Complete mitogenome sequence of black carp (Mylopharyngodon piceus) and its use for molecular phylogeny of leuciscine fishes

Molecular Biology Reports

Volumn 39, Issue 5, 2012, Pages 6337-6342

  Chenghui, Wang ^a   Wang, Jun ^a   Yang, Jinquan ^a   Lu, Guoqing ^b   Song, Xiao ^a   Chen, Qin ^a   Xu, Jiawei ^a   Yang, Qinling ^a   Li, Sifa ^a  

^a SHANGHAI OCEAN UNIVERSITY   (China)

^b UNIVERSITY OF NEBRASKA AT OMAHA   (United States)

Author keywords

Leuciscinae; Mitochondrial genome; Mylopharyngodon piceus; Phylogeny

Indexed keywords

RIBOSOME RNA; TRANSFER RNA; NUCLEOTIDE; SPACER DNA;

ARTICLE; CARP; CONTROLLED STUDY; CTENOPHARYNGODON IDELLUS; FISH GENETICS; GENE NUMBER; GENETIC CODE; GENETIC MARKER; GENOME ANALYSIS; MITOCHONDRIAL GENE; MITOGENICITY; MOLECULAR PHYLOGENY; MYLOPHARYNGODON PICEUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; ANIMAL; BAYES THEOREM; CLASSIFICATION; DNA SEQUENCE; FISH; GENETIC POLYMORPHISM; GENETICS; MITOCHONDRIAL GENOME; OPEN READING FRAME; STATISTICAL MODEL;

CTENOPHARYNGODON; CTENOPHARYNGODON IDELLA; CYPRINIDAE; LEUCISCINAE; MYLOPHARYNGODON PICEUS; PISCES; VERTEBRATA;

ANIMALS; BASE SEQUENCE; BAYES THEOREM; CARPS; DNA, INTERGENIC; FISHES; GENES, MITOCHONDRIAL; GENOME, MITOCHONDRIAL; LIKELIHOOD FUNCTIONS; NUCLEOTIDES; OPEN READING FRAMES; PHYLOGENY; POLYMORPHISM, GENETIC; RNA, TRANSFER; SEQUENCE ANALYSIS, DNA;

EID: 84863768028     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-012-1455-9     Document Type: Article

References (38)

