title: 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.
authors.affiliation: 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China.
authors.forename: Hongyu
authors.initials: H
authors.lastname: Ma
authors.affiliation: 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China.
authors.forename: Chunyan
authors.initials: C
authors.lastname: Ma
authors.affiliation: College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China.
authors.forename: Chenhong
authors.initials: C
authors.lastname: Li
authors.affiliation: 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China.
authors.forename: Jianxue
authors.initials: J
authors.lastname: Lu
authors.affiliation: 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China.
authors.forename: Xiong
authors.initials: X
authors.lastname: Zou
authors.affiliation: 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China.
authors.forename: Yangyang
authors.initials: Y
authors.lastname: Gong
authors.affiliation: 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
authors.affiliation: 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.affiliation: 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China.
authors.forename: Lingbo
authors.initials: L
authors.lastname: Ma
authors.affiliation: 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China [2] Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, Shanghai 200090, China.
authors.forename: Lianjun
authors.initials: L
authors.lastname: Xia
mesh_terms: D000818:Animals; D001483:Base Sequence; D030541:Databases, Genetic; D033364:Decapoda / Q000145:classification / Q000235:genetics*; D003576:Electron Transport Complex IV / Q000737:chemistry / Q000235:genetics; D014644:Genetic Variation; D005828:Genetics, Population; D054629:Genome, Mitochondrial; D006239:Haplotypes; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000737:chemistry / Q000302:isolation & purification; D012343:RNA, Transfer / Q000737:chemistry / Q000302:isolation & purification; D017422:Sequence Analysis, DNA
chemical_list: D012335:RNA, Ribosomal; D012343:RNA, Transfer; D003576:Electron Transport Complex IV