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        <td align="left">Gene ID:</td>
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Text Content

 * Home
   * News
   
 * Genome Browsers
   * S. tuberosum group Phureja DM1-3 v6.1
   * S. tuberosum cv. Atlantic v3
   * S. tuberosum cv. Castle Russet v2
   * S. tuberosum group Tuberosum RH89-039-16 v3
   * Doubled Monoploid DM1S1
   * Diploid potato 'Jan' v1.1
   * S. tuberosum cv. Cooperation-88
   * S. tuberosum cv. Otava v1
   * Solanum candolleanum v1.0
   * Solanum chacoense M6 v5.0
   * Potato 2.0 Dihaploids
 * Search Tools
 * Analyses
   * Gene Expression
   * Gene Coexpression
   * Syntelogs
 * Download
 * Contact


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.


DM V6.1 QUICK SEARCH

Gene ID:     

Search terms:     



WHAT'S NEW

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.






This work is supported by grants from the National Science Foundation (IOS-
2140176), U.S. Department of Agriculture (2019-51181-30021), and funds from the
Georgia Research Alliance, Georgia Seed Development, and University of Georgia.