메뉴 건너뛰기




Volumn 42, Issue 22, 2014, Pages

Multiplex sequencing of pooled mitochondrial genomes - A crucial step toward biodiversity analysis using mito-metagenomics

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIODIVERSITY; CONTROLLED STUDY; DNA DETERMINATION; DROSOPHILA; GENE LOCUS; GENE SEQUENCE; GENETIC DISTANCE; GENOME ANALYSIS; GENOMICS; HIGH THROUGHPUT SEQUENCING; INSECT GENOME; METAGENOMICS; MITOCHONDRIAL GENOME; MITOGENOMICS; NONHUMAN; PHYLOGENOMICS; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SIMULATION; VALIDATION PROCESS; ANIMAL; COMPUTER SIMULATION; DNA SEQUENCE; GENETICS; MOLECULAR GENETICS; PROCEDURES;

EID: 84927611164     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku917     Document Type: Article
Times cited : (233)

References (41)
  • 1
    • 84859598363 scopus 로고    scopus 로고
    • Towards next-generation biodiversity assessment using DNA metabarcoding
    • Taberlet, P., Coissac, E., Pompanon, F., Brochmann, C. and Willerslev, E. (2012) Towards next-generation biodiversity assessment using DNA metabarcoding. Mol. Ecol., 21, 2045-2050.
    • (2012) Mol. Ecol. , vol.21 , pp. 2045-2050
    • Taberlet, P.1    Coissac, E.2    Pompanon, F.3    Brochmann, C.4    Willerslev, E.5
  • 3
    • 77954336858 scopus 로고    scopus 로고
    • ITS as an environmental DNA barcode for fungi: An in silico approach reveals potential PCR biases
    • Bellemain, E., Carlsen, T., Brochmann, C., Coissac, E., Taberlet, P. and Kauserud, H. (2010) ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiol., 10, 189.
    • (2010) BMC Microbiol. , vol.10 , pp. 189
    • Bellemain, E.1    Carlsen, T.2    Brochmann, C.3    Coissac, E.4    Taberlet, P.5    Kauserud, H.6
  • 4
    • 84865657400 scopus 로고    scopus 로고
    • Limited efficiency of universal mini-barcode primers for DNA amplification from desert reptiles, birds and mammals
    • Arif, I. A., Khan, H. A., Al Sadoon, M. and Shobrak, M. (2011) Limited efficiency of universal mini-barcode primers for DNA amplification from desert reptiles, birds and mammals. Genet. Mol. Res., 10, 3559-3564.
    • (2011) Genet. Mol. Res. , vol.10 , pp. 3559-3564
    • Arif, I.A.1    Khan, H.A.2    Al Sadoon, M.3    Shobrak, M.4
  • 6
    • 84883191674 scopus 로고    scopus 로고
    • Improved inference of taxonomic richness from environmental DNA
    • Morgan, M. J., Chariton, A. A., Hartley, D. M., Court, L. N. and Hardy, C. M. (2013) Improved inference of taxonomic richness from environmental DNA. PLoS One, 8, e71974.
    • (2013) PLoS One , vol.8 , pp. e71974
    • Morgan, M.J.1    Chariton, A.A.2    Hartley, D.M.3    Court, L.N.4    Hardy, C.M.5
  • 7
    • 84889639970 scopus 로고    scopus 로고
    • SOAPBarcode: Revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons
    • Liu, S., Li, Y., Lu, J., Su, X., Tang, M., Zhang, R., Zhou, L., Zhou, C., Yang, Q. and Ji, Y. (2013) SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons. Methods Ecol. Evol., 4, 1142-1150.
    • (2013) Methods Ecol. Evol. , vol.4 , pp. 1142-1150
    • Liu, S.1    Li, Y.2    Lu, J.3    Su, X.4    Tang, M.5    Zhang, R.6    Zhou, L.7    Zhou, C.8    Yang, Q.9    Ji, Y.10
  • 8
    • 84866642478 scopus 로고    scopus 로고
    • Biodiversity soup: Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring
    • Yu, D. W., Ji, Y., Emerson, B. C., Wang, X., Ye, C., Yang, C. and Ding, Z. (2012) Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods Ecol. Evol., 3, 613-623.
