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Complete mitochondrial DNA sequence and phylogenetic analysis of Zhikong scallop Chlamys farreri (Bivalvia: Pectinidae)

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Abstract

The complete mitochondrial genome of Zhikong scallop Chlamys farreri is 21,695 bp in length and contains 12 protein-coding genes (the atp8 gene is absent, as in most bivalves), 2 ribosomal RNA genes, and 22 transfer RNA genes. The heavy strand has an overall A+T content of 58.7%. GC and AT skews for the mt genome of C. farreri are 0.337 and −0.184, respectively, indicating the nucleotide bias against C and A. The mitochondrial gene order of C. farreri differs drastically from the scallops Argopecten irradians, Mimachlamys nobilis and Placopecten magellanicus, which belong to the same family Pectinidae. 6623 bp non-coding nucleotides exist intergenically in the mitogenome of C. farreri, with a large continuous sequence (4763 bp) between tRNA Val and tRNA Asn. Two repeat families are found in the large continuous sequence, which seems to be a common feature of scallops. Phylogenetic analysis based on 12 concatenated amino acid sequences of protein-coding genes supports the monophyly of Pectinidae and paraphyletic Pteriomorphia with respect to Heteroconchia.

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References

  1. Wolstenholme DR, Jeon KW (1992) A survey of cell biology. Int Rev Cytol 141:173–232

    Article  PubMed  CAS  Google Scholar 

  2. Hoffmann RJ, Boore JL, Brown WM (1992) A novel mitochondrial genome organization for the blue mussel, Mytilus edulis. Genetics 131:397–412

    PubMed  CAS  Google Scholar 

  3. Brown WM (1985) The mitochondrial genome of animals. In: Macintyre RJ (ed) Molecular evolutionary genetics. Plenum Press, New York, pp 95–130

    Google Scholar 

  4. Harrison RG (1989) Animal mitochondrial DNA as a genetic marker in population and evolutionary biology. Trends Ecol Evol 4:6–11

    Article  PubMed  CAS  Google Scholar 

  5. Moritz C, Brown WM (1986) Tandem duplication of Dloop and ribosomal RNA sequences in lizard mitochondrial DNA. Science 233:1425–1427

    Article  PubMed  CAS  Google Scholar 

  6. Moritz C, Brown WM (1987) Tandem duplications in animal mitochondrial DNAs: variation in incidence and gene content among lizards. Proc Natl Acad Sci USA 84:7183–7187

    Article  PubMed  CAS  Google Scholar 

  7. Zevering CE, Moritz C, Heideman A, Sturm RA (1991) Parallel origins of duplications and the ormation of pseudogenes in mitochondrial DNA from parthenogenetic lizards (Heteronotia binoei; Gekkonidae). J Mol Evol 33:431–441

    Article  PubMed  CAS  Google Scholar 

  8. Zhou Y, Zhang JY, Zheng RQ, Yu BG, Yang G (2009) Complete nucleotide sequence and gene organization of the mitochondrial genome of Paa spinosa (Anura: Ranoidae). Gene. doi:10.1016/j.gene.2009.07.009

  9. Saccone C, Giorgi CD, Gissi C, Pesole G, Reyes A (1999) Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system. Gene 238:195–209

    Article  PubMed  CAS  Google Scholar 

  10. Yamanoue Y, Miya M, Matsuura K, Yagishita N, Mabuchi K, Sakai H (2007) Phylogenetic position of tetraodontiform fishes within the higher teleosts: Bayesian inferences based on 44 whole mitochondrial genome sequences. Mol Phylogenet Evol 45:89–101

    Article  PubMed  CAS  Google Scholar 

  11. Gjetvaj B, Cook DI, Zouros E (1992) Repeated sequences and large-scale size variation of mitochondrial DNA: a common feature among scallops (Bivalvia: Pectinidae). Mol Biol Evol 9:106–124

    CAS  Google Scholar 

  12. Smith DR, Snyder M (2007) Complete mitochondrial DNA sequence of the scallop Placopecten magellanicus: evidence of transposition leading to an uncharacteristically large mitochondrial genome. J Mol Evol 65:380–391

    Article  PubMed  CAS  Google Scholar 

  13. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucl Acids Res 25:955–964

    Article  PubMed  CAS  Google Scholar 

  14. Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–3255

    Article  PubMed  CAS  Google Scholar 

  15. Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucl Acids Res 27:573–580

    Article  PubMed  CAS  Google Scholar 

  16. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 25:4876–4882

    Article  PubMed  CAS  Google Scholar 

  17. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552

    PubMed  CAS  Google Scholar 

  18. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704

    Article  PubMed  Google Scholar 

  19. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574

    Article  PubMed  CAS  Google Scholar 

  20. Abascal F, Zardoya R, Posada D (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21:2104–2105

    Article  PubMed  CAS  Google Scholar 

  21. Milbury CA, Gaffney PM (2005) Complete mitochondrial DNA sequence of the eastern oyster Crassostrea virginica. Mar Biotechnol 7:697–712

    Article  PubMed  CAS  Google Scholar 

  22. Perna NT, Kocher TD (1995) Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol 41:353–358

    Article  PubMed  CAS  Google Scholar 

  23. Boore JL (1999) Animal mitochondrial genomes. Nucl Acids Res 27:1767–1780

    Article  PubMed  CAS  Google Scholar 

  24. Boore JL, Medina M, Rosenberg LA (2004) Complete sequences of the highly rearranged molluscan mitochondrial genomes of the scaphopod Graptacme eborea and the bivalve Mytilus edulis. Mol Biol Evol 21:1492–1503

