Extensive duplication events account for multiple control regions and pseudo-genes in the mitochondrial genome of the velvet worm Metaperipatus inae (Onychophora, Peripatopsidae)

The phylogeny of Onychophora (velvet worms) is unresolved and even the monophyly of the two major onychophoran subgroups, Peripatidae and Peripatopsidae, is uncertain. Previous studies of complete mitochondrial genomes from two onychophoran species revealed two strikingly different gene arrangement patterns from highly conserved in a representative of Peripatopsidae to highly derived in a species of Peripatidae, suggesting that these data might be informative for clarifying the onychophoran phylogeny. In order to assess the diversity of mitochondrial genomes among onychophorans, we analyzed the complete mitochondrial genome of Metaperipatus inae, a second representative of Peripatopsidae from Chile. Compared to the proposed ancestral gene order in Onychophora, the mitochondrial genome of M. inae shows dramatic rearrangements, although all protein-coding and ribosomal RNA genes are encoded on the same strands as in the ancestral peripatopsid genome. The retained strand affiliation of all protein-coding and ribosomal RNA genes and the occurrence of three control regions and several pseudo-genes suggest that the derived mitochondrial gene arrangement pattern in M. inae evolved by partial genome duplications, followed by a subsequent loss of redundant genes. Our findings, thus, confirm the diversity of the mitochondrial gene arrangement patterns among onychophorans and support their utility for clarifying the phylogeography of Onychophora, in particular of the Peripatopsidae species from South Africa and Chile.