The complete mitochondrial genome of the Atlantic ghost crab Ocypode quadrata (Fabricius, 1787) (Brachyura: Ocypodidae: Ocypodinae)

Abstract

Abstract The semi-terrestrial Atlantic ghost crab Ocypode quadrata (Fabricius, 1787) is a medium-sized species that inhabits the supralittoral zone in sandy temperate and tropical beaches of the western Atlantic Ocean. Despite the relevant ecological role of O. quadrata and its use as a bio-indicator, there are currently few genetic and genomic resources for this species. This study assembled and characterized in detail the complete mitochondrial genome of O. quadrata from Illumina short paired-end reads. The software NOVOplasty assembled and circularized the complete mitochondrial genome of the Atlantic ghost crab with an average coverage of 162×, per nucleotide. The AT-rich mitochondrial genome of O. quadrata is 15,547 bp in length, consisting of 13 protein coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA genes (rrnL and rrnS). A single 685 bp long non-coding nucleotide region is assumed to be the D-loop/control region. The observed gene order in O. quadrata is identical to that reported for all congeneric species with known mitochondrial genomes. A selective pressure analysis indicates that all the PCGs are under purifying selection. Differences in KA/KS ratios among genes indicate strong purifying selection in the cox1, cox2, cox3, and atp6 genes, and weaker purifying selection in the atp8 gene. The 22 tRNA genes range from 64 to 70 bp in length, and all the tRNAs show a conventional “cloverleaf” secondary structure except for trnS1 that is missing the D-arm, in agreement to that reported for other brachyuran crabs with tRNA secondary depictions published. A maximum likelihood phylogenetic analysis based on all PCGs that included a total of 18 species of crabs fully supported the monophyly of the family Ocypodidae. The monophyly of the subfamilies Ocypodinae and Ucinidae was also highly supported by the analysis. These results suggest that mitochondrial PCGs have “phylogenetic signal” to reveal natural relationships at high taxonomic levels in crabs belonging to the family Ocypodidae. This study represents a new genomic resource for this ecologically relevant bioindicator ghost crab.