    Article  PubMed  CAS  Google Scholar 

  25. Serb JM, Lydeard C (2003) Complete mtDNA sequence of the North American freshwater mussel, Lampsilis ornata (Unionidae): an examination of the evolution and phylogenetic utility of mitochondrial genome organisation in Bivalvia (Mollusca). Mol Biol Evol 20:1854–1866

    Article  PubMed  CAS  Google Scholar 

  26. Dreyer H, Steiner G (2006) The complete sequence and gene organization 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

    Article  PubMed  Google Scholar 

  27. Schneider A, Marechal-Drouard L (2000) Mitochondrial tRNA import: are there distinct mechanisms? Trends Cell Biol 10:509–513

    Article  PubMed  CAS  Google Scholar 

  28. Faber JE, Stepien CA (1998) Tandemly repeated sequences in the mitochondrial DNA control region and phylogeography of the Pike-Perches Stizostedion. Mol Phylogenet Evol 10:310–322

    Article  PubMed  CAS  Google Scholar 

  29. Wilkinson GS, Mayer F, Kerth G, Petri B (1997) Evolution of repeated sequence arrays in the D-Loop region of bat mitochondrial DNA. Genetics 146:1035–1048

    PubMed  CAS  Google Scholar 

  30. Matsumoto M, Hayami I (2000) Phylogenetic analysis of the family Pectinidae (Bivalvia) based on mitochondrial cytochrome C oxidase subunit I. J Molluscan Stud 66:477–488

    Article  Google Scholar 

  31. Matsumoto M (2003) Phylogenetic analysis of the subclass Pteriomorphia (Bivalvia) from mtDNA COI sequences. Mol Phylogenet Evol 27:429–440

    Article  PubMed  CAS  Google Scholar 

  32. Puslednik L, Serb JM (2008) Molecular phylogenetics of the Pectinidae (Mollusca: Bivalvia) and effect of increased taxon sampling and outgroup selection on tree topology. Mol Phylogenet Evol 48:1178–1188

    Article  PubMed  CAS  Google Scholar 

  33. Waller TR (1991) Evolutionary relationships among commercial scallops (Mollusca: Bivalvia: Pectinidae). In: Shumway SE (ed) Scallops: biology, ecology and aquaculture. Elsevier, New York, pp 1–73

    Google Scholar 

  34. Waller TR (2006) New phylogenies of the Pectinidae (Mollusca: Bivalvia): reconciling morphological and molecular approaches. In: Shumway SE, Parsons GJ (eds) Scallops: biology, ecology and aquaculture. Elsevier BV, Amsterdam, pp 1–43

    Chapter  Google Scholar 

  35. Barucca M, Olmo E, Schiaparelli S, Canapa A (2004) Molecular phylogeny of the family Pectinidae (Mollusca: Bivalvia) based on mitochondrial 16S and 12S rRNA. Mol Phylogenet Evol 31:89–95

    Article  PubMed  CAS  Google Scholar 

  36. Waller TR (1998) Origin of the molluscan class Bivalvia and a phylogeny of major groups. In: Johnston PA, Haggart JW (eds) Bivalves: an eon of evolution. University of Calgary Press, Calgary, pp 1–45

    Google Scholar 

  37. Cope JCW (1997) The early phylogeny of the class Bivalvia. Palaeontology 40:713–746

    Google Scholar 

  38. Adamkewicz SL, Harasewych MG, Blake J, Saudek D, Bult CJ (1997) A molecular phylogeny of the bivalve mollusks. Mol Biol Evol 14:619–629

    PubMed  CAS  Google Scholar 

  39. Campbell DC, Hoekstra KJ, Carter JG (1998) 18S ribosomal DNA and evolutionary relationships within the Bivalvia. In: Johnston PA, Haggart JW (eds) Bivalves: an eon of evolution. University of Calgary Press, Calgary, pp 75–85

    Google Scholar 

  40. Carter JG, Campbell DC, Campbell MR (2000) Cladistic perspectives on early bivalve evolution. In: Harper EM, Taylor JD, Crame JA (eds) The evolutionary biology of the bivalvia. The Geological Society of London, London, pp 47–79

    Google Scholar 

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Acknowledgments

The study was supported by the grants from National High Technology Research and Development Program (2007AA09Z433), and Chinese Ministry of Education (707041).

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Authors and Affiliations

  1. Fisheries College, Ocean University of China, 266003, Qingdao, China

    Kefeng Xu, Hong Yu & Qi Li

  2. Laboratory of Integrative Aquatic Biology, Graduate School of Agriculture Science, Tohoku University, Onagawa, Miyagi, 9862242, Japan

    Manami Kanno & Akihiro Kijima

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  1. Kefeng Xu
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  2. Manami Kanno
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  3. Hong Yu
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  4. Qi Li
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  5. Akihiro Kijima
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Correspondence to Qi Li.

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Xu, K., Kanno, M., Yu, H. et al. Complete mitochondrial DNA sequence and phylogenetic analysis of Zhikong scallop Chlamys farreri (Bivalvia: Pectinidae). Mol Biol Rep 38, 3067–3074 (2011). https://doi.org/10.1007/s11033-010-9974-8

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