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Volumn 10, Issue 4, 2010, Pages 615-627

Assessing the effects of primer specificity on eliminating numt coamplification in DNA barcoding: A case study from Orthoptera (Arthropoda: Insecta)

Author keywords

DNA barcoding; Numt; Orthoptera; Primer specificity

Indexed keywords

ARTHROPODA; HEXAPODA; INSECTA; ORTHOPTERA;

EID: 77954742750     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2009.02823.x     Document Type: Article
Times cited : (115)

References (42)
  • 1
    • 28644444059 scopus 로고    scopus 로고
    • Discovery of a large number of previously unrecognized mitochondrial pseudogenes in fish genomes
    • Antunes A, Ramos MJ. Discovery of a large number of previously unrecognized mitochondrial pseudogenes in fish genomes. Genomics 2005, 86:708-717.
    • (2005) Genomics , vol.86 , pp. 708-717
    • Antunes, A.1    Ramos, M.J.2
  • 4
    • 0033999959 scopus 로고    scopus 로고
    • Frequent assimilation of mitochondrial DNA by grasshopper nuclear genomes
    • Bensasson D, Zhang DX, Hewitt GM. Frequent assimilation of mitochondrial DNA by grasshopper nuclear genomes. Molecular Biology and Evolution 2000, 17:406-415.
    • (2000) Molecular Biology and Evolution , vol.17 , pp. 406-415
    • Bensasson, D.1    Zhang, D.X.2    Hewitt, G.M.3
  • 7
    • 33748948266 scopus 로고    scopus 로고
    • Who will actually use DNA barcoding and what will it cost?
    • Cameron S, Rubinoff D, Will K. Who will actually use DNA barcoding and what will it cost? Systematic Biology 2006, 55:844-847.
    • (2006) Systematic Biology , vol.55 , pp. 844-847
    • Cameron, S.1    Rubinoff, D.2    Will, K.3
  • 8
    • 33845866870 scopus 로고    scopus 로고
    • A mitochondrial genome phylogeny of Diptera: whole genome sequence data accurately resolve relationships over broad timescales with high precision
    • Cameron SL, Lambkin CL, Barker SC, Whiting MF. A mitochondrial genome phylogeny of Diptera: whole genome sequence data accurately resolve relationships over broad timescales with high precision. Systematic Entomology 2007, 32:40-59.
    • (2007) Systematic Entomology , vol.32 , pp. 40-59
    • Cameron, S.L.1    Lambkin, C.L.2    Barker, S.C.3    Whiting, M.F.4
  • 9
    • 3042666256 scopus 로고    scopus 로고
    • Muscle: multiple sequence alignment with high accuracy and high throughput
    • Edgar RC. muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 2004, 32:1792-1797.
    • (2004) Nucleic Acids Research , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 10
    • 33847708768 scopus 로고    scopus 로고
    • The complete mitochondrial genome sequence of the Mormon cricket (Anabrus simplex: Tettigoniidae: Orthoptera) and an analysis of control region variability
    • Fenn JD, Cameron SL, Whiting MF. The complete mitochondrial genome sequence of the Mormon cricket (Anabrus simplex: Tettigoniidae: Orthoptera) and an analysis of control region variability. Insect Molecular Biology 2007, 16:239-252.
    • (2007) Insect Molecular Biology , vol.16 , pp. 239-252
    • Fenn, J.D.1    Cameron, S.L.2    Whiting, M.F.3
  • 11
    • 52049118280 scopus 로고    scopus 로고
    • A preliminary mitochondrial genome phylogeny of Orthoptera (Insecta) and approaches to maximizing phylogenetic signal found within mitochondrial genome data
    • Fenn JD, Song H, Cameron SL, Whiting MF. A preliminary mitochondrial genome phylogeny of Orthoptera (Insecta) and approaches to maximizing phylogenetic signal found within mitochondrial genome data. Molecular Phylogenetics and Evolution 2008, 49:59-68.
    • (2008) Molecular Phylogenetics and Evolution , vol.49 , pp. 59-68
    • Fenn, J.D.1    Song, H.2    Cameron, S.L.3    Whiting, M.F.4
  • 12
    • 0029619268 scopus 로고
    • The sequence, organization, and evolution of the Locusta migratoria mitochondrial genome
    • Flook PK, Rowell CH, Gellissen G. The sequence, organization, and evolution of the Locusta migratoria mitochondrial genome. Journal of Molecular Evolution 1995, 41:928-941.
    • (1995) Journal of Molecular Evolution , vol.41 , pp. 928-941
