title: Comparative mitogenomic analysis reveals cryptic species: A case study in Mactridae (Mollusca: Bivalvia).
abstract: The Chinese surf clam Mactra chinensis Philippi, 1846 is a commercially important marine bivalve belonging to the family Mactridae (Mollusca: Bivalvia). In this study, the M. chinensis mitochondrial genomic features are analyzed. The genome has 34 genes on the same strand, lacking atp8 and both trnS (trnS1 and trnS2) as compared with the typical gene content of metazoan mitochondrial genomes. The A+T content of M. chinensis mitochondrial genome is 63.72%, which is slightly lower than that of M. veneriformis (67.59%) and Coelomactra antiquata (64.33% and 64.14% for the samples from Ri Zhao, Shandong Province, and Zhang Zhou, Fujian Province, China, respectively) in the same family. There are 22 NCRs in the M. chinensis mitochondrial genome, accounting for 12.91% of the genome length. The longest NCR (1,075bp in length) is located between trnT and trnQ. A TRS (127bp×8.15) accounts for 96.3% (1,035/1,075) of this NCR. The occurrence of TRS in NCR is shared by the two Mactra mitochondrial genomes, but is not found in the two Coelomactra mitochondrial genomes. A phylogenetic tree constructed based on 12 PCGs of 25 bivalve mitochondrial genomes shows that all seven genera (Mactra, Coelomactra, Paphia, Meretrix, Solen, Mytilus, and Crassostrea) constitute monophyletic groups with very high support values. Pairwise genetic distance analyses indicate that the genetic distance of C. antiquata from the two localities is 0.084, which is greater than values between congeneric species, such as those in Mactra, Mytilus, Meretrix, and Crassostrea. The results show that the C. antiquata from the two localities represent cryptic species.
authors.affiliation: Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China; Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Shen
authors.affiliation: Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China. Electronic address: mxp2002@hotmail.com.
authors.forename: Xue Ping
authors.initials: XP
authors.lastname: Meng
authors.affiliation: Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.
authors.forename: Ka Hou
authors.initials: KH
authors.lastname: Chu
authors.affiliation: Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China; Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Na Na
authors.initials: NN
authors.lastname: Zhao
authors.affiliation: Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China.
authors.forename: Mei
authors.initials: M
authors.lastname: Tian
authors.affiliation: Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China.
authors.forename: Meng
authors.initials: M
authors.lastname: Liang
authors.affiliation: Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China.
authors.forename: Jue
authors.initials: J
authors.lastname: Hao
mesh_terms: D000818:Animals; D049872:Bivalvia / Q000166:cytology / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000235:genetics; D023061:Gene Order; D054629:Genome, Mitochondrial; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000235:genetics
chemical_list: D004272:DNA, Mitochondrial; D012335:RNA, Ribosomal
keywords: Cryptic species; Mactra chinensis; Mactridae; Mitochondrial genome; Phylogeny