Mitochondrial genomes of the land hermit crab Coenobita clypeatus (Anomura: Paguroidea) and the mole crab Emerita talpoida (Anomura: Hippoidea) with insights into phylogenetic relationships in the Anomura (Crustacea: Decapoda)

The infraorder Anomura is a species-rich clade of decapod crustaceans recognized by its remarkable disparity in terms of morphology, anatomy, ecology, physiology, and behavior. This study assembled and characterized the complete mitochondrial genomes of two anomuran species, the hermit crab Coenobita clypeatus and the mole crab Emerita talpoida. The AT-rich mitochondrial genomes of C. clypeatus and E. talpoida are 16,469 bp and 15,810 bp long, respectively, and are composed of 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. A 1,390 bp and 553 bp long intergenic space is assumed to be the D-loop in C. clypeatus and E. talpoida, respectively. Mitochondrial synteny in C. clypeatus is identical to that reported in other congeneric hermit crabs while synteny in E. talpoida is identical to that described for the confamilial mole crab Stemonopa insignis. No major differences occur between the studied species and their respective congeneric / cofamilial species in terms of nucleotide composition and codon usage profiles of PCGs. Selective pressure analysis in PCGs, rarely conducted in anomuran crabs, indicate that all these mitochondrial PCGs experience purifying selection and that this purifying selection is stronger in some (i.e., cox family genes and cob) compared to other PCGs (e.g., atp8). Most of the tRNA genes exhibited a typical 'cloverleaf' secondary structure with few exceptions in the two studied species. In C. clypeatus, tRNA-Ser1 lacks the thymine pseudouracil cytosine (TY'C) loop while tRNA-Phe and tRNA-Tyr each exhibit a deletion of the dihydroxyuridine (DHU) loop but not the arm. In turn, in E. talpoida, tRNA-Phe and tRNA-Arg exhibit a deletion of the DHU loop but not the arm while tRNA-Ser1 lacks the TY'C arm. A phylogenomic analysis based on translated PCGs confirms the monophyly of the infraorder Anomura and re-trieves most/all relationships at the superfamily and family level previously reported for anomurans. The analysis supports the monophyletic status of the families Albuneidae, Lithodidae, Coenobitidae, and Porcella-nidae. In turn, the superfamily Paguroidea, and the families Paguridae and Diogenidae are polyphyletic.

Automated summary

This study characterized the complete mitochondrial genomes of two anomuran species and found that their genome structures and codon usage profiles are similar to other congeneric species. The selective pressure analysis on protein-coding genes revealed that these genes have undergone purifying selection. Furthermore, the phylogenomic analysis based on translated protein-coding genes confirmed the monophyly of the infraorder Anomura and provided more detailed relationships at the genus level.