메뉴 건너뛰기




Volumn 8, Issue 4, 2013, Pages

Parallel Tagged Next-Generation Sequencing on Pooled Samples - A New Approach for Population Genetics in Ecology and Conservation

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE;

EID: 84876308901     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0061471     Document Type: Article
Times cited : (7)

References (36)
  • 1
    • 65449162673 scopus 로고    scopus 로고
    • Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing
    • Abdelkrim J, Robertson BC, Stanton J-AL, Gemmell NJ, (2009) Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing. Biotechniques 46: 185-192.
    • (2009) Biotechniques , vol.46 , pp. 185-192
    • Abdelkrim, J.1    Robertson, B.C.2    Stanton, J.-A.L.3    Gemmell, N.J.4
  • 3
    • 84856619292 scopus 로고    scopus 로고
    • A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses
    • Goto H, Ryder OA, Fisher AR, Schultz B, KosakovskyPond SL, et al. (2011) A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses. Genome Biology and Evolution 3: 1096-1106.
    • (2011) Genome Biology and Evolution , vol.3 , pp. 1096-1106
    • Goto, H.1    Ryder, O.A.2    Fisher, A.R.3    Schultz, B.4    KosakovskyPond, S.L.5
  • 4
    • 79954599493 scopus 로고    scopus 로고
    • Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore
    • article 10
    • Knaus BJ, Cronn R, Liston A, Pilgrim K, Schwartz MK (2011) Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore. BMC Ecology 11: article 10.
    • (2011) BMC Ecology , vol.11
    • Knaus, B.J.1    Cronn, R.2    Liston, A.3    Pilgrim, K.4    Schwartz, M.K.5
  • 5
    • 79957800445 scopus 로고    scopus 로고
    • Characterization of the transcriptome of a wild great tit Parus major population by next generation sequencing
    • article 283
    • Santure AW, Gratten J, Mossman JA, Sheldon BC, Slate J (2011) Characterization of the transcriptome of a wild great tit Parus major population by next generation sequencing. BMC Genomics 12: article 283.
    • (2011) BMC Genomics , vol.12
    • Santure, A.W.1    Gratten, J.2    Mossman, J.A.3    Sheldon, B.C.4    Slate, J.5
  • 6
    • 84856420280 scopus 로고    scopus 로고
    • De novo transcriptome assembly and polymorphism detection in the flowering plant Silene vulgaris (Caryophyllaceae)
    • Sloan DB, Keller SR, Berardi AE, Sanderson BJ, Karpovich JF, et al. (2012) De novo transcriptome assembly and polymorphism detection in the flowering plant Silene vulgaris (Caryophyllaceae). Molecular Ecology Resources 12: 333-343.
    • (2012) Molecular Ecology Resources , vol.12 , pp. 333-343
    • Sloan, D.B.1    Keller, S.R.2    Berardi, A.E.3    Sanderson, B.J.4    Karpovich, J.F.5
  • 7
    • 77951973196 scopus 로고    scopus 로고
    • A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies
    • Galan M, Guivier E, Caraux G, Charbonnel N, Cosson J-F, (2010) A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies. BMC Genomics 11: 296.
    • (2010) BMC Genomics , vol.11 , pp. 296
    • Galan, M.1    Guivier, E.2    Caraux, G.3    Charbonnel, N.4    Cosson, J.-F.5
  • 8
    • 34547834963 scopus 로고    scopus 로고
    • The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing
    • Binladen J, Gilbert MTP, Bollback JP, Panitz F, Bendixen C, et al. (2007) The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS ONE 2: e197.
    • (2007) PLoS ONE , vol.2
    • Binladen, J.1    Gilbert, M.T.P.2    Bollback, J.P.3    Panitz, F.4    Bendixen, C.5
  • 9
    • 39449089394 scopus 로고    scopus 로고
    • Parallel tagged sequencing on the 454 platform
    • Meyer M, Stenzel U, Hofreiter M, (2008) Parallel tagged sequencing on the 454 platform. Nature Protocols 3: 267-278.
    • (2008) Nature Protocols , vol.3 , pp. 267-278
    • Meyer, M.1    Stenzel, U.2    Hofreiter, M.3
  • 10
    • 82955249064 scopus 로고    scopus 로고
    • Gene conversion rapidly generates major histocompatibility complex diversity in recently founded bird populations
    • Spurgin LG, van Oosterhout C, Illera JC, Bridgett S, Gharbi K, et al. (2011) Gene conversion rapidly generates major histocompatibility complex diversity in recently founded bird populations. Molecular Ecology 20: 5213-5225.
    • (2011) Molecular Ecology , vol.20 , pp. 5213-5225