1. Li SZ, Fang F (1990) On the geographical distribution of the four kinds of pond-cultured carps in China. Acta Zool Sinica 36:244-248 (In Chinese with English abstract)
2. Chen YY (1998) Fauna Sinica, Osteichthyes, Cypriniformes II. Science Press, Beijing, pp 1-16
3. Li SF (1998) Genetic characterization of major freshwater culture fishes in China. Shanghai Scientific & Technical Publishers, Shanghai, pp 142-147
4. Ben-Ami F, Heller J (2001) Biological control of aquatic pest snails by the black carp, Mylopharyngodon piceus. Biol Cont 22:131-138
5. Nico LG, Williams JD, Jelks HL (2005) Black carp: biological synopsis and risk assessment of an introduced fish. American Fisheries Society, Bethesda, p 337
6. Nelson JS (2006) Fishes of the world, 4th edn. Wiley, Hoboken, p 142
7. He S, Liu H, Chen Y, Kuwahara M, Nakajima T, Zhong Y (2004) Molecular phylogenetic relationships of Eastern Asian Cyprinidae (Pisces: Cypriniformes) inferred from cytochrome b sequences. Sci China Ser C Life Sci 47:130-138
8. Wang X, Li J, He S (2007) Molecular evidence for the monophyly of East Asian groups of Cyprinidae (Teleostei: Cypriniformes) derived from the nuclear recombination activating gene 2 sequences. Mol Phylogenet Evol 42:157-170
9. He S, Mayden RL, Wang X, Wang W, Tang KL, Chen W, Chen Y (2008) Molecular phylogenetics of the family Cyprinidae (Actinopterygii: Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: further evidence from a nuclear gene of the systematic chaos in the family. Mol Phylogenet Evol 46:818-829
10. Tao W, Zou M, Wang X, Gan X, Mayden RL, He S (2010) Phylogenomic analysis resolves the formerly intractable adaptive diversification of the endemic clade of east Asian Cyprinidae (Cypriniformes). PLoS ONE 5:e13508
11. Howes GJ (1981) Anatomy and phylogeny of the Chinese major carps Ctenopharyngodon Steind., 1866 and Hypophthalmichthys Blkr, 18 60. Bull Br Mus (Nat Hist) Zool 41:1-52
12. Avise JC (1994) Molecular marker, natural history and evolution. Chapman & Hall, New York
13. Avise JC (2000) Phylogeography: the history and formation of species. Harvard University Press, Cambridge
14. Boore J (1999) Animal mitochondrial genomes. Nucleic Acids Res 27:1767-1780
15. Yue G, Liew W, Orban L (2006) The complete mitochondrial genome of a basal teleost, the Asian arowana (Scleropages formosus, Osteoglossidae). BMC Genom 7:242
16. Zhu ZY, Yue GH (2008) The complete mitochondrial genome of red grouper Plectropomus leopardus and its applications in identification of grouper species. Aquaculture 276:44-49
17. Catanese G, Infante C, Manchado M (2008) Complete mitochondrial DNA sequences of the frigate tuna Auxis thazard and the bullet tuna Auxis rochei. DNA Seq 19:159-166
18. Wang C, Chen Q, Lu G, Xu J, Yang Q, Li S (2008) Complete mitochondrial genome of the grass carp (Ctenopharyngodon idella, Teleostei): insight into its phylogenic position within Cyprinidae. Gene 424:96-101
19. Peng Z, Wang J, He S (2006) The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes. Gene 376:290-297
20. Catanese G, Manchado M, Infante C (2010) Evolutionary relatedness of mackerels of the genus Scomber based on complete mitochondrial genomes: strong support to the recognition of Atlantic Scomber colias and Pacific Scomber japonicus as distinct species. Gene 452:35-43
21. Jondeung A, Karinthanyakit W (2010) The complete mitochondrial DNA sequence of the short mackerel (Rastrelliger brachysoma), and its phylogenetic position within Scombroidei, Perciformes. Mitochondrial DNA 21:36-47
22. Sambrook Jl, Russell DW (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, New York, pp 479-483
23. Chang YS, Huang FL, Lo TB (1994) The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome. J Mol Evol 38:138-155
24. Mabuchi K, Miya M, Senou H, Suzuki T, Nishida M (2006) Complete mitochondrial DNA sequence of the Lake Biwa wild strain of common carp (Cyprinus carpio L.): further evidence for an ancient origin. Aquaculture 257:68-77
25. Murakami M, Yamashita Y, Fujitani H (1998) The complete sequence of mitochondrial genome from a gynogenetic triploid "ginbuna" (Carassius auratus langsdorfi). Zool Sci 15:335-337
26. Saitoh K, Sado T, Mayden R, Hanzawa N, Nakamura K, Nishida M, Miya M (2006) Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): the first evidence toward resolution of higher-level relationships of the world's largest freshwater fish clade based on 59 whole mitogenome sequences. J Mol Evol 63:826-841
27. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acid Symp Ser 41:95-98
28. Ojala D, Merkel C, Gelfand R, Attardi G (1980) The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA. Cell 22:393-403
29. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
30. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574
31. Jobb G, von Haeseler A, Strimmer K (2004) TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol 4:18
32. Posada D, Buckley TR (2004) Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests. Syst Biol 53:793-808
33. Posada D (2008) jModeltest: phylogenetic model averaging. Mol Biol Evol 25:1253-1256
34. Li SF, Xu JW, Yang QL, Wang CH, Chen Q, Chapman DC, Lu G (2009) A comparison of complete mitochondrial genomes of silver carp Hypophthalmichthys molitrix and bighead carp Hypophthalmichthys nobilis: implications for their taxonomic relationship and phylogeny. J Fish Biol 74:1787-1803
35. Kartavtsev YP, Jung SO, Lee YM, Byeon HK, Lee JS (2007) Complete mitochondrial genome of the bullhead torrent catfish, Liobagrus obesus (Siluriformes, Amblycipididae): genome description and phylogenetic considerations inferred from the Cyt b and 16S rRNA genes. Gene 396:13-27
36. Hixson JE, Wong TW, Clayton DA (1986) Both the conserved stem-loop and divergent 5'-flanking sequences are required for initiation at the human mitochondrial origin of light-strand DNA replication. J Biol Chem 261:2384-2390
37. He AY, Lou YJ, Yang H, Liu LP, Li SF, Wang CH (2011) Complete mitochondrial DNA sequences of the Nile tilapia (Oreochromis niloticus) and Blue tilapia (Oreochromis aureus): Genome characterization and phylogeny applications. Mol Biol Rep 38:2015-2021
38. Galtier N, Nabholz B, Glemin S, Hurst GDD (2009) Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Mol Ecol 18:4541-4550