Solanaceae Genomics Resource

September 16, 2024 - The SpudDB website has been updated. The genome browsers for all the genome assemblies have been updated to Jbrowse2. The DM v6.1 gene expression and coexpression data and webpages have also been updated. There is also a new DM v6.1 syntelogs page for an updated potato syntelog data set. The website has also been upgraded to use HTTPS for security and better compatibility with modern web browsers.

Potato Genomic Tools

Potato (Solanum tuberosum L.) is the fourth most important crop in the world, behind wheat, rice, and maize. In 2022, worldwide potato production exceeded 374 million metric tons. Potato also produces more food energy and value per unit of land area than any other crop. Compared to grain crops, potato is a superior source of nutrition; however, among major crop plants, potato is arguably the most intensively managed. In addition, tuber quality requirements are complex and must be maintained during harvest and storage. The genome sequence of potato was released and published in 2011 by the International Potato Genome Sequencing Consortium (PGSC) of the doubled monoploid S. tuberosum Group Phureja DM1-3 516 R44 (hereafter DM).

In 2020, an improved genome assembly of DM (v6.1) (based on Oxford Nanopore long-read sequencing) and improved genome annotation was released and published. The new assembly represents 741.6 Mb of sequence (87.8%) of the estimated 844 Mb genome, of which 741.5 Mb is non-gapped with 731.2 Mb anchored to the 12 chromosomes. The new assembly has improved contiguity with a 595-fold increase in N50 contig size, 99% reduction in the number of contigs, a 44-fold increase in N50 scaffold size, and an LTR Assembly Index score of 13.56.

Spud DB houses potato genome browsers for the updated DM v6.1 pseudomolecules and a suite of other completed potato genomes. The potato genome browsers also contain data from potato RNA-Seq libraries from the SRA, and SolCAP SNP information , and SolCAP SNP information (Hamilton et al. 2011) (Felcher et al. 2012).

The updated SpudDB Search Tools provide a BLAST server to search the assembly, annotation, and legacy data sets. Annotation searches by assigned functional annotation, InterPro, GO and PFAM are also available.

Spud DB is maintained and hosted by the Buell Lab in the Department of Crop and Soil Sciences at University of Georgia.