    • Spurgin, L.G.1    van Oosterhout, C.2    Illera, J.C.3    Bridgett, S.4    Gharbi, K.5
  • 11
    • 84861480746 scopus 로고    scopus 로고
    • Differentiated population structure of a genetically depauperate mangrove species Ceriops tagal revealed by both Sanger and deep sequencing
    • Huang Y, Zhu C, Li X, Li X, Hu L, et al. (2012) Differentiated population structure of a genetically depauperate mangrove species Ceriops tagal revealed by both Sanger and deep sequencing. Aquatic Botany 101: 46-54.
    • (2012) Aquatic Botany , vol.101 , pp. 46-54
    • Huang, Y.1    Zhu, C.2    Li, X.3    Li, X.4    Hu, L.5
  • 12
    • 78751665708 scopus 로고    scopus 로고
    • The next generation of molecular markers from massively parallel sequencing of pooled DNA samples
    • Futschik A, Schlötterer C, (2010) The next generation of molecular markers from massively parallel sequencing of pooled DNA samples. Genetics 186: 207-218.
    • (2010) Genetics , vol.186 , pp. 207-218
    • Futschik, A.1    Schlötterer, C.2
  • 13
    • 77951702343 scopus 로고    scopus 로고
    • Genetic heterogeneity in human disease
    • McClellan J, King M-C, (2010) Genetic heterogeneity in human disease. Cell 141: 210-217.
    • (2010) Cell , vol.141 , pp. 210-217
    • McClellan, J.1    King, M.-C.2
  • 14
    • 54249110308 scopus 로고    scopus 로고
    • Evaluation of human gene variant detection in amplicon pools by the GC-FLX parallel pyrosequencer
    • article 464
    • Bordoni R, Bonnal R, Rizzi E, Carrera P, Benedetti S, et al. (2008) Evaluation of human gene variant detection in amplicon pools by the GC-FLX parallel pyrosequencer. BMC Genomics 9: article 464.
    • (2008) BMC Genomics , vol.9
    • Bordoni, R.1    Bonnal, R.2    Rizzi, E.3    Carrera, P.4    Benedetti, S.5
  • 17
    • 84867007629 scopus 로고    scopus 로고
    • Estimating allele frequency from next-generation sequencing of pooled mitochondrial DNA samples
    • article 51
    • Wang T, Pradhan K, Ye K, Wong LJ, Rohan TE (2011) Estimating allele frequency from next-generation sequencing of pooled mitochondrial DNA samples. Frontiers in Genetics 2: article 51.
    • (2011) Frontiers in Genetics , vol.2
    • Wang, T.1    Pradhan, K.2    Ye, K.3    Wong, L.J.4    Rohan, T.E.5
  • 18
    • 79960220058 scopus 로고    scopus 로고
    • Amplicon-based high-throughput pooled sequencing identifies mutations in CYP7B1 and SPG7 in sporadic spastic paraplegia patients
    • Schlipf NA, Schüle R, Klimpe S, Karle KN, Synofzik M, et al. (2011) Amplicon-based high-throughput pooled sequencing identifies mutations in CYP7B1 and SPG7 in sporadic spastic paraplegia patients. Clinical Genetics 80: 148-160.
    • (2011) Clinical Genetics , vol.80 , pp. 148-160
    • Schlipf, N.A.1    Schüle, R.2    Klimpe, S.3    Karle, K.N.4    Synofzik, M.5
  • 19
    • 80955151523 scopus 로고    scopus 로고
    • Discovery of polymorphisms in starch-related genes in rice germplasm by amplification of pooled DNA and deeply parallel sequencing
    • Kharabian-Masouleh A, Waters DLE, Reinke RF, Henry RJ, (2011) Discovery of polymorphisms in starch-related genes in rice germplasm by amplification of pooled DNA and deeply parallel sequencing. Plant Biotechnology Journal 9: 1074-1085.
    • (2011) Plant Biotechnology Journal , vol.9 , pp. 1074-1085
    • Kharabian-Masouleh, A.1    Waters, D.L.E.2    Reinke, R.F.3    Henry, R.J.4
  • 20
    • 80051668334 scopus 로고    scopus 로고
    • Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation Ecotilling
    • Marroni F, Pinosio S, Di Centa E, Jurman I, Boerjan W, et al. (2011) Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation Ecotilling. The Plant Journal 67: 736-745.
    • (2011) The Plant Journal , vol.67 , pp. 736-745
    • Marroni, F.1    Pinosio, S.2    Di Centa, E.3    Jurman, I.4    Boerjan, W.5
  • 21
    • 84860524333 scopus 로고    scopus 로고
    • RNA-Seq identifies SNP markers for growth traits in rainbow trout
    • Salem M, Vallejo RL, Leeds TD, Palti Y, Liu SX, et al. (2012) RNA-Seq identifies SNP markers for growth traits in rainbow trout. PLoS ONE 7: e36264.
    • (2012) PLoS ONE , vol.7
    • Salem, M.1    Vallejo, R.L.2    Leeds, T.D.3    Palti, Y.4    Liu, S.X.5
  • 22
    • 84859613736 scopus 로고    scopus 로고
