Complete mitochondrial genome of Coelomactra antiquata (Mollusca: Bivalvia): The first representative from the family Mactridae with novel gene order and unusual tandem repeats

Xueping Meng1, Nana Zhao1,2, Xin Shen1, Jue Hao1, Meng Liang1, Xiaolin Zhu1, Hanliang Cheng1, Binlun Yan1, Zhaopu Liu2
1Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China
2Key Laboratory of Marine Biology of Jiangsu Province, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China

Tài liệu tham khảo

Abascal, 2005, ProtTest: selection of best-fit models of protein evolution, Bioinformatics, 21, 2104, 10.1093/bioinformatics/bti263 Abascal, 2007, MtArt: a new model of amino acid replacement for Arthropoda, Mol. Biol. Evol., 24, 1, 10.1093/molbev/msl136 Benson, 1999, Tandem repeats finder: a program to analyze DNA sequences, Nucleic Acids Res., 27, 573, 10.1093/nar/27.2.573 Burger, 2007, Sequencing complete mitochondrial and plastid genomes, Nat. Protocols, 2, 603, 10.1038/nprot.2007.59 Dreyer, 2006, The complete sequences and gene organisation of the mitochondrial genomes of the heterodont bivalves Acanthocardia tuberculata and Hiatella arctica—and the first record for a putative Atpase subunit 8 gene in marine bivalves, Front. Zool., 3, 13, 10.1186/1742-9994-3-13 Guindon, 2003, A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood, Syst. Biol., 52, 696, 10.1080/10635150390235520 He, 2011, The complete mitochondrial genome of the hard clam Meretrix meretrix, Mol. Biol. Rep., 38, 3401, 10.1007/s11033-010-0449-8 Kong, 2009, Genetic evidence for the existence of cryptic species in an endangered clam Coelomactra antiquata, Mar. Biol., 156, 1507, 10.1007/s00227-009-1190-5 La Roche, 1990, Molecular characterization of a repeat element causing large-scale size variation in the mitochondrial DNA of the sea scallop Placopecten magellanicus, Mol. Biol. Evol., 7, 45 Liu, 2006, The clam, Xishi tongue Coelomactra antiquata (Spengler), a promising new candidate for aquaculture in China, Aquaculture, 255, 402, 10.1016/j.aquaculture.2005.12.027 Lowe, 1997, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Res., 25, 955, 10.1093/nar/25.5.955 Palumbi, 1991 Perna, 1995, Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes, J. Mol. Evol., 41, 353, 10.1007/BF01215182 Ren, 2009, The complete mitochondrial genome of the clam Meretrix petechialis (Mollusca: Bivalvia: Veneridae), Mitochondrial DNA, 20, 78, 10.1080/19401730902964425 Ren, 2010, The mitochondrial genomes of two scallops, Argopecten irradians and Chlamys farreri (Mollusca: Bivalvia): the most highly rearranged gene order in the family Pectinidae, J. Mol. Evol., 70, 57, 10.1007/s00239-009-9308-4 Shen, 2009, A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculenta, BMC Genomics, 10, 136, 10.1186/1471-2164-10-136 Soroka, 2010, Complete sequences of maternally inherited mitochondrial genomes in mussels Unio pictorum (Bivalvia, Unionidae), J. Appl. Genet., 51, 469, 10.1007/BF03208876 Thompson, 1997, The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucleic Acids Res., 25, 4876, 10.1093/nar/25.24.4876 Wang, 2010, Complete mtDNA of Meretrix lusoria (Bivalvia: Veneridae) reveals the presence of an atp8 gene, length variation and heteroplasmy in the control region, Comp. Biochem. Physiol. D, 5, 256 Wu, 2009, Phylogenetic analyses of complete mitochondrial genome of Urechis unicinctus (Echiura) support that echiurans are derived annelids, Mol. Phylogenet. Evol., 52, 558, 10.1016/j.ympev.2009.03.009 Wyman, 2004, Automatic annotation of organellar genomes with DOGMA, Bioinformatics, 20, 3252, 10.1093/bioinformatics/bth352