Complete mitochondrial genome of Clistocoeloma sinensis (Brachyura: Grapsoidea): Gene rearrangements and higher-level phylogeny of the Brachyura

Abstract

Deciphering the animal mitochondrial genome (mitogenome) is very important to understand their molecular evolution and phylogenetic relationships. In this study, the complete mitogenome of Clistocoeloma sinensis was determined. The mitogenome of C. sinensis was 15,706 bp long, and its A+T content was 75.7%. The A+T skew of the mitogenome of C. sinensis was slightly negative (−0.020). All the transfer RNA genes had the typical cloverleaf structure, except for the trnS1 gene, which lacked a dihydroxyuridine arm. The two ribosomal RNA genes had 80.2% A+T content. The A+T-rich region spanned 684 bp. The gene order within the complete mitogenome of C. sinensis was identical to the pancrustacean ground pattern except for the translocation of trnH. Additionally, the gene order of trnItrnQ-trnM in the pancrustacean ground pattern becomes trnQ-trnI-trnM in C. sinensis. Our phylogenetic analysis showed that C. sinensis and Sesarmops sinensis cluster together with high nodal support values, indicating that C. sinensis and S. sinensis have a sister group relationship. The results support that C. sinensis belongs to Grapsoidea, Sesarmidae. Our findings also indicate that Varunidae and Sesarmidae species share close relationships. Thus, mitogenomes are likely to be valuable tools for systematics in other groups of Crustacea.Mitochondrial DNA (mtDNA) is a typically closed circular molecule approximately ranging in size from 14 to 18 kb. It contains 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and control region (CR) 1, 2 . mtDNA is characterized by maternal inheritance, simple structure, a small genome size, conserved gene content and organization, high mutation rate, and accelerated rate of nucleotide substitution [3][4][5][6][7] . The mitogenomes of animal mtDNA can provide important information on rearrangement laws and phylogenetic analysis because of their rapid evolutionary rate and lack of genetic recombination 1 . It is becoming increasingly common to use complete animal mitogenomes for phylogenetic reconstruction [8][9][10]

A comprehensive phylogenetic analysis of Grapsoidea crabs (Decapoda: Brachyura) based on mitochondrial cytochrome oxidase subunit 1 (CO1) genes

“…Sesarma and Clistocoeloma are part of Sesarmidae, Grapsoidea. These findings are in keeping with previous reports (Von Hagen, 1978;Tang et al, 2017;Xin et al, 2017a) We present evidence that both Helice species are significantly closer to most Varunidae genera than to the Sesarmidae based on the CO1 genes sequences, which is in accordance with the findings reported by Guinot (1978) and Schubart et al ( , 2000. Preliminary results show that the genus Varuna clusters with the other Varunidae species based on its 16S rRNA sequence (Schubart et al, , 2000.…”

The complete mitochondrial genomes of two vent squat lobsters, Munidopsis lauensis and M. verrilli: Novel gene arrangements and phylogenetic implications

“…Comparative analysis of mitochondrial gene order has been proved to be a valuable phylogenetic tool in crustaceans (Shen, Tsang, Chu, Achituv, & Chan, ; Xin et al, ). Based on the comparative analysis of mitochondrial gene arrangement within Sessilia, Shen et al () found that Amphibalanus amphitrite (Balanidae) should cluster with Striatobalanus amaryllis (Archaeobalanidae) and Nobia grandis (Pyrgomatidae) instead of Megabalanus (Balanidae), resulting in nonmonophyly of the family Balanidae.…”

“…Based on the comparative analysis of mitochondrial gene arrangement within Sessilia, Shen et al () found that Amphibalanus amphitrite (Balanidae) should cluster with Striatobalanus amaryllis (Archaeobalanidae) and Nobia grandis (Pyrgomatidae) instead of Megabalanus (Balanidae), resulting in nonmonophyly of the family Balanidae. Xin et al () examined the mitochondrial gene arrangements of infraorder Brachyura and suggested that Clistocoeloma sinensis may belong to the group Sesarmidae of the superfamily Grapsoidea and that C. sinensis and Sesarmops sinensis probably belong to sister groups.…”

“…These results are consistent with the conclusion from the gene order-based phylogenetic tree ( Figure 5). M. lauensis and M. verrilli showed a closest Comparative analysis of mitochondrial gene order has been proved to be a valuable phylogenetic tool in crustaceans (Shen, Tsang, Chu, Achituv, & Chan, 2015;Xin et al, 2017). Based on the compara-…”

A review of the brachyuran deep-sea vent community of the western Pacific, with two new species of Austinograea Hessler & Martin, 1989 (Crustacea, Decapoda, Brachyura, Bythograeidae) from the Lau and North Fiji Back-Arc Basins

“…In a series of papers on the complete mitogenome of brachyuran species, the genomes of A. alayseae, A. rodriguezensis, Gandalfus yunohana and G. puia were downloaded from GenBank and included in reconstructed phylogenetic trees, all showing occurrence of T and A nucleotides that differed from that all of other studied Brachyura (Xin et al 2017a: 309;2017b;Tang et al 2017).…”