A novel gene rearrangement in the mitochondrial genome of Coenobita brevimanus (Anomura: Coenobitidae) and phylogenetic implications for Anomura

Background: Gene arrangement in vertebrate mitochondrial genomes (mitogenomes) is relatively conserved and fewer gene arrangement is discovered. In contrast, that in invertebrate mitogenomes is relatively common. Although a gradually growing number of gene rearrangement in hermit crabs (Paguridae) has been discovered, it is surprising that gene rearrangement in its close relatives, the terrestrial hermit crab (Coenobitidae), was overlooked until 2018. So far, only few studies focused on the phylogenetic studies of Anomura based on molecular evidences. Results: In the present study, the complete mitogenome of a terrestrial hermit crab, Coenobita brevimanus, was sequenced, and large-scale gene rearrangements were observed. The genomic features of this terrestrial hermit crab were different from those of any other studied crabs. Five gene clusters (or genes) including eleven tRNAs and two PCGs were found to be rearranged with respect to the pancrustacean ground pattern gene order, which was characterized by multiple translocations and inversions. Two phylogenetic trees (ML and BI tree) arrived at a similar topology based on the nucleotide sequences of the 13 concatenated PCGs. Conclusions: We propose tandem duplication-random loss and recombination model to explain the large-scale gene rearrangements in C. brevimanus mitogenome. The phylogenetic trees showed that all Coenobitidae species clustered into one clade. The polyphyly of Paguroidea was well supported, whereas the non-monophyly of Galatheoidea was not in consistence with previous findings. The phylogenetic relationships of Pylochelidae, Lomidae, and Albuneidae were controversial.