Mitochondrial genome of the Chinese mitten crab Eriocheir japonica sinenesis (Brachyura: Thoracotremata: Grapsoidea) reveals a novel gene order and two target regions of gene rearrangements.

We determined the complete 16,354 bp mitochondrial DNA sequence of the Chinese mitten crab Eriocheir japonica sinesnesis. It consists of 13 protein coding genes (PCGs), 2 rRNAs, and 22 tRNAs, typical of metazoan mitochondrial genomes. With respect to the ancestral crustacean mt gene order, a PCG, the rRNAs, and 12 of the tRNAs appear to be rearranged. This rearrangement is novel in the arthropods and suggests an accelerated rate of mt genome rearrangement in this brachyuran lineage based on the relative rate of gene rearrangement. It is typical in arthropods that all of the rearranged genes or gene blocks take place at both nad3-nad5 and nad5-nad4 gene junctions. Such occurrence additionally revealed two target regions of frequent rearrangement in mitochondrial genomes of decapods, even in that of the non-hexapod arthropods according to our comparative studies among 32 taxa. Additionally, selective constraint on sharing the single introducing location is apparent for most of the rearrangements that occurred at the nad3-nad5 gene junction of these taxa. The gene arrangement features at both gene junctions allow the reconstruction of relationships among the advanced decapods. These features are therefore characteristic molecular markers in phylogenetic inference. The genomic organization differences at both gene junctions provide new evidence of extremely divergence between Heterotremata and Thoracotremata in brachyuran crabs. A duplication/loss (random and nonrandom)-recombination model was proposed to account for the generation of the gene order in E. japonica sinesnesis under the guide of intergenic spacers.