The first mitochondrial genome of Melastoma dodecandrum resolved structure evolution in Melastomataceae and micro inversions from inner horizontal gene transfer

Melastoma dodecandrum is recognized as an ideal industrial subshrub in Melastoma with special characters, like medicinal component, edible fruits, bizarre heteromorphic stamen flowers. Because of strong tolerance to drought and poor land, now it is gradually domesticated into functional economic crops. These special development characters and reported abundant metabolites are suspected to have influence by the mitochondria. To get a better understand of this potential species, we first generated the circle mitochondrial genome with Pacbio-Illumina hybrid sequencing strategy. Finally, the 411,944 bp physical map of M. dodecandrum displayed a long intergenic region segmentation structure and from the comparison with other plant mitogenomes, we unveiled large-scale rearrangements of conserved genes caused by micro inversions. A new insight highlighted the lateral gene transfer from nuclear, chloroplast to mitochondrial genome, consistent fragments captured functional genes like Cytb6f. In the generalized analysis of energy and metabolism genes, we detected a loss of ccmFN and a repeat of cox1 in the whole mitogenome, making it contain relatively complete energy metabolic system. Abnormal selective pressure occurred among the genes in mitogenome and chloroplast, inferring different driving forces of selection existed in the transfer of organic and nuclear genetic materials from hybridization event. This manifested a phylogenetic conflict between the mitochondrial gene and chloroplast gene tree. Eventually, our newly assembled mitogenome will add the knowledge of general trends in mitogenome evolution within dicotyledons and lay solid foundation to the future industrial development.