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Volumn 2, Issue 1, 2010, Pages 410-424

Index-free de novo assembly and deconvolution of mixed mitochondrial genomes

Author keywords

Control region; Informatic deconvolution; Molluscs; Multiplex sequencing; Noncomplementary

Indexed keywords

MITOCHONDRIAL DNA; PRIMER DNA;

EID: 77958511708     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evq029     Document Type: Article
Times cited : (26)

References (44)
  • 1
    • 33244495720 scopus 로고    scopus 로고
    • Extensive mitochondrial gene arrangements in coleoid Cephalopoda and their phylogenetic implications
    • Akasaki T, et al. 2006. Extensive mitochondrial gene arrangements in coleoid Cephalopoda and their phylogenetic implications. Mol Phylogenet Evol. 38:648-658.
    • (2006) Mol. Phylogenet Evol. , vol.38 , pp. 648-658
    • Akasaki, T.1
  • 2
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul SF, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 3
    • 0019423856 scopus 로고
    • Sequence and organization of the human mitochondrial genome
    • Anderson S, et al. 1981. Sequence and organization of the human mitochondrial genome. Nature. 290:457-465.
    • (1981) Nature , vol.290 , pp. 457-465
    • Anderson, S.1
  • 4
    • 33746575087 scopus 로고    scopus 로고
    • Complete mitochondrial DNA sequence of a Conoidean gastropod, Lophiotoma (Xenuroturris) cerithiformis: Gene order and gastropod phylogeny
    • Bandyopadhyay PK, Stevenson BJ, Cady MT, Olivera BM, Wolstenholme DR. 2006. Complete mitochondrial DNA sequence of a Conoidean gastropod, Lophiotoma (Xenuroturris) cerithiformis: gene order and gastropod phylogeny. Toxicon. 48:29-43.
    • (2006) Toxicon , vol.48 , pp. 29-43
    • Bandyopadhyay, P.K.1    Stevenson, B.J.2    Cady, M.T.3    Olivera, B.M.4    Wolstenholme, D.R.5
  • 5
    • 37249024664 scopus 로고    scopus 로고
    • The mitochondrial genome of Conus textile, coxI-coxII intergenic sequences and Conoidean evolution
    • Bandyopadhyay PK, et al. 2008. The mitochondrial genome of Conus textile, coxI-coxII intergenic sequences and Conoidean evolution. Mol Phylogenet Evol. 46:215-223.
    • (2008) Mol. Phylogenet Evol. , vol.46 , pp. 215-223
    • Bandyopadhyay, P.K.1
  • 7
  • 8
    • 33745988233 scopus 로고    scopus 로고
    • The use of genome-level characters for phylogenetic reconstruction
    • Boore JL. 2006. The use of genome-level characters for phylogenetic reconstruction. Trends Ecol Evol. 21:439-446.
    • (2006) Trends Ecol. Evol. , vol.21 , pp. 439-446
    • Boore, J.L.1
  • 9
    • 0034760329 scopus 로고    scopus 로고
    • A clone-array pooled shotgun strategy for sequencing large genomes
    • Cai W-W, Chen R, Gibbs RA, Bradley A. 2001. A clone-array pooled shotgun strategy for sequencing large genomes. Genome Res. 11:1619-1623.
    • (2001) Genome Res. , vol.11 , pp. 1619-1623
    • Cai, W.-W.1    Chen, R.2    Gibbs, R.A.3    Bradley, A.4
  • 10
    • 4544263565 scopus 로고    scopus 로고
    • Fragment assembly with short reads
    • Chaisson M, Pevzner P, Tang H. 2004. Fragment assembly with short reads. Bioinformatics. 20:2067-2074.
    • (2004) Bioinformatics , vol.20 , pp. 2067-2074
    • Chaisson, M.1    Pevzner, P.2    Tang, H.3
  • 11
    • 70349120372 scopus 로고    scopus 로고
    • Neogastropod phylogenetic relationships based on entire mitochondrial genomes
    • Cunha R, Grande C, Zardoya R. 2009. Neogastropod phylogenetic relationships based on entire mitochondrial genomes. BMC Evol Biol. 9:210.
    • (2009) BMC Evol. Biol. , vol.9 , pp. 210
    • Cunha, R.1    Grande, C.2    Zardoya, R.3
  • 12
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    • Dohm JC, Lottaz C, Borodina T, Himmelbauer H. 2008. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 36: e105.
