First mitochondrial genome for the red crab (Charybdis feriata) with implication of phylogenomics and population genetics

Abstract

In this study, we first described the complete mitochondrial genome for the red crab (Charybdis feriata), elucidated its phylogenetic relationship among 20 species within Decapoda, and estimated the population genetic diversity. The mitochondrial genome was 15,660 bp in size and encoded 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and two ribosomal RNA genes. The gene arrangement of the mitochondrial genome was the same as that of its sister species, C. japonica. Phylogenomic analysis suggested that genus Charybdis should be classified into subfamily Portuninae but not into subfamily Thalamitinae. Moreover, a total of 33 haplotypes of complete cytochrome c oxidase subunit I gene were defined in 70 individuals of C. feriata derived from three localities. Haplotype diversity and nucleotide diversity values among three localities indicated a high level of genetic diversity in C. feriata. AMOVA analysis suggested a low level of genetic differentiation among the three localities (FST = 0.0023, P > 0.05). Neutrality tests and mismatch analysis revealed that C. feriata might have undergone a population expansion event that possibly occurred in the last 61,498 to 43,814 years. This study should be helpful to better understand the evolutionary status, and population genetic diversity of C. feriata and related species.

Characterization of the complete mitochondrial genome of Portunus pelagicus with implications for phylogenomics

“…The anticodon loop was 7 bp long in all of the tRNA genes, except for tRNA Ser(UCN) . Seventeen unmatched base pairs were detected in the 22 tRNA genes, which is more than that found in the tRNA genes of C. feriata (Ma et al, 2015). As in related species, both 16S rRNA and 12S rRNA were located on the light strand of the mitochondrial genome.…”

“…In the mitochondrial genome of Myrmeleon immanis, four types of start codons have been detected (Yan et al, 2014). Two incomplete stop codons have been found in the C. feriata mitochondrial genome (Ma et al, 2015), and one was detected in the S. paramamosain mitochondrial genome (Ma et al, 2013). Post-transcriptional polyadenylation may result in an incomplete stop codon (Ojala et al, 1981).…”

“…Nine protein-coding genes (ATP6, ATP8, ND1,ND2,ND3,ND4,ND4L,ND5,and ND6) ended with a typical stop codon (TAA or TAG), whereas an incomplete stop codon (T-) was detected in the remaining four genes (COI, COII, COIII, and Cytb). Variable start codons and incomplete stop codons exist in the mitochondrial genomes of many species (Ma et al, 2013(Ma et al, , 2015. In the mitochondrial genome of Myrmeleon immanis, four types of start codons have been detected (Yan et al, 2014).…”

The complete mitochondrial genome of the swimming crab Charybdis natator (Herbst) (Decapoda: Brachyura: Portunidae) and its phylogeny

“…The gene arrangement and genome structure were accordant to those of the published species of Portunids. The overall base composition of the mitogenome was 34.00% for A, 11.06% for G, 36.36% for T, and 18.58% for C, respectively, with a higher A þ T content (70.36%), just as in Charybdis feriata (Ma et al 2015) and C. japonica (Liu and Cui 2010). The 13 protein-coding genes had a varying length from 162 to 1728 bp and encoded 3714 amino acids in total.…”

Identification of the complete mitochondrial genome of Monomia gladiator (Decapoda: Brachyura: Portunidae) and its phylogenetic relationship

“…Of the 37 genes, 23 were encoded by the heavy strand, while 14 were encoded by the light strand. The arrangement and composition of the mitochondrial genome were similar to those of Charybdis feriata (Ma et al 2015) and Thalamita crenata (Tan et al 2016). The length of the 13 protein-coding genes ranged from 162 bp (ATP8) to 1728 bp (ND5).…”