Comparative genomics reveal species-specific variation in the mitochondrial genomes of Dothistroma septosporum and Dothistroma pini.

Nante, R.*¹, Postma, A.¹, Heinzelmann, R.^2,3, Hamelin, R. C.^3,4, Coetzee, M. P. A.¹, Barnes, I.¹

¹ Department of Biochemistry Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, South Africa.
² Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Switzerland.
³ Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Canada.
⁴ Institute of Integrative and Systems Biology (IBIS), Université Laval, Canada. 2Research & Development division, Naktuinbouw, Roelofarendsveen, The Netherlands

Mitochondrial genomes have been used in phylogenetic studies, population genetics, and tracing the relatedness of populations. Dothistroma pini and D. septosporum are two pathogens that cause Dothistroma needle blight (DNB); a disease that affects pine species. The pathogens cause the same symptoms yet differ in geographical distribution and number of infected hosts such that they can be distinguished based on several nuclear gene regions. This study aimed to determine if there were any species-specific variations in the mitochondrial genomes of the DNB pathogens that could, in future, be used for population and evolution-based studies. The two isolates from each species included in the study were selected based on differences in mating types and geographic origin. Illumina sequencing was used to obtain short-read genome sequences for isolates of D. septosporum from Canada and South Africa and for D. pini isolates from North Dakota and Hungary. PacBio sequencing of the D. pini Hungary isolate and D. septosporum South African isolate was used to obtain long-read sequences. The assembled D. pini mitochondrial genomes were 34.7 Kb and those of D. septosporum 33.4 Kb. The increased genome size of D. pini was due to large intergenic regions and homing endonuclease genes of type GIY. All the genomes had the 14 protein-coding genes that are typically harboured on fungal mitochondrial genomes. Mitochondrial gene duplication and pseudogenization was observed in D. septosporum while gene rearrangement was observed across the species. The large amount of species-specific variation observed in the mitochondrial genomes would need to be validated in populations, but could be useful in future population studies to determine the evolutionary history of these, and other closely related species.