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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #397007
Research Project: Mapping Crop Genome Functions for Biology-Enabled Germplasm Improvement

Location: Plant, Soil and Nutrition Research

Title: SorghumBase: supporting the sorghum community with pangenomes resources and community news

Author
item BRAYNEN, JANEED - Cold Spring Harbor Laboratory
item Ware, Doreen

Submitted to: American Society of Plant Biologists Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 6/2/2022
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: SorghumBase (https://www.sorghumbase.org) is a USDA-ARS funded resource for the curated genomic and genetic data sets as well as relevant news and events for the sorghum research community. The current pangenome browser includes 18 assembled and annotated sorghum genomes and 7 additional species, including Arabidopsis, rice, maize, and poplar to support cross-species comparisons. Protein-coding gene trees were built with more than 31K proteins. The resulting gene trees support information on orthology, paralogy, and candidate copy numbers variation (CNVs). The information on CNVs can be observed within the gene neighborhood views available from the search interface. The gene trees are also used to identify potential annotation artifacts, and can support future community curation efforts. SorghumBase hosts over 17 million genetic variants aligned to the Sorghum BTx623 accession, including natural variants, as well as novel EMS-induced point mutations. These can be visualized on gene-based views for their impact on a transcript, capturing functional effects in over 23.5K genes. The Sorghum BTx623 accession also provides access to baseline gene expression data from the EBI-Expression Atlas, orthology-based protein pathway projections from the Plant Reactome and trait data from the Sorghum Atlas QTLs. SorghumBase is working closely with the community to support stewardship of sorghum genomic data, establishing best-practices on managing the data and coordination with the community. In the last six months, 41 news items related to Sorghum have been released, including highlights on recent publications, conferences and community news. News items on publications are indexed and searchable, and include information on how to access data related to the articles from the site. An user guide is available from the site and feedback may be provided via a contact form. Individual training sessions may be scheduled at request. This work is supported by the USDA-ARS (8062-21000-041-00D).