SorghumBase release 4 is out with updated gene and transcript names and synonyms for BTx623

Submitted by marcela.karey on Mon, 07/18/2022 - 17:21

SorghumBase (https://www.sorghumbase.org/) has just announced its 4th release (see release notes #4). This release included the genome assembly and annotation of the poplar tree, Populus trichocarpa v4.1 from JGI Phytozome, a dicot model plant that like sorghum, is also studied for drought tolerance and bioenergy production. Poplar is the 8th outgroup species that together with the genomes of 18 sorghum varieties was used to generate 31,210 protein-coding gene family trees to support phylogenetic analyses and cross-species comparisons.

At the instance of the sorghum community, gene and transcript names of the sorghum BTx623 reference models were updated as follows:

* Gene names of the form Sobic.nnn (in use at the Phytozome database) were added as synonyms of their corresponding SORBI_3nnn counterparts, and are now given as the display name for gene models in the SorghumBase search interface and genome browser.

* Transcript names were modified to the conventional format of appending to Ensembl gene names of the form SORBI_3nnn, a dot followed by a digit suffix. For example, transcripts for the gene ‘SORBI_3004G141800’ are SORBI_3004G141800.1, SORBI_3004G141800.2, SORBI_3004G141800.3, and SORBI_3004G141800.4. This is in contrast to their corresponding (GenBank) names such as KXG30174, OQU84910, OQU84911, and OQU84912, currently in use by the Gramene and Plant Ensembl database, see SORBI_3004G141800 example.

See some examples of the corresponding Gene and Transcript pages for this gene in this release.

Also, a mapping file to convert sorghum gene identifiers of the forms Sobic.nnn, SORBI_3nnn, and SbNNN was made available in the SorghumBase’s FTP site.

The SorghumBase publications database grew to 420 papers, 16 of which have been highlighted in recent News posts, together with 71 relevant Events for the sorghum research community.

Core funding for the project is provided by the Agricultural Research Service of the U.S. Department of Agriculture (USDA ARS 8062-21000-041-00D).