    • (2008) Nucleic Acids Res. , vol.36
    • Dohm, J.C.1    Lottaz, C.2    Borodina, T.3    Himmelbauer, H.4
  • 13
    • 67349165358 scopus 로고    scopus 로고
    • cited 2008 December 22. Available from
    • Drummond AJ, et al. 2008. Geneious v4.0 [cited 2008 December 22]. Available from http://www.geneious.com/.
    • (2008) Geneious v4.0
    • Drummond, A.J.1
  • 14
    • 67650047735 scopus 로고    scopus 로고
    • DNA Sudoku-harnessing high-throughput sequencing for multiplexed specimen analysis
    • Erlich Y, et al. 2009. DNA Sudoku-harnessing high-throughput sequencing for multiplexed specimen analysis. Genome Res. 19:1243-1253.
    • (2009) Genome Res. , vol.19 , pp. 1243-1253
    • Erlich, Y.1
  • 15
    • 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. 2008. A preliminary mitochondrial genome phylogeny of Orthoptera (Insecta) and approaches to maximizing phylogenetic signal found within mitochondrial genome data. Mol Phylogenet Evol. 49:59-68.
    • (2008) Mol. Phylogenet Evol. , vol.49 , pp. 59-68
    • Fenn, J.D.1    Song, H.2    Cameron, S.L.3    Whiting, M.F.4
  • 16
    • 70749085913 scopus 로고    scopus 로고
    • BARCRAWL and BARTAB: Software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing
    • Frank DN. 2009. BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. BMC Bioinformatics. 10:362.
    • (2009) BMC Bioinformatics , vol.10 , pp. 362
    • Frank, D.N.1
  • 17
    • 63849091245 scopus 로고    scopus 로고
    • Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
    • Fullwood MJ, Wei C-L, Liu ET, Ruan Y. 2009. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 19:521-532.
    • (2009) Genome Res. , vol.19 , pp. 521-532
    • Fullwood, M.J.1    Wei, C.-L.2    Liu, E.T.3    Ruan, Y.4
  • 18
    • 0034274870 scopus 로고    scopus 로고
    • An open graph visualization system and its applications to software engineering
    • Gansner ER, North SC. 2000. An open graph visualization system and its applications to software engineering. Software Pract Exper. 30:1203-1233.
    • (2000) Software Pract. Exper , vol.30 , pp. 1203-1233
    • Gansner, E.R.1    North, S.C.2
  • 19
    • 33845873317 scopus 로고    scopus 로고
    • Mitochondrial genomes and avian phylogeny: Complex characters and resolvability without explosive radiations
    • Gibb GC, Kardailsky O, Kimball RT, Braun EL, Penny D. 2007. Mitochondrial genomes and avian phylogeny: complex characters and resolvability without explosive radiations. Mol Biol Evol. 24:269-280.
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 269-280
    • Gibb, G.C.1    Kardailsky, O.2    Kimball, R.T.3    Braun, E.L.4    Penny, D.5
  • 20
    • 43149085041 scopus 로고    scopus 로고
    • De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer
    • Hernandez D, Francois P, Farinelli L, Osterås M, Schrenzel J. 2008. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res. 18:802-809.
    • (2008) Genome Res. , vol.18 , pp. 802-809
    • Hernandez, D.1    Francois, P.2    Farinelli, L.3    Osterås, M.4    Schrenzel, J.5
  • 21
    • 38749149152 scopus 로고    scopus 로고
    • Whole-genome sequencing and variant discovery in C. elegans
    • Hillier LW, et al. 2008. Whole-genome sequencing and variant discovery in C. elegans. Nat Methods. 5:183-188.
    • (2008) Nat. Methods , vol.5 , pp. 183-188
    • Hillier, L.W.1
  • 22
    • 0034619822 scopus 로고    scopus 로고
    • Mitochondrial genome variation and the origin of modern humans
    • Ingman M, Kaessmann H, Pääbo S, Gyllensten U. 2000. Mitochondrial genome variation and the origin of modern humans. Nature. 408:708-713.
    • (2000) Nature , vol.408 , pp. 708-713
    • Ingman, M.1    Kaessmann, H.2    Pääbo, S.3    Gyllensten, U.4
  • 23
    • 21744458548 scopus 로고    scopus 로고
