Molecular characterization and phylogenetic analysis of crabs (Crustacea: Decapoda: Brachyura) based on mitochondrial COI and 16S rRNA genes

This study aims to know the efficiency of the partial sequence of COI and 16S rRNA genes for the identification of crab species and to determine their phylogenetic relationships. A total of 36 sequences of 14 different species of crab were generated, belonging to 9 genera and 7 families. The average %GC content was higher in the sequences of the COI gene compared to the 16S rRNA. A large variation of the GC content was found at the 3rd codon position of the COI sequences. All the species were discriminated by COI and 16S rRNA when an intraspecific threshold of 2% K2P was used. The mean congeneric divergence was 72 and 94-fold higher than mean conspecific divergence for the COI and 16S rRNA markers, respectively. However, K2P% between closely related species was higher in COI compared to 16S rRNA. The Maximum Likelihood (ML) phylogenetic tree constructed based on COI and 16S rRNA gene sequences showed that the same species were clustered together under a single clade, supporting that both the markers were efficient in discriminating crab species. The ML tree of the COI sequences showed long-branch attraction and clustering of the species from different genus together. Such incongruence was not found in the tree topology of the 16S rRNA, providing phylogenetic relationships among species with a true divergence rate. The study revealed that the COI gene would be much efficient in discriminating closely related species, and 16S rRNA would be superior to COI in phylogenetic analysis.