Release Notes 64 (September 2021)

Table of Contents

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

The Gramene Knowledgebase Team is pleased to announce its Release #64 with the Genome section providing access to information on 114 reference genomes and 123,064 gene family trees. We are adding 21 new reference genomes, including Persian wheat, sesame and new varieties of potato and barley. For the complete list, see below. With these new genomes, our comparative genomics collection has reached a total of 340 pairwise DNA alignments and 80 synteny maps. Updates were applied to maize, banana, Arabidopsis, earthmoss, white Guinea yam, and Peruvian cotton.

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 106 species including crops and model plants, lower plants and single-cell photoautotrophs. This release is a maintenance release with one new addition. The gene homology-based projections were added for the version #5 of the reference maize genome (Zea mays version v5). Maize v4 pathway projections are also available for comparison and continued access. In total, Plant Reactome is currently hosting 320 rice curated pathways and their gene-orthology based projection for 106 species.  

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:
  • Asparagus officinalis (garden asparagus)
  • Chenopodium quinoa (quinoa)
  • Eucalyptus grandis (flooded gum)
  • Eutrema salsugineum (saltwater cress)
  • Hordeum vulgare var. Morex (barley MOREX cultivar, TRITEX assembly)
  • Juglans regia (persian walnut)
  • Kalanchoe fedtschenkoi (lavender scallops)
  • Papaver somniferum (opium poppy)
  • Quercus lobata (white oak)
  • Sesamum indicum (sesame)
  • Solanum tuberosum var. RH8903916 (diploid potato cultivar)
  • Triticum aestivum (bread wheat) cultivars:
    • T. aestivum var. Arinalrfor
    • T. aestivum var. Jagger
    • T. aestivum var. Julius
    • T. aestivum var. Lancer
    • T. aestivum var. Landmark
    • T. aestivum var. Mace
    • T. aestivum var. Mattis
    • T. aestivum var. Norin61
    • T. aestivum var. Stanley
  • Triticum spelta (spelt)
• Updated genomes:
  • Zea mays. The assembly and annotation of the B73 maize reference genome was updated to Zm-B73-REFERENCE-NAM-5.0 (RefGen_V5) (Hufford et al, 2021).
  • Musa acuminata. The assembly and annotation of the banana reference genome was updated to V2 from the Banana Genome Hub.
  • Dioscorea rotundata (white yam) assembly and annotation updated to V2.
  • Gossypium raimondii (Peruvian cotton) assembly and anotation updated to V6.
• New & Updated data:
  • New variation data for soybean (Glycine max) and black bean (Phaseolus vulgaris) from the European Variation Archive. This data is not yet available via Gramene Mart.
  • Maize variation data as well as V3, V4 and curated genes remapped to V5.
  • Earthmoss Physcomitrella patens renamed Physcomitrium patens.
  • Updated cross-references for Arabidopsis thaliana.
  • Updated split gene predictions from peptide comparative genomics.
  • Updated repeated element annotation for selected plants using a custom plant library (nrTEplants).
• Updated software:
  • Updated genome browser, database schema, and API to Ensembl 104 software.
• Summary of Compara analysis:
  • Protein gene tree analysis
  • Whole-genome alignments

  Note: A maximum of 100 genomes is included in the Compara Gene Family Trees analysis, which will change depending on data available for each release. You can find the list of included genomes in Ensembl Plant's github repository.

Compara

Gene Trees

The EnsemblCompara GeneTree database updated. A total of total of 123,064 GeneTree families were constructed comprising 2,956,404 individual genes from 90 plant genomes with 3,256,006 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 340 pairwise genomic alignments.

Synteny data

There are 80 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 21; Gramene r64) Summary:

Here, we provide a summary of Gramene Release 64.  This release is a maintenance release with one new addition. The gene homology-based projections were added for the version #5 of the reference maize genome (Zea mays version v5). We also provide the Maize v4 pathway projections for comparison and continued access. Plant Reactome now hosts 320 rice curated pathways and their gene-orthology based projection for 106 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 106 projected species hosted by Plant Reactome.

Pathway Projection Statistics

We have extended orthology-based pathway projections for version #5 of the reference maize genome (Zea mays version v5). In total, 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 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.

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. Hufford MB, Seetharam AS, Woodhouse MR, Chougule KM, Ou S, Liu J, Ricci WA, Guo T, Olson A, Qiu Y, Coletta RD, Tittes S, Hudson AI, Marand AP, Wei S, Lu Z, Wang B, Tello-Ruiz MK, Piri RD, Wang N, Kim DK, Zeng Y, O’Connor CH, Li X, Gilbert AM, Baggs E, Krasileva KV, II JLP, Cannon EKS, Andorf CM, Manchanda N, Snodgrass SJ, Hufnagel DE, Jiang Q, Pedersen S, Syring ML, Kudrna DA, Llaca V, Fengler K, Schmitz RJ, Ross-Ibarra J, Yu J, Gent JI, Hirsch CN, Ware D, Dawe RK. (2021) De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science. 373(6555):655-662. doi: 10.1126/science.abg5289.
2. Naithani S, D.A. Dikeman, P. Garg, N. Al-Bader, and P. Jaiswal (2021). Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily. PeerJ 9:e11052, doi:10.7717/peerj.11052
3. 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
4. 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.
5. 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
6. 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
7. 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.