    • Flook, P.K.1    Rowell, C.H.2    Gellissen, G.3
  • 13
    • 0028528103 scopus 로고
    • DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates
    • Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology & Biotechnology 1994, 3:294-299.
    • (1994) Molecular Marine Biology & Biotechnology , vol.3 , pp. 294-299
    • Folmer, O.1    Black, M.2    Hoeh, W.3    Lutz, R.4    Vrijenhoek, R.5
  • 14
    • 1942485857 scopus 로고    scopus 로고
    • Origin of intra-individual variation in PCR-amplified mitochondrial cytochrome oxidase I of Thrips tabaci (Thysanoptera: Thripidae): mitochondrial heteroplasmy or nuclear integration?
    • Frey JE, Frey B. Origin of intra-individual variation in PCR-amplified mitochondrial cytochrome oxidase I of Thrips tabaci (Thysanoptera: Thripidae): mitochondrial heteroplasmy or nuclear integration? Hereditas 2004, 140:92-98.
    • (2004) Hereditas , vol.140 , pp. 92-98
    • Frey, J.E.1    Frey, B.2
  • 15
    • 84969429196 scopus 로고
    • Mitochondrial DNA sequences in the nuclear genome of a locust
    • Gellissen G, Bradfield JY, White BN, Wyatt GR. Mitochondrial DNA sequences in the nuclear genome of a locust. Nature 1983, 24:774-786.
    • (1983) Nature , vol.24 , pp. 774-786
    • Gellissen, G.1    Bradfield, J.Y.2    White, B.N.3    Wyatt, G.R.4
  • 16
    • 45749124657 scopus 로고    scopus 로고
    • Tnt, a free program for phylogenetic analysis
    • Goloboff PA, Farris JS, Nixon KC. tnt, a free program for phylogenetic analysis. Cladistics 2008, 24:774-786.
    • (2008) Cladistics , vol.24 , pp. 774-786
    • Goloboff, P.A.1    Farris, J.S.2    Nixon, K.C.3
  • 18
    • 31344432889 scopus 로고    scopus 로고
    • The promise of DNA barcoding for taxonomy
    • Hebert PD, Gregory TR. The promise of DNA barcoding for taxonomy. Systematic Biology 2005, 54:852-859.
    • (2005) Systematic Biology , vol.54 , pp. 852-859
    • Hebert, P.D.1    Gregory, T.R.2
  • 23
    • 0030807901 scopus 로고    scopus 로고
    • Novel and dynamic evolution of equine infectious anemia virus genomic quasispecies associated with sequential disease cycles in an experimentally infected pony
    • Leroux C, Issel CJ, Montelaro RC. Novel and dynamic evolution of equine infectious anemia virus genomic quasispecies associated with sequential disease cycles in an experimentally infected pony. Journal of Virology 1997, 71:9627-9639.
    • (1997) Journal of Virology , vol.71 , pp. 9627-9639
    • Leroux, C.1    Issel, C.J.2    Montelaro, R.C.3
  • 24
    • 0028363062 scopus 로고
    • Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat
    • Lopez JV, Yuhki N, Masuda R, Modi W, O'Brien SJ. Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. Journal of Molecular Evolution 1994, 39:174-190.
    • (1994) Journal of Molecular Evolution , vol.39 , pp. 174-190
    • Lopez, J.V.1    Yuhki, N.2    Masuda, R.3    Modi, W.4    O'Brien, S.J.5
  • 25
    • 0036134760 scopus 로고    scopus 로고
    • Using secondary structure to identify ribosomal numts: cautionary examples from the human genome
    • Olson LE, Yoder AD. Using secondary structure to identify ribosomal numts: cautionary examples from the human genome. Molecular Biology and Evolution 2002, 19:93-100.
    • (2002) Molecular Biology and Evolution , vol.19 , pp. 93-100
    • Olson, L.E.1    Yoder, A.D.2
  • 28
    • 0041386108 scopus 로고    scopus 로고
    • Mrbayes 3: Bayesian phylogenetic inference under mixed models
    • Ronquist F, Huelsenbeck JP. mrbayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 29
    • 33845914892 scopus 로고    scopus 로고
    • A genomic perspective on the shortcomings of mitochondrial DNA for " barcoding" identification
    • Rubinoff D, Cameron S, Will K. A genomic perspective on the shortcomings of mitochondrial DNA for " barcoding" identification. Journal of Heredity 2006, 97:581-594.
    • (2006) Journal of Heredity , vol.97 , pp. 581-594
    • Rubinoff, D.1    Cameron, S.2    Will, K.3
  • 31
    • 54149095095 scopus 로고    scopus 로고
    • A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles
    • Sheffield NC, Song H, Cameron SL, Whiting MF. A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles. Molecular Biology & Evolution 2008, 25:2499-2509.
