Release Notes 63 (October 2020)

Table of Contents

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

The Gramene Knowledgebase Team is pleased to announce its Release #63 with the Genome section providing access to information on 93 reference genomes and 122,947 gene family trees. We are adding 26 new reference genomes, including pineapple, cantaloupe, watermelon, Golden apple, clementine, sweet cherry, almond, pistachio, olive tree, cannabis or marijuana, tobacco, a relative of sugar cane, five varieties of European wheat, and new varieties of barley and cocoa. With these new genomes, our comparative genomics collection has reached a total of 382 pairwise DNA alignments and 84 synteny maps. We have also added SNP variation datasets for sunflower, Golden apple, and durum wheat.

The Plant Reactome is the pathway knowledgebase of Gramene. We utilize the Reactome pathway data model to represent plant metabolic, transport and signaling pathways, developmental processes, organ differentiation, and transcriptional regulatory networks. Manual biocuration is conducted in the reference species rice (O. sativa) and pathways are then projected via gene orthology to other species including crops and model plants, lower plants and single-cell photoautotrophs. In this release, we have extended orthology-based pathway projections for 9 new species; added 13 newly curated pathways; and updated 8 pathways in the reference species Oryza sativa.  In total, Plant Reactome is currently hosting  320 rice curated pathways and their gene-orthology based projection for 106 species ranging from unicellular autotrophs to higher plants.  

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 Agricultural Research Service of the U.S. Department of Agriculture (USDA ARS 1907-21000-030-00D), and the National Science Foundation (NSF IOS-1127112).

GENOMES Release Notes 

• New genomes:

1. Arabis alpina (alpine rock-cress)
2. Camelina sativa (camelina, gold-of-pleasure or false flax)
3. Cannabis sativa (cannabis or marijuana)
4. Citrullus lanatus (watermelon)
5. Cucumis melo (cantaloupe or muskmelon, smooth-skinned)
6. Nymphaea colorata (a tropical water lily)
7. Prunus dulcis (almond)
8. Rosa chinensis (China or Chinese rose; Bengal rose, crimson or beauty)
9. Setaria viridis (wild or green foxtail millet, green bristlegrass )
10. Citrus clementina (clementine; citrus fruit hybrid between mandarin and sweet orange)
11. Ipomoea triloba (morning glory, a relative of sweet potato )
12. Malus domestica (Golden apple)
13. Olea europaea sylvestris (wild olive tree)
14. Pistacia vera (pistachio)
15. Prunus avium (sweet cherry)
16. Ananas comosus (pineapple)
17. Eragrostis curvula (weeping lovegrass)
18. Saccharum spontaneum (a sugar-poor relative of sugarcane)
19. Chara braunii (Braun's stonewort, an ecorticated streptophyte algae)
20. Hordeum vulgare subsp. GoldenPromise (barley var. GoldenPromise)
21. Theobroma cacao subsp. Matina 1-6 (Matina cocoa, cacao or chocolate tree)
22. Triticum aestivum subsp. Cadenza
23. Triticum aestivum subsp. Claire
24. Triticum aestivum subsp. Paragon
25. Triticum aestivum subsp. Robigus
26. Triticum aestivum subsp. Weebill

• Updated genomes:

1. Renamed almond gene names.

• New & updated data: 

1. Added new variation data for sunflower, apple and durum wheat.
2. New whole-genome alignments, see summary here.
3. New synteny maps, see summary here.
4. Updated split gene predictions from peptide comparative genomics.
5. A total of 122,947 GeneTree families were constructed comprising 2,875,432 individual genes from 93 plant genomes with 3,169,866 input proteins.

• Updated software: 

Updated genome browser, database schema, and API to Ensembl 101 software.

NOTE: We are aware about the filter to select chromosome for a given region in sorghum being missing in the current release 63. This will be fixed in the next release 64. Meantime, users are encouraged to use the "Multiple regions (Chr:Start:End:Strand) [Max 250 advised]" filter for one or many regions. Examples of formatted entries are:

4:10000:1000000:-1

7:150000:250000:1

Here is a complete list of Genomes with every data category available for it in Gramene's genome browser.

Compara

Gene Trees

The EnsemblCompara GeneTree database updated. A total of total of 122,947 GeneTree families were constructed comprising 2,875,432 individual genes from 93 plant genomes with 3,169,866 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

There are 382 pairwise genomic alignments.

Synteny data

There are 84 synteny maps.

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 20; Gramene r63) Summary:

Here, we provide a summary of Gramene Release 63 including website and coding updates, a list of new & updated pathways, information on new species, and projection statistics. Plant Reactome now hosts pathway projections for 105 plant species. 

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 13 newly curated pathways, 8 updated pathways, and 1 "container" pathways, resulting in a total of 320 reference rice pathways. In this release, we focused on updates to rice metabolic pathways and curation of cell-cycle events.

Pathway Projection Statistics

We have extended orthology-based pathway projections for 9 new species (in bold below). Plant Reactome now hosts pathway projections for 106 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

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. Tello-Ruiz MK, Naithani S, Gupta P, Olson A, Wei S, Preece S, Jiao Y, Wang B, Chougule K, Garg P, Elser J, Kumari S, Kumar V, Contreras-Moreira B, Naamati G, George N, Cook J, Bolser D, D’Eustachio P, Stein LD, Gupta A, Xu W, Regala J, Papatheodorou I, Kersey PJ, Flicek P, Taylor C, Jaiswal P, and Ware D. (2021). Gramene 2021: Harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Research 49(D1): D1452–D1463. 10.1093/nar/gkaa979
2. 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 (2020). Plant Reactome: A knowledgebase and resource for comparative pathway analysis. Nucleic Acids Res. 10.1093/nar/gkz996.
3. 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 (2020). Ensembl Genomes 2020—enabling non-vertebrate genomic research. Nucleic Acids Res., gkz890, 10.1093/nar/gkz890
4. 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. 10.1371/journal.pone.0224086
5. 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, 10.1093/database/bay146

Please let us know if you have questions or suggestions.

The Gramene Team
www.gramene.org.