Release Notes 62 (November 2019)

Table of Contents

• Genomes Release Notes
• Pathways Release Notes 
• Infrastructure Updates
• Recent publications

The Gramene Knowledgebase Team is pleased to announce its Release #62 with the Genome section providing access to information on 96,607 GeneTree families comprising 2,146,774 individual genes from 67 plant genomes with 2,365,624 input proteins. It includes six new reference genomes: robusta coffee (Coffea canephora), hot pepper (Capsicum annuum), global artichoke (Cynara cardunculus), eragrostis tef (Eragrostis tef), durum wheat (Triticum turgidum, tetraploid AABB), and common liverwort (Marchantia polymorpha), and one updated genome: criollo cocoa, cacao or chocolate tree (Theobroma cacao).

The Plant Reactome, Gramene's pathway portal, hosts pathway projections for 97 species ranging from unicellular autotrophs to higher plants. In this release, we have extended orthology-based pathway projections for 15 new species; added 6 newly curated pathways; and updated 11 pathways in tthe reference species Oryza sativa (resulting in a total of 306 rice pathways). In the following sections we provide detailed summary of updates in the Gramene Knowledgebase. 

The 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. Robusta coffee (Coffea canephora): assembly and annotation GCA_900059795.1.
2. Hot pepper (Capsicum annuum): assembly and annotation GCA_000512255.2.
3. Global artichoke (Cynara cardunculus): assembly and annotation GCA_001531365.1.
4. Eragrostis tef (Eragrostis tef): assembly from ENA (GCA_000970635.1) and community annotation.
5. Durum wheat (Triticum turgidum, tetraploid AABB).
6. Common liverwort (Marchantia polymorpha): assembly and annotation GCA_003032435.1.

• Updated genomes:

1. Criollo cocoa, cacao or chocolate tree (Theobroma cacao): assembly update GCA_000208745.2.

• New & Updated data: 

1. New whole genome alignments for robusta coffee (Coffea canefora), hot pepper (Capsicum annuum), global artichoke (Cynara cardunculus), eragrostis tef (Eragrostis tef), durum wheat (Triticum turgidum), common liverwort (Marchantia polymorpha), and chocolate tree (Theobroma cacao); see summary here.
2. New synteny data for robusta coffee (Coffea canefora), hot pepper (Capsicum annuum), and chocolate tree (Theobroma cacao); see summary here.
3. Updated split gene predictions from peptide comparative genomics.
4. The Pan-taxonomic Compara set of gene trees was updated with two new plant species added (Marchantia polymorpha and Brachypodium distachyon), and one removed (Chondrus crispus).
5. Updated metadata for wheat EMS-induced mutations.
6. KASP marker information for the TILLING population is being displayed on the genetic variation pages for wheat.

• Updated software: Updated genome browser, database schema, and API to Ensembl 98 software.

List of Genomes (Genome browser)

Compara

Gene Trees

The EnsemblCompara GeneTree database updated. A total of 96,607 GeneTree families comprising 2,146,774 individual genes from 67 plant genomes with 2,365,624 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 299 genomic alignments.

 New whole-genome alignments between:

• Robusta coffee (Coffea canefora) and Arabidopsis / Grape / Rice / Tomato.
• Hot pepper (Capsicum annuum) and Arabidopsis / Grape / Rice / Tomato.
• Global artichoke (Cynara cardunculus) and Arabidopsis / Grape / Rice / Tomato.
• Eragrostis tef (Eragrostis tef) and Arabidopsis / Grape / Rice.
• Durum wheat (Triticum turgidum) and Arabidipsis / Brachypodium / Grape / Rice.
• Common liverwort (Marchantia polymorpha) and Arabidopsis / Grape / Rice.
• Chocolate tree (Theobroma cacao) and Arabidopsis thaliana, A. lyrata, A. halleri / Brassica napus, B. oleracea, B. rapa / Corchorus capsularis / Gossypium raimondii / Grape / Rice.

Synteny data

 Here is a summary of all 66 synteny maps. The following synteny maps are new.

• Robusta coffee (Coffea canefora) with Grape / Tomato.
• Hot pepper (Capsicum annuum) with Tomato.
• Chocolate tree (Theobroma cacao) with Grape.

Protein Annotation, GO, Xref Protein domain information 

These were generated for the new and updated genomes.

