Solanaceae Genomics Resource

  • September 14, 2021 - The chromosome-scale and haplotype-resolved genome assembly and annotation of a heterozygous tetraploid potato Otava is now available on SpudDB. More information about the assembly, download links, and a Jbrowse instance are available on the data access page.
  • December 1, 2020 - The SpudDB search tools have been updated with the DM v6.1 annotation.
  • September 23, 2020 - The paper "Construction of a chromosome-scale long-read reference genome assembly for potato" describing the DM v6.1 assembly and annotation has now been published in Gigascience. The DM 6.1 genome assembly, annotation, and Jbrowse are available on the data access page
  • June 4, 2020 - The genome annotation for the updated long-read chromosome-scale genome assembly (v6.1) for the doubled monoploid potato S. tuberosum Group Phureja DM 1-3 516 R44 is now available. The DM v6.1 genome assembly, annotation, and Jbrowse are available on the data access page.
  • May 22, 2020 - The Buell Lab at Michigan State University is pleased to make available an updated long-read chromosome-scale genome assembly (v6.1) for the doubled monoploid potato S. tuberosum Group Phureja DM 1-3 516 R44. The genome assembly is available on the DM v6.1 data access page.
  • March 14, 2020 - The haplotype resolved genome assembly and annotation of the heterozygous diploid potato RH89-039-16 is now available on SpudDB. More information about the assembly, download links, and a Jbrowse instance are available on the data access page.
  • February 5, 2018 - The paper Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity been published in The Plant Journal. The genome assembly and annotation are available from the Data Dryad data repository.
  • March 28, 2014 - A paper describing the resources, tools and data available in Spud DB has been published in the journal The Plant Genome.

Potato Genomic Tools

Potato (Solanum tuberosum L.) is the fourth most important crop in the world, behind wheat, rice, and maize. In 2004, worldwide potato production exceeded 327 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). The assembled potato genome is that of the doubled monoploid S. tuberosum Group Phureja DM1-3 (DM; AEWC00000000); the genome assembly represents 726 MB, of which 86%, is anchored to the genetic map and contains 39,031 annotated genes. In addition, BAC and whole genome shotgun sequences were released from a second clone, S. tuberosum Group Tuberosum RH89-039-16 (RH; ERP000627).

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 the legacy PGSC v4.03 pseudomolecules. 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.



We welcome input from outside researchers. If there is some way in which we can improve this resource, we would like to hear from you. Please use the comment form on our contact page to send us your suggestions.

Funding has been provided by awards from the U.S. Department of Agriculture (2008-35300-18671) and the U.S. National Science Foundation (DBI-0604907, DBI-0834044, and 1202724). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Spud DB is maintained and hosted by the Buell Lab in the Plant Biology Department at Michigan State University.

DM v6.1 Quick Search

Gene ID:
    
Search terms:
    

What's New

September 14, 2021

The chromosome-scale and haplotype-resolved genome assembly and annotation of a heterozygous tetraploid potato Otava is now available on SpudDB. More information about the assembly, download links, and a Jbrowse instance are available on the data access page.

December 1, 2020

The SpudDB search tools have been updated with the DM v6.1 annotation.

September 23, 2020

The paper "Construction of a chromosome-scale long-read reference genome assembly for potato" describing the DM v6.1 assembly and annotation has now been published in Gigascience. The DM 6.1 genome assembly, annotation, and Jbrowse are available on the data access page.

June 4, 2020

The genome annotation for the updated long-read chromosome-scale genome assembly (v6.1) for the doubled monoploid potato S. tuberosum Group Phureja DM 1-3 516 R44 is now available. The v6.1 genome assembly, annotation, and Jbrowse are available on the data access page.

May 22, 2020

An updated and improved long-read chromosome-scale genome assembly (v6.1) for the doubled monoploid potato S. tuberosum Group Phureja DM 1-3 516 R44 is now available. See the data access page for more information.

March 14, 2020

The haplotype resolved genome assembly and annotation of the heterozygous diploid potato RH89-039-16 is now available on SpudDB. More information about the assembly, download links, and a Jbrowse instance are available on the data access page..

February 5, 2018

The paper Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity been published in The Plant Journal. The genome assembly and annotation are available from the Data Dryad data repository.

February 1, 2016

The Buell Lab has released v4.04 of the DM pseudomolecules. More information can be found on the Download page


Maintenance Notice

We have planned server maintenance on the first Wednesday of every month and therefore, Spud DB web pages may be unavailable or only partially functional during server maintenance.