    • (2008) Molecular Biology & Evolution , vol.25 , pp. 2499-2509
    • Sheffield, N.C.1    Song, H.2    Cameron, S.L.3    Whiting, M.F.4
  • 32
    • 51649110939 scopus 로고    scopus 로고
    • Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified
    • Song H, Buhay JE, Whiting MF, Crandall KA. Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proceedings of the National Academy of Sciences USA 2008, 105:13486-13491.
    • (2008) Proceedings of the National Academy of Sciences USA , vol.105 , pp. 13486-13491
    • Song, H.1    Buhay, J.E.2    Whiting, M.F.3    Crandall, K.A.4
  • 33
    • 0031884718 scopus 로고    scopus 로고
    • Numts: a challenge for avian systematics and population biology
    • Sorenson MD, Quinn TW. Numts: a challenge for avian systematics and population biology. Auk 1998, 115:214-221.
    • (1998) Auk , vol.115 , pp. 214-221
    • Sorenson, M.D.1    Quinn, T.W.2
  • 34
    • 34547781750 scopus 로고    scopus 로고
    • Mega4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    • Tamura K, Dudley J, Nei M, Kumar S. mega4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology & Evolution 2007, 24:1596-1599.
    • (2007) Molecular Biology & Evolution , vol.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 35
    • 52649138494 scopus 로고    scopus 로고
    • Strong host preference of ectomycorrhizal fungi in a Tasmanian wet sclerophyll forest as revealed by DNA barcoding and taxon-specific primers
    • Tedersoo L, Jairus T, Horton BM. Strong host preference of ectomycorrhizal fungi in a Tasmanian wet sclerophyll forest as revealed by DNA barcoding and taxon-specific primers. New Phytologist 2008, 180:479-490.
    • (2008) New Phytologist , vol.180 , pp. 479-490
    • Tedersoo, L.1    Jairus, T.2    Horton, B.M.3
  • 38
    • 0034907535 scopus 로고    scopus 로고
    • Mitochondrial Pseudogenes Are Pervasive and Often Insidious in the Snapping Shrimp Genus Alpheus
    • Williams ST, Knowlton N. Mitochondrial Pseudogenes Are Pervasive and Often Insidious in the Snapping Shrimp Genus Alpheus. Molecular Biology & Evolution 2001, 18:1484-1493.
    • (2001) Molecular Biology & Evolution , vol.18 , pp. 1484-1493
    • Williams, S.T.1    Knowlton, N.2
  • 39
    • 33747083455 scopus 로고    scopus 로고
    • DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: implications for desert spring conservation
    • Witt JD, Threloff DL, Hebert PD. DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: implications for desert spring conservation. Molecular Ecology 2006, 15:3073-3082.
    • (2006) Molecular Ecology , vol.15 , pp. 3073-3082
    • Witt, J.D.1    Threloff, D.L.2    Hebert, P.D.3
  • 40
    • 0030116955 scopus 로고    scopus 로고
    • Highly conserved nuclear copies of the mitochondrial control region in the desert locust Schistocerca gregaria: some implications for population studies
    • Zhang DX, Hewitt GM. Highly conserved nuclear copies of the mitochondrial control region in the desert locust Schistocerca gregaria: some implications for population studies. Molecular Ecology 1996a, 5:295-300.
    • (1996) Molecular Ecology , vol.5 , pp. 295-300
    • Zhang, D.X.1    Hewitt, G.M.2
  • 41
    • 0000387373 scopus 로고    scopus 로고
    • Nuclear integrations: challenges for mitochondrial DNA markers
    • Zhang DX, Hewitt GM. Nuclear integrations: challenges for mitochondrial DNA markers. Trends in Ecology & Evolution 1996b, 11:247-251.
    • (1996) Trends in Ecology & Evolution , vol.11 , pp. 247-251
    • Zhang, D.X.1    Hewitt, G.M.2
  • 42
    • 0030952282 scopus 로고    scopus 로고
    • Insect mitochondrial control region: a review of its structure, evolution and usefulness in evolutionary studies
    • Zhang DX, Hewitt GM. Insect mitochondrial control region: a review of its structure, evolution and usefulness in evolutionary studies. Biochemical Systematics and Ecology 1997, 25:99-120.
    • (1997) Biochemical Systematics and Ecology , vol.25 , pp. 99-120
    • Zhang, D.X.1    Hewitt, G.M.2


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