Potato Genome Sequence and Annotation Resource

To improve our understanding of potato, we are participating in the International Potato Genome Sequencing Consortium (PGSC). The PGSC has sequenced two potato species: the heterozygous diploid S. tuberosum Group Tuberosum cultivar, RH89-039-16 (RH), and the doubled monoploid S. tuberosum Group Phureja clone DM1-3 516R44 (DM). The DM genome has been assembled, annotated and released. You can access the genome through this site and/or through the Potato Genome Sequencing Consortium. The current potato genome assembly represents 726 Mb of which 86% is anchored to the genetic map. A total of 39,031 genes have been annotated in the DM genome. To aid in the annotation of the potato genome, we initiated a comprehensive whole transcriptome sequencing project for the DM clone in which 32 libraries were sequenced using RNA-seq. The RH genome has also been sequenced and next generation sequencing reads have been mapped to the DM genome assembly. Reads for the RH genome are available through EBI.

Personnel

Principal Investigator (PI):
C. Robin Buell, Michigan State University
Co-Principal Investigator (coPI):
Chris Town, J Craig Venter Institute
Collaborator:
Jiming Jiang, University of Wisconsin-Madison
Collaborator:
Christine Flanagan, U. S. Botanic Garden

Project Resources

You can access the PGSC data through potatogenome.net. The sequence can be downloaded from our web site, searched using our BLAST tool, and the annotation viewed through our genome browser.

The RH BACs sequenced in our NSF funded project can be viewed on our BAC summary page.

DM and RH BAC end sequences are available for download from our ftp site.

Annotation of the potato BAC sequences is accessible through our Solanaceae comparative genome database.

View a table of DM tissues sequenced in our transcriptome sequencing efforts.

This project was initiated at TIGR on October 1, 2006, and as of October 1, 2007 moved to Michigan State University.

This material is based upon work supported by the National Science Foundation under Grant No. DBI-0604907 and DBI-0834044. Any opinions, findings and conclusions or recomendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation (NSF).