    • The complete nucleotide sequence and gene organization of the mitochondrial genome of the oriental mole cricket, Gryllotalpa orientalis (Orthoptera: Gryllotalpidae)
    • Kim I, et al. 2005. The complete nucleotide sequence and gene organization of the mitochondrial genome of the oriental mole cricket, Gryllotalpa orientalis (Orthoptera: Gryllotalpidae). Gene. 353:155-168.
    • (2005) Gene , vol.353 , pp. 155-168
    • Kim, I.1
  • 24
    • 76749117156 scopus 로고    scopus 로고
    • Assembly complexity of prokaryotic genomes using short reads
    • Kingsford C, Schatz MC, Pop M. 2010. Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics. 11:21.
    • (2010) BMC Bioinformatics , vol.11 , pp. 21
    • Kingsford, C.1    Schatz, M.C.2    Pop, M.3
  • 25
    • 0025770417 scopus 로고
    • The transcription of DNA in chicken mitochondria initiates from one major bidirectional promoter
    • L'Abbé D, Duhaime JF, Lang BF, Morais R. 1991. The transcription of DNA in chicken mitochondria initiates from one major bidirectional promoter. J Biol Chem. 266:10844-10850.
    • (1991) J. Biol. Chem. , vol.266 , pp. 10844-10850
    • L'Abbé, D.1    Duhaime, J.F.2    Lang, B.F.3    Morais, R.4
  • 26
    • 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. 1994. Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. J Mol Evol. 39:174-190.
    • (1994) J. Mol. Evol. , vol.39 , pp. 174-190
    • Lopez, J.V.1    Yuhki, N.2    Masuda, R.3    Modi, W.4    O'Brien, S.J.5
  • 27
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated highdensity picolitre reactors
    • Margulies M, et al. 2005. Genome sequencing in microfabricated highdensity picolitre reactors. Nature. 437:376-380.
    • (2005) Nature , vol.437 , pp. 376-380
    • Margulies, M.1
  • 28
    • 33746207763 scopus 로고    scopus 로고
    • Multiplex sequencing of paired-end ditags (MS-PET): A strategy for the ultra-high-throughput analysis of transcriptomes and genomes
    • Ng P, et al. 2006. Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes. Nucleic Acids Res. 34: e84.
    • (2006) Nucleic Acids Res. , vol.34
    • Ng, P.1
  • 29
    • 0035400648 scopus 로고    scopus 로고
    • Gene trees and species trees are not the same
    • Nichols R. 2001. Gene trees and species trees are not the same. Trends Ecol Evol. 16:358-364.
    • (2001) Trends Ecol. Evol. , vol.16 , pp. 358-364
    • Nichols, R.1
  • 30
    • 0347380991 scopus 로고    scopus 로고
    • Radiation of extant marsupials after the K/T boundary: Evidence from complete mitochondrial genomes
    • Nilsson MA, Gullberg A, Spotorno AE, Arnason U, Janke A. 2003. Radiation of extant marsupials after the K/T boundary: evidence from complete mitochondrial genomes. J Mol Evol. 57: S3-S12.
    • (2003) J. Mol. Evol. , vol.57
    • Nilsson, M.A.1    Gullberg, A.2    Spotorno, A.E.3    Arnason, U.4    Janke, A.5
  • 31
    • 58449087343 scopus 로고    scopus 로고
    • Toward resolving deep Neoaves phylogeny: Data, signal enhancement, and priors
    • Pratt RC, et al. 2009. Toward resolving deep Neoaves phylogeny: data, signal enhancement, and priors. Mol Biol Evol. 26:313-326.
    • (2009) Mol. Biol. Evol. , vol.26 , pp. 313-326
    • Pratt, R.C.1
  • 32
    • 70149113077 scopus 로고    scopus 로고
    • R Development Core Team, Vienna, Austria: R Foundation for Statistical Computing
    • R Development Core Team. 2009. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing.
    • (2009) R: A Language and Environment for Statistical Computing
  • 33
    • 0037115476 scopus 로고    scopus 로고
    • The crocodilian mitochondrial control region: General structure, conserved sequences, and evolutionary implications
    • Ray DA, Densmore L. 2002. The crocodilian mitochondrial control region: general structure, conserved sequences, and evolutionary implications. J Exp Zool. 294:334-345.