    • (2012) Methods Ecol. Evol. , vol.3 , pp. 613-623
    • Yu, D.W.1    Ji, Y.2    Emerson, B.C.3    Wang, X.4    Ye, C.5    Yang, C.6    Ding, Z.7
  • 9
    • 85006186573 scopus 로고    scopus 로고
    • Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification
    • Zhou, X., Li, Y., Liu, S., Yang, Q., Su, X., Zhou, L., Tang, M., Fu, R., Li, J. and Huang, Q. (2013) Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. Gigascience, 2, 4.
    • (2013) Gigascience , vol.2 , pp. 4
    • Zhou, X.1    Li, Y.2    Liu, S.3    Yang, Q.4    Su, X.5    Zhou, L.6    Tang, M.7    Fu, R.8    Li, J.9    Huang, Q.10
  • 10
    • 69149084832 scopus 로고    scopus 로고
    • A DNA barcode for land plants
    • CBOL Plant Working Group (2009) A DNA barcode for land plants. Proc. Natl. Acad. Sci. U. S. A., 106, 12794-12797.
    • (2009) Proc. Natl. Acad. Sci. U. S. A. , vol.106 , pp. 12794-12797
  • 11
    • 84894282696 scopus 로고    scopus 로고
    • Evaluation of 11 single-locus and seven multilocus DNA barcodes in Lamium L. (Lamiaceae)
    • Krawczyk, K., Szczecińska, M. and Sawicki, J. (2013) Evaluation of 11 single-locus and seven multilocus DNA barcodes in Lamium L. (Lamiaceae). Mol. Ecol. Resour., 14, 272-285.
    • (2013) Mol. Ecol. Resour. , vol.14 , pp. 272-285
    • Krawczyk, K.1    Szczecińska, M.2    Sawicki, J.3
  • 12
    • 84876285048 scopus 로고    scopus 로고
    • A multi-locus approach to barcoding in the Anopheles strodei subgroup (Diptera: Culicidae)
    • Bourke, B. P., Oliveira, T. P., Suesdek, L., Bergo, E. S. and Sallum, M. A. (2013) A multi-locus approach to barcoding in the Anopheles strodei subgroup (Diptera: Culicidae). Parasit. Vectors, 6, 111.
    • (2013) Parasit. Vectors , vol.6 , pp. 111
    • Bourke, B.P.1    Oliveira, T.P.2    Suesdek, L.3    Bergo, E.S.4    Sallum, M.A.5
  • 13
    • 78650424081 scopus 로고    scopus 로고
    • Multilocus species identification and fungal DNA barcoding: Insights from blue stain fungal symbionts of the mountain pine beetle
    • Roe, A. D., Rice, A. V., Bromilow, S. E., Cooke, J. E. and Sperling, F. A. (2010) Multilocus species identification and fungal DNA barcoding: insights from blue stain fungal symbionts of the mountain pine beetle. Mol. Ecol. Resour., 10, 946-959.
    • (2010) Mol. Ecol. Resour. , vol.10 , pp. 946-959
    • Roe, A.D.1    Rice, A.V.2    Bromilow, S.E.3    Cooke, J.E.4    Sperling, F.A.5
  • 14
    • 84866236892 scopus 로고    scopus 로고
    • Multi-locus species delimitation in closely related animals and fungi: One marker is not enough
    • Dupuis, J. R., Roe, A. D. and Sperling, F. A. (2012) Multi-locus species delimitation in closely related animals and fungi: one marker is not enough. Mol. Ecol., 21, 4422-4436.
    • (2012) Mol. Ecol. , vol.21 , pp. 4422-4436
    • Dupuis, J.R.1    Roe, A.D.2    Sperling, F.A.3
  • 15
    • 84905983626 scopus 로고    scopus 로고
    • Performance comparison of genetic markers for high-throughput sequencing-based biodiversity assessment in complex communities
    • Zhan, A., Bailey, S. A., Heath, D. D. and Macisaac, H. J. (2014) Performance comparison of genetic markers for high-throughput sequencing-based biodiversity assessment in complex communities. Mol. Ecol. Resour., 14, 1049-1059.
    • (2014) Mol. Ecol. Resour. , vol.14 , pp. 1049-1059
    • Zhan, A.1    Bailey, S.A.2    Heath, D.D.3    Macisaac, H.J.4
  • 16
    • 84859333161 scopus 로고    scopus 로고
    • Coalescent-based DNA barcoding: Multilocus analysis and robustness
    • David, O., Laredo, C., Leblois, R., Schaeffer, B. and Vergne, N. (2012) Coalescent-based DNA barcoding: multilocus analysis and robustness. J. Comput. Biol., 19, 271-278.
