Improved Assembly of Potato Mitochondrial DNA, and Comparative Analysis of Cytoplasmic Types

Some of the important traits of cultivated potato exhibit cytoplasmic patterns of inheritance, suggesting that variation in extrachromosomal genetic material in this important crop is of interest for breeding. While the chloroplast genome of Solanum tuberosum has been sequenced and assembled completely, the mtDNA assembly remained incomplete, thus preventing detailed molecular characterisation of variation among cultivars. The difficulty with assembly is due to the size and complexity of potato mtDNA, which is typical of solanaceous species, with extensive history of exchange between chromosomes and mtDNA. We have previously deeply sequenced a large number of potato cultivars as part of MASPOTII project, and used a combination of approaches to improve the existing mtDNA collection of contigs, including the recently published in silico differential coverage binning of multiple metagenomes approach (Albertsen et al, 2013), and the genome finishing module of CLC bio’s Genomics Workbench. We will report preliminary analysis of variation among three cultivars, representing the main cytoplasmic types.