Identifying Mitochondrial Genomes in Draft Whole-Genome Shotgun Assemblies of Six Gymnosperm Species

Abstract: Sequencing efforts for gymnosperm genomes typically focus on nuclear and chloroplast DNA, with only three complete mitochondrial genomes published as of 2017. The availability of additional mitochondrial genomes would aid biological and evolutionary understanding of gymnosperms. Identifying mtDNA from existing whole genome sequencing (WGS) data (i.e. contigs) negates the need for additional experimental work but previous classification methods show limitations in sensitivity or accuracy, particularly in difficult cases. In this thesis I present a classification pipeline based on (1) kmer probability scoring and (2) SVM classification applied to the available contigs. Using this pipeline the mitochondrial genomes of six gymnosperm species were obtained: Abies sibirica, Gnetum gnemon, Juniperus communis, Picea abies, Pinus sylvestris and Taxus baccata. Cross-validation experiments showed a satisfying and forsome species excellent degree of accuracy.