    • (2002) J. Exp. Zool. , vol.294 , pp. 334-345
    • Ray, D.A.1    Densmore, L.2
  • 34
    • 2442637641 scopus 로고    scopus 로고
    • NUMTs in sequenced eukaryotic genomes
    • Richly E, Leister D. 2004. NUMTs in sequenced eukaryotic genomes. Mol Biol Evol. 21:1081-1084.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1081-1084
    • Richly, E.1    Leister, D.2
  • 35
    • 55049136427 scopus 로고    scopus 로고
    • Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes
    • Robins JH, et al. 2008. Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes. Mol Phylogenet Evol. 49:460-466.
    • (2008) Mol. Phylogenet Evol. , vol.49 , pp. 460-466
    • Robins, J.H.1
  • 36
    • 9944235433 scopus 로고    scopus 로고
    • Phylogenetic relationships of discoglossid frogs (Amphibia: Anura: Discoglossidae) based on complete mitochondrial genomes and nuclear genes
    • San Mauro D, García-París M, Zardoya R. 2004. Phylogenetic relationships of discoglossid frogs (Amphibia:Anura:Discoglossidae) based on complete mitochondrial genomes and nuclear genes. Gene. 343:357-366.
    • (2004) Gene , vol.343 , pp. 357-366
    • Mauro, D.S.1    García-París, M.2    Zardoya, R.3
  • 38
    • 0033025011 scopus 로고    scopus 로고
    • Gene contents and organization of a mitochondrial DNA segment of the squid Loligo bleekeri
    • Sasuga J, et al. 1999. Gene contents and organization of a mitochondrial DNA segment of the squid Loligo bleekeri. J Mol Evol. 48:692-702.
    • (1999) J. Mol. Evol. , vol.48 , pp. 692-702
    • Sasuga, J.1
  • 39
    • 33646066557 scopus 로고    scopus 로고
    • Rolling circle amplification of metazoan mitochondrial genomes
    • Simison WB, Lindberg DR, Boore JL. 2006. Rolling circle amplification of metazoan mitochondrial genomes. Mol Phylogenet Evol. 39:562-567.
    • (2006) Mol. Phylogenet Evol. , vol.39 , pp. 562-567
    • Simison, W.B.1    Lindberg, D.R.2    Boore, J.L.3
  • 40
    • 24044447664 scopus 로고    scopus 로고
    • Automated generation of heuristics for biological sequence comparison
    • Slater G S C, Birney E. 2005. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics. 6:31.
    • (2005) BMC Bioinformatics , vol.6 , pp. 31
    • Slater, G.S.C.1    Birney, E.2
  • 41
    • 0035203374 scopus 로고    scopus 로고
    • Complete nucleotide sequence and gene rearrangement of the mitochondrial genome of the Japanese pond frog Rana nigromaculata
    • Sumida M, et al. 2001. Complete nucleotide sequence and gene rearrangement of the mitochondrial genome of the Japanese pond frog Rana nigromaculata. Genes Genet Syst. 76:311-325.
    • (2001) Genes Genet. Syst. , vol.76 , pp. 311-325
    • Sumida, M.1
  • 42
    • 0032581682 scopus 로고    scopus 로고
    • SerGCU: Molecular basis for assignment of AGA/AGG codons as serine in invertebrate mitochondria
    • SerGCU: molecular basis for assignment of AGA/AGG codons as serine in invertebrate mitochondria. Biochim Biophys Acta. 1399:78-82.
    • (1998) Biochim. Biophys. Acta , vol.1399 , pp. 78-82
    • Tomita, K.1    Ueda, T.2    Watanabe, K.3
  • 43
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821-829.
    • (2008) Genome Res. , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 44
    • 0002287019 scopus 로고    scopus 로고
    • Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide
    • Barciszewski J, Clark BFC, editors, NATO ASI Series, Dordrecht NL: Kluwer Academic Publishers
    • Zuker M, et al. 1999. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In Barciszewski J, Clark BFC, editors. RNA biochemistry and biotechnology. NATO ASI Series, Dordrecht (NL): Kluwer Academic Publishers. 11-43.
    • (1999) RNA Biochemistry and Biotechnology , pp. 11-43
    • Zuker, M.1


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