    • (2012) J. Comput. Biol. , vol.19 , pp. 271-278
    • David, O.1    Laredo, C.2    Leblois, R.3    Schaeffer, B.4    Vergne, N.5
  • 17
    • 84885627471 scopus 로고    scopus 로고
    • Heuristic optimization for global species clustering of DNA sequence data from multiple loci
    • Chesters, D., Yu, F., Cao, H., Dai, Q., Wu, Q., Shi, W., Zheng, W. and Zhu, C. (2013) Heuristic optimization for global species clustering of DNA sequence data from multiple loci. Methods Ecol. Evol., 4, 961-970.
    • (2013) Methods Ecol. Evol. , vol.4 , pp. 961-970
    • Chesters, D.1    Yu, F.2    Cao, H.3    Dai, Q.4    Wu, Q.5    Shi, W.6    Zheng, W.7    Zhu, C.8
  • 18
    • 84860508725 scopus 로고    scopus 로고
    • Assessment of three mitochondrial genes (16S, Cytb, CO1) for identifying species in the Praomyini tribe (Rodentia: Muridae)
    • Nicolas, V., Schaeffer, B., Missoup, A. D., Kennis, J., Colyn, M., Denys, C., Tatard, C., Cruaud, C. and Laredo, C. (2012) Assessment of three mitochondrial genes (16S, Cytb, CO1) for identifying species in the Praomyini tribe (Rodentia: Muridae). PLoS One, 7, e36586.
    • (2012) PLoS One , vol.7 , pp. e36586
    • Nicolas, V.1    Schaeffer, B.2    Missoup, A.D.3    Kennis, J.4    Colyn, M.5    Denys, C.6    Tatard, C.7    Cruaud, C.8    Laredo, C.9
  • 19
    • 84899060897 scopus 로고    scopus 로고
    • Sequence analysis of mitochondrial ND1 gene can reveal the genetic structure and origin of Bactrocera dorsalis s.s
    • Wu, Z., Li, H., Bin, S., Ma, J., He, H., Li, X., Gong, F. and Lin, J. (2014) Sequence analysis of mitochondrial ND1 gene can reveal the genetic structure and origin of Bactrocera dorsalis s.s. BMC Evol. Biol., 14, 55.
    • (2014) BMC Evol. Biol. , vol.14 , pp. 55
    • Wu, Z.1    Li, H.2    Bin, S.3    Ma, J.4    He, H.5    Li, X.6    Gong, F.7    Lin, J.8
  • 20
    • 84884591564 scopus 로고    scopus 로고
    • Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae)
    • Botero-Castro, F., Tilak, M. K., Justy, F., Catzeflis, F., Delsuc, F. and Douzery, E. J. (2013) Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae). Mol. Phylogenet. Evol., 69, 728-739.
    • (2013) Mol. Phylogenet. Evol. , vol.69 , pp. 728-739
    • Botero-Castro, F.1    Tilak, M.K.2    Justy, F.3    Catzeflis, F.4    Delsuc, F.5    Douzery, E.J.6
  • 21
    • 84891906859 scopus 로고    scopus 로고
    • Insect mitochondrial genomics: Implications for evolution and phylogeny
    • Cameron, S. L. (2014) Insect mitochondrial genomics: implications for evolution and phylogeny. Annu. Rev. Entomol., 59, 95-117.
    • (2014) Annu. Rev. Entomol. , vol.59 , pp. 95-117
    • Cameron, S.L.1
  • 23
    • 84902684348 scopus 로고    scopus 로고
    • How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research
    • Cameron, S. L. (2014) How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research. Syst. Entomol., 39, 400-411.
    • (2014) Syst. Entomol. , vol.39 , pp. 400-411
    • Cameron, S.L.1
  • 24
    • 84887243551 scopus 로고    scopus 로고
    • The complete mitochondrial genome of a turbinid vetigastropod from MiSeq Illumina sequencing of genomic DNA and steps towards a resolved gastropod phylogeny
    • Williams, S., Foster, P. and Littlewood, D. (2014) The complete mitochondrial genome of a turbinid vetigastropod from MiSeq Illumina sequencing of genomic DNA and steps towards a resolved gastropod phylogeny. Gene, 533, 38-47.
