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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 #402304
Research Project: Mapping Crop Genome Functions for Biology-Enabled Germplasm Improvement

Location: Plant, Soil and Nutrition Research

Title: Sorghumbase: an integrated pan-genome resource on sorghum genomics and genetics data set for the sorghum community

Author
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item KUMAR, VIVEK - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item OLSON, AUDRA - Cold Spring Harbor Laboratory
item TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory
item VAN BUREN, PETER - Cold Spring Harbor Laboratory
item WEI, SHARON - Cold Spring Harbor Laboratory
item Ware, Doreen
item ZHANG, LIFANG - Cold Spring Harbor Laboratory

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 11/6/2022
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: SorghumBase (https://www.sorghumbase.org) is a USDA-ARS funded pan-genome resource on the curated genomics, genetics and related data resources for the sorghum crop research community. SorghumBase is working closely with the community to support stewardship of sorghum genomics data, establishing best-practices on managing the data and coordination with the community. It contains the most recent genetic, physical and genomic sequence maps integrated with professionally curated gene expression atlas, pathway and QTL data. In addition, it provides the literature database and wealth of the information through news and events to sorghum researchers. The current pan-genome 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.