Solanum tuberosum Assembly and Gene Annotation

About Solanum tuberosum

Solanum tuberosum (potato) is the worlds fourth most important food crop after rice, wheat and maize. Potatoes were first introduced outside the Andes four centuries ago, and it is estimated that by the year 2020 over two billion people will depend on it for food, feed, or income. It belongs to the Solanaceae, a diverse family of agriculturally important species, including tomato, eggplant, pepper, tobacco, and petunia. The potato genome consists of 12 chromosomes and has a (haploid) length of approximately 840 Mb, making it a medium-sized plant genome. While many potato lines are tetraploid, this sequenced accession corresponds to homozygous diploid line (double haploid) S. tuberosum phureja DM1-3 516 R44.

Assembly

Genome sequencing was performed by the Potato Genome Sequencing Consortium using a BAC libary, fingerprinted and aligned into physical map contigs. This was complemented by whole genome shotgun approaches with 454 and Illumina sequencing.

Annotation

Annotation was carried out by the Potato Genome Sequencing Consortium using Cyrille2.

Additional analysis was carried out in house: non coding RNA genes have been annotated using tRNAScan-SE, Rfam, and RNAmmer.

Regulation

• Mapping using GSNAP of transcriptomics sequences from 16 samples from different tissues submitted to the ENA SRA as part of study ERP000527.
• ~194,000 EST sequences have been aligned to the genome with Exonerate.

References

1. Genome sequence and analysis of the tuber crop potato.
   The Potato Genome Sequencing Consortium. 2011. Nature. 475:189-195.
2. Sequencing the Potato Genome: Outline and First Results to Come from the Elucidation of the Sequence of the Worlds Third Most Important Food Crop.
   Visser RichardGF, Bachem ChristianWB, Boer JanMde, Bryan GlennJ, Chakrabati SwarupK, Feingold Sergio, Gromadka Robert, Ham RoelandCHJvan, Huang Sanwen, Jacobs JeanneME et al. 2009. Am. J. Potato Res. 86:417-429.
3. Analyzing the potato abiotic stress transcriptome using expressed sequence tags.
   Rensink W, Hart A, Liu J, Ouyang S, Zismann V, Buell CR. 2005. Genome. 48:598-605.
4. Gene expression profiling of potato responses to cold, heat, and salt stress.
   Rensink WA, Iobst S, Hart A, Stegalkina S, Liu J, Buell CR. 2005. Funct. Integr. Genomics. 5:201-207.
5. Image credit: Scott Bauer, USDA ARS [Public domain], via Wikimedia Commons.
   

More information

General information about this species can be found in Wikipedia.