Comparative mitochondrial genomics within sea cucumber (Apostichopus japonicus): Provide new insights into relationships among color variants

To investigate genetic relationships among three color variants (Red, Green and Black) of sea cucumber Apostichopus japonicus, complete mitochondrial (mt) genomes of two Red and one Green individuals of A. japonicus were sequenced and compared with those of other eight individuals (two Red, two Black and four Green) from GenBank. All the eleven A. japonicus mitogenomes share an identical gene complement, consisting of 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes, arranged in the same order. Comparative genomic analyses reveal that non-coding intergenic regions have the highest mutation rate (7.36% of sites were variable), while tRNA genes have the lowest mutation rates (0.99%). Three hundred and eighty-six single-nucleotide polymorphism sites are observed in protein-coding genes across the eleven mt sequences. The overall mean genetic distance for the complete mtDNA of the eleven individuals is 0.76% (p-distance). For all protein-coding genes, the pairwise p-distances among the eleven A. japonicus range from 0.04% to 1.55%. As the consequences of extremely low levels of divergence, they strongly support that the assertion that the three color variants of sea cucumber belong to a single species A. japonicus.