Gramene Mart

• New Plant Gene and Variation Marts

PATHWAYS Release Notes
(Plant Reactome Version 19; Gramene r62) Summary:

This release represents a significant expansion in the number of curated pathways, projected species, and associated inferred pathways, reactions and genes (~25% data increase). Plant Reactome now hosts pathway projections for 97 plant species. Here, we provide a summary of Gramene Release 62 including website and coding updates, a list of new & updated pathways, information on new species, and projection statistics.

Website and coding updates

This release utilizes an updated ortho-inference process, converted to Java from Perl and revised for efficiency. The script uses the rules previously set up for ortho-inference while containing minor adjustments to facilitate changes in the underlying Reactome data schema and take advantage of new features and functionalities present in our partner Reactome site.

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 97 projected species hosted by Plant Reactome.

Curation of reference rice pathways

We have added 6 newly curated pathways, 11 updated pathways, and 2 "container" pathways, resulting in a total of 306 reference rice pathways. In this release, we focused on updates to rice metabolic pathways and curation of cell-cycle events.

Below: An example of newly curated cell-cycle pathways representing G1/S transition during mitosis. Our data model represents various steps of this event within the nucleoplasm (assembly of the pre-replication complex, activation of the pre-replication complex, and G1/S-specific transcription). Clickable elements allow the user to highlight a subset of reactions. For example, in this pathway, highlighted blue lines show "Activation of the pre-replication complex in G1/S transition":

Pathway Projection Statistics

We have extended orthology-based pathway projections for 15 new species (in bold below). Plant Reactome now hosts pathway projections for 97 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 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 ortho-inference at this time, although we are actively working to enhance the projection process to include these elements on projected pathways in future releases.

Plant Reactome mirror at Powered-by-CyVerse

We continue to leverage the resources made available in the Powered-by-CyVerse virtual server environment by providing the Plant Reactome database mirror (https://plantreactome.cyverse.org) to facilitate training, education, and integration with the CyVerse platform and user community.

Recent Publications:

1. Naithani S., P. Gupta, J. Preece, P. D'Eustachio, J. Elser, J. Kiff, P. Garg, D.A. Dikeman$, A.J. Olson, S. Wei, M.K. Tello-Ruiz, J. Cook, A. Fabregat, T. Cheng, E. Bolton, A.F. Muñoz-Pomer, S. Mohammed, I. Papatheodorou, L. Stein, D. Ware, and P. Jaiswal (2019). Plant Reactome: A knowledgebase and resource for comparative pathway analysis. Nucleic Acids Res. https://doi.org/10.1093/nar/gkz996.
2. Howe K.L., B. Contreras-Moreira, N. De Silva, G. Maslen, W. Akanni, J. Allen, J. Alvarez-Jarreta, M. Barba, D.M. Bolser, L. Cambell, M. Carbajo, M. Chakiachvili, M. Christensen, C. Cummins, A. Cuzick, P. Davis, S. Fexova, A. Gall, N. George, L. Gil, P. Gupta, K. E. Hammond-Kosack, E. Haskell, S. E. Hunt, P. Jaiswal, S. H. Janacek, P. J. Kersey, N. Langridge, U. Maheswari, T. Maurel, M. D. McDowall, B. Moore, M. Muffato, G. Naamati, S. Naithani, A. Olson, I. Papatheodorou, M. Patricio, M. Paulini, H. Pedro, E. Perry, J. Preece, M. Rosello, M. Russell, V. Sitnik, D. M. Staines, J. Stein, M. K. Tello-Ruiz, S. J. Trevanion, M. Urban, S. Wei, D. Ware, G. Williams, A. D. Yates, P. Flicek (2019). Ensembl Genomes 2020—enabling non-vertebrate genomic research. Nucleic Acids Res., gkz890, https://doi.org/10.1093/nar/gkz890
3. Tello-Ruiz MK, Marco CF, Hsu FM, Khangura RS, Qiao P, et al. (2019) Double triage to identify poorly annotated genes in maize: The missing link in community curation. PLOS ONE 14(10): e0224086. https://doi.org/10.1371/journal.pone.0224086
4. Naithani S, P. Gupta, J. Preece, P. Garg, V. Fraser, L.K. Padgitt-Cobb, M. Martin, K. Vining and P. Jaiswal (2019). Involving community in genes and pathway curation. Database, 2019:1-8,  https://doi.org/10.1093/database/bay146

Please let us know if you have questions or suggestions.

The Gramene Team
www.gramene.org.