PhD Oral Defence: Genome assembly and discovery of structural variation in cultivated potato taxa
PhD Oral Defence of Maria Kyriakidou, Plant Science
The common potato (Solanum tuberosum L.) is an important staple crop, with a highly complex, heterozygous, tetraploid genome. It has its origins in South America, where potato has a large secondary gene pool consisting of wild relatives of diverse ploidy levels. Significant efforts have previously been made to sequence and construct a double monoploid (S. tuberosum Group Phureja – DM1-3) and two wild (S. commersonii and S. chacoense clone M6) reference genomes. However, it is uncertain how well the potato genome diversity is captured in these three genomes, as the genetic riches of the S. America taxa are not represented. This work focuses on the genomic analyses of 12 native S. American potato genomes (ten taxa) of various ploidy (2n – 5n). Their comparisons with two reference genomes (DM1-3, M6) unraveled a great number of copy number variation (CNV) impacted genes, including disease resistance genes. Additionally, these genomes have been assembled de novo. The diploid potato genomes along with the three reference genomes have been used for the construction of a diploid potato pan-genome. Within the pan-genome, there are self-incompatibility and other genes that are absent from the DM1-3 genome. This work reflects only a part of the tremendous variability of the S. American potato taxa.