    • (2014) Gene , vol.533 , pp. 38-47
    • Williams, S.1    Foster, P.2    Littlewood, D.3
  • 25
    • 84858710282 scopus 로고    scopus 로고
    • The complete mitogenome of Cylindrus obtusus (Helicidae, Ariantinae) using Illumina next generation sequencing
    • Groenenberg, D. S., Pirovano, W., Gittenberger, E. and Schilthuizen, M. (2012) The complete mitogenome of Cylindrus obtusus (Helicidae, Ariantinae) using Illumina next generation sequencing. BMC Genomics, 13, 114.
    • (2012) BMC Genomics , vol.13 , pp. 114
    • Groenenberg, D.S.1    Pirovano, W.2    Gittenberger, E.3    Schilthuizen, M.4
  • 26
    • 84855845962 scopus 로고    scopus 로고
    • Rapid sequencing of the bamboo mitochondrial genome using Illumina technology and parallel episodic evolution of organelle genomes in grasses
    • Ma, P., Guo, Z. and Li, D. (2012) Rapid sequencing of the bamboo mitochondrial genome using Illumina technology and parallel episodic evolution of organelle genomes in grasses. PLoS One, 7, e30297.
    • (2012) PLoS One , vol.7 , pp. e30297
    • Ma, P.1    Guo, Z.2    Li, D.3
  • 27
    • 84880527958 scopus 로고    scopus 로고
    • Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads-a baiting and iterative mapping approach
    • Hahn, C., Bachmann, L. and Chevreux, B. (2013) Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads-a baiting and iterative mapping approach. Nucleic Acids Res., 41, e129-e129.
    • (2013) Nucleic Acids Res. , vol.41 , pp. e129-e129
    • Hahn, C.1    Bachmann, L.2    Chevreux, B.3
  • 29
    • 84871314939 scopus 로고    scopus 로고
    • Conveniently pre-tagged and pre-packaged: Extended molecular identification and metagenomics using complete metazoan mitochondrial genomes
    • Dettai, A., Gallut, C., Brouillet, S., Pothier, J., Le COintre, G. and Debruyne, R. (2012) Conveniently pre-tagged and pre-packaged: extended molecular identification and metagenomics using complete metazoan mitochondrial genomes. PLoS One, 7, e51263.
    • (2012) PLoS One , vol.7 , pp. e51263
    • Dettai, A.1    Gallut, C.2    Brouillet, S.3    Pothier, J.4    Cointre, G.5    Debruyne, R.6
  • 30
    • 33751313616 scopus 로고    scopus 로고
    • An inexpensive, automation-friendly protocol for recovering high-quality DNA
    • Ivanova, N. V., Dewaard, J. R. and Hebert, P. D. (2006) An inexpensive, automation-friendly protocol for recovering high-quality DNA. Mol. Ecol. Notes, 6, 998-1002.
    • (2006) Mol. Ecol. Notes , vol.6 , pp. 998-1002
    • Ivanova, N.V.1    Dewaard, J.R.2    Hebert, P.D.3
  • 31
    • 84942887758 scopus 로고    scopus 로고
    • SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler
    • Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Y. et al. (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience, 1, 18.
    • (2012) Gigascience , vol.1 , pp. 18
    • Luo, R.1    Liu, B.2    Xie, Y.3    Li, Z.4    Huang, W.5    Yuan, J.6    He, G.7    Chen, Y.8    Pan, Q.9    Liu, Y.10
  • 34
    • 84861760530 scopus 로고    scopus 로고
    • IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
    • Peng, Y., Leung, H. C., Yiu, S. M. and Chin, F. Y. (2012) IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics, 28, 1420-1428.
    • (2012) Bioinformatics , vol.28 , pp. 1420-1428
    • Peng, Y.1    Leung, H.C.2    Yiu, S.M.3    Chin, F.Y.4
  • 37
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J. D., Higgins, D. G. and Gibson, T. J. (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.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 38
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol., 28, 2731-2739.
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5    Kumar, S.6
  • 39
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 41
    • 84865591846 scopus 로고    scopus 로고
    • A tale of three next generation sequencing platforms: Comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers
    • Quail, M. A., Smith, M., Coupland, P., Otto, T. D., Harris, S. R., Connor, T. R., Bertoni, A., Swerdlow, H. P. and Gu, Y. (2012) A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics, 13, 341.
    • (2012) BMC Genomics , vol.13 , pp. 341
    • Quail, M.A.1    Smith, M.2    Coupland, P.3    Otto, T.D.4    Harris, S.R.5    Connor, T.R.6    Bertoni, A.7    Swerdlow, H.P.8    Gu, Y.9


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.