services are now available over https. The latest Plant Reactome pathway data has also 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 82 projected species currently hosted by Plant Reactome.
• Curation of reference rice pathways: 
  • We have added 4 newly curated pathways, 2 updated pathways and 1 "container" pathway, resulting in a total of 298 reference rice pathways.
  • New Pathways:
    • Root hair development
    • Phytic Acid biosynthesis (lipid independent)
    • Response to aluminum stress
    • Root-specific gene-network of NAC10_TF induced by drought, salinity, and ABA
  • Updated pathways:
    • HSFA7-regulatory network induced by drought and ABA
    • SNAC1 transcription network involved in drought and salinity tolerance

Example of recently curated rice pathway: Response to aluminum stress

• Pathway Projection Statistics: We have extended orthology-based pathway projections for three new species: Actinidia chinensis (kiwi fruit), Panicum hallii FIL2 ("Hall's panicgrass"), and Panicum hallii var. hallii HAL2. Plant Reactome now hosts pathway projections for 82 species ranging from unicellular autotrophs to higher 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 the 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