Mitochondrial genome assembly in strawberry (Fragaria) leads to discovery of a genus-wide cytoplasmic male-sterility locus

Cytoplasmic male-sterility (CMS) genes are chimeras created by mitochondrial genomic rearrangement and produce novel peptides that interfere with pollen development. Sex determination in some gynodioecious species involves complex genetic interactions between CMS and nuclear-restorer genes that leave a unique signature of selection on CMS and other mitochondrial genes. We assembled the mitochondrial exome from whole-genome shotgun sequence for the gynodioecious diploid wild strawberry Fragaria vesca subsp. bracteata (Rosaceae), and discovered a chimeric ORF (atp8-orf225) with the genomic hallmarks of known CMS genes. Moreover, it is present in all other species in the genus. The chimeric ORF in F. vesca subsp. bracteata and other sexually dimorphic species within the Fragaria octoploid clade showed evidence of positive selection (dN/dS >1) compared to other mitochondrial housekeeping genes. The phylogenetic histories derived from mitochondrial and chloroplast genomes, in combination with chimeric ORF phylogeny, support Pacific Northwest F. vesca subsp. bracteata as the maternal donor of octoploid strawberries. However, incongruities between cytoplasmic genomes suggest paternal mitochondrial leakage during the evolution of the octoploids. These results provide insight into the origin of sex determination in octoploids as well as other sexually dimorphic species in Fragaria.