The SorghumBase Team looks forward to meeting with plant researchers at the 2022 ASA, CSSA & SSSA International Annual Meeting from November 6th to the 9th. You will be able to meet Dr. Sunita Kumari at the Plant Genetic Resources posters session II on Wednesday, November 9th, from 2:30 PM – 4:30 PM in the Baltimore Convention Center, Exhibit Hall A-D, to learn everything you always wanted to know about SorghumBase and didn’t get to ask. Dr. Kumari’s poster #1277 is titled: “Sorghumbase: An Integrated Pan-Genome Resource on Sorghum Genomics and Genetics Data Set for the Sorghum Community”. The abstract for this USDA-funded poster (USDA-ARS 8062-21000-041-00D) follows:
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.
To get more details and hands-on training experience, a user-guide is available on the SorghumBase site (https://www.sorghumbase.org/guides) and feedback (https://www.sorghumbase.org/contact) may be provided via a contact form. Individual training sessions may be scheduled at request.
Have a safe trip and see you soon in Baltimore!
On behalf of the SorghumBase Team