The potato genome sequencing project 2 years on: Comparison of strategies with related projects and perspectives for the future of the world's 3rd food crop"

The PGSC started in 2006 with the aim of completing the potato genome sequence by 2010 using a BAC-by-BAC, chromosome-by-chromosome approach. The basis for this project was a BAC library and physical map from the diploid potato genotype RH89-039-16 (RH). With the rapid advancement of genome sequencing technologies, in 2008, the consortium decided to adopt whole genome shotgun (WGS) sequencing as a faster way to achieve the compete genome. Of the developing methods available the Illumina system was chosen in combination with the Roche 454 technologies to produce long-range scaffolding data. To achieve a rapid high quality assembly an additional homozygous potato genotype (DM1-3 516R44) was used for sequencing using next generation sequencing technology only. The sequence and analysis of the potato genome was published in mid 2011 (PGSC, 2011). The DM1-3 516R44 and RH89-039-16 genomes represent three alleles of potato, with DM1-3 516R44 being a S. phureja and RH89-039-16 being a S. tuberosum. This allows a three-genome comparison and the differences and similarities of the alleles being highlighted. In addition to the genome sequences (nuclear and organelles) a large volume of mRNA sequencing was also carried out on DM1-3 516R44 and RH89-039-16. The cDNA libraries were isolated from the main plant tissues such as root, stem, tuber, leaf and various generative tissues and additionally from various biotic and abiotic stress treatments. The analysis of this RNA-seq data will be presented. The strategies of sequencing and analysis of the genomes of potato and tomato will be discussed.