The complete mitochondrial genome of Sesarmops sinensis reveals gene rearrangements and phylogenetic relationships in Brachyura

• Published in: PloS one 2017-06, Vol.12 (6), p.e0179800-e0179800
• Main Authors: Tang, Bo-Ping, Xin, Zhao-Zhe, Liu, Yu, Zhang, Dai-Zhen, Wang, Zheng-Fei, Zhang, Hua-Bin, Chai, Xin-Yue, Zhou, Chun-Lin, Liu, Qiu-Ning
• Format: Article
• Language: English
• Subjects: Amino acids; Analysis; Animals; Arthropod Proteins - genetics; Biology and life sciences; Bismuth; Brachyura; Brachyura - genetics; Coding; Computer and Information Sciences; Crustaceans; Gene rearrangement; Gene Rearrangement - physiology; Genes; Genes, Mitochondrial - physiology; Genetic aspects; Genome, Mitochondrial - physiology; Genomes; Genomics; Mitochondria; Mitochondrial DNA; Mitochondrial Proteins - genetics; Molecular evolution; Molecular structure; Nucleotides; Phylogeny; Physiological aspects; Research and Analysis Methods; Ribonucleic acid; RNA; RNA - genetics; RNA, Mitochondrial; RNA, Ribosomal - genetics; RNA, Transfer - genetics; rRNA; Transcription; Trees; tRNA
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0179800

Mitochondrial genome (mitogenome) is very important to understand molecular evolution and phylogenetics. Herein, in this study, the complete mitogenome of Sesarmops sinensis was reported. The mitogenome was 15,905 bp in size, and contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR). The AT skew and the GC skew are both negative in the mitogenomes of S. sinensis. The nucleotide composition of the S. sinensis mitogenome was also biased toward A + T nucleotides (75.7%). All tRNA genes displayed a typical mitochondrial tRNA cloverleaf structure, except for the trnS1 gene, which lacked a dihydroxyuridine arm. S. sinensis exhibits a novel rearrangement compared with the Pancrustacean ground pattern and other Brachyura species. Based on the 13 PCGs, the phylogenetic analysis showed that S. sinensis and Sesarma neglectum were clustered on one branch with high nodal support values, indicating that S. sinensis and S. neglectum have a sister group relationship. The group (S. sinensis + S. neglectum) was sister to (Parasesarmops tripectinis + Metopaulias depressus), suggesting that S. sinensis belongs to Grapsoidea, Sesarmidae. Phylogenetic trees based on amino acid sequences and nucleotide sequences of mitochondrial 13 PCGs using BI and ML respectively indicate that section Eubrachyura consists of four groups clearly. The resulting phylogeny supports the establishment of a separate subsection Potamoida. These four groups correspond to four subsections of Raninoida, Heterotremata, Potamoida, and Thoracotremata.