    • Ecological Genomics of Anopheles gambiae along a latitudinal cline: a population-resequencing approach
    • Cheng C, White BJ, Kamdem C, Mockaitis K, Costantini C, et al. (2012) Ecological Genomics of Anopheles gambiae along a latitudinal cline: a population-resequencing approach. Genetics 190: 1417-1432.
    • (2012) Genetics , vol.190 , pp. 1417-1432
    • Cheng, C.1    White, B.J.2    Kamdem, C.3    Mockaitis, K.4    Costantini, C.5
  • 23
    • 0035544509 scopus 로고    scopus 로고
    • Adaptive evolutionary conservation: towards a unified concept for defining conservation units
    • Fraser DJ, Bernatchez L, (2001) Adaptive evolutionary conservation: towards a unified concept for defining conservation units. Molecular Ecology 10: 2741-2752.
    • (2001) Molecular Ecology , vol.10 , pp. 2741-2752
    • Fraser, D.J.1    Bernatchez, L.2
  • 24
    • 77952879875 scopus 로고    scopus 로고
    • Phylogeography of Leiopelma hochstetteri reveals strong genetic structure and suggests new conservation priorities
    • Fouquet A, Green DM, Waldman B, Bowsher JH, McBride KP, et al. (2010) Phylogeography of Leiopelma hochstetteri reveals strong genetic structure and suggests new conservation priorities. Conservation Genetics 11: 907-919.
    • (2010) Conservation Genetics , vol.11 , pp. 907-919
    • Fouquet, A.1    Green, D.M.2    Waldman, B.3    Bowsher, J.H.4    McBride, K.P.5
  • 25
    • 65649117685 scopus 로고    scopus 로고
    • DnaSP v5: a software for comprehensive analysis of DNA polymorphism data
    • Librado P, Rozas J, (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
    • (2009) Bioinformatics , vol.25 , pp. 1451-1452
    • Librado, P.1    Rozas, J.2
  • 26
    • 0026709389 scopus 로고
    • Estimation of levels of gene flow from DNA sequence data
    • Hudson RR, Slatkin M, Maddison WP, (1992) Estimation of levels of gene flow from DNA sequence data. Genetics 132: 583-589.
    • (1992) Genetics , vol.132 , pp. 583-589
    • Hudson, R.R.1    Slatkin, M.2    Maddison, W.P.3
  • 27
    • 85007110786 scopus 로고    scopus 로고
    • Arlequin ver. 3.0: an integrated software package for population genetics data analysis
    • Excoffier L, Laval G, Schneider S, (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1: 4.
    • (2005) Evolutionary Bioinformatics Online , vol.1 , pp. 4
    • Excoffier, L.1    Laval, G.2    Schneider, S.3
  • 28
    • 84890417804 scopus 로고
    • The genetical structure of populations
    • Wright S, (1951) The genetical structure of populations. Annals of Eugenics 15: 323-354.
    • (1951) Annals of Eugenics , vol.15 , pp. 323-354
    • Wright, S.1
  • 29
    • 0000862605 scopus 로고
    • The interpretation of population structure by F-statistics with special regards to systems of mating
    • Wright S, (1965) The interpretation of population structure by F-statistics with special regards to systems of mating. Evolution 19: 395-420.
    • (1965) Evolution , vol.19 , pp. 395-420
    • Wright, S.1
  • 31
    • 0028151986 scopus 로고
    • Defining 'Evolutionarily Significant Units' for conservation
    • Moritz C, (1994) Defining 'Evolutionarily Significant Units' for conservation. Trends in Ecology and Evolution 9: 373-375.
    • (1994) Trends in Ecology and Evolution , vol.9 , pp. 373-375
    • Moritz, C.1
  • 32
    • 79961135005 scopus 로고    scopus 로고
    • R Core Development Team, version 2.12.2. Vienna: R Foundation for Statistical Computing. Available at
    • R Core Development Team (2011) R: A language and environment for statistical computing, version 2.12.2. Vienna: R Foundation for Statistical Computing. Available at http://cran.r-project.org/.
    • (2011) R: A language and environment for statistical computing
  • 33
    • 0035153070 scopus 로고    scopus 로고
    • Pyrosequencing sheds light on DNA sequencing
    • Ronaghi M, (2001) Pyrosequencing sheds light on DNA sequencing. Genome Research 11: 3-11.
    • (2001) Genome Research , vol.11 , pp. 3-11
    • Ronaghi, M.1
  • 34
    • 40149098690 scopus 로고    scopus 로고
    • SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries
    • Van Tassel CP, Smith TPL, Matukumalli LK, Taylor JF, Schnabel RD, et al. (2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nature Methods 5: 247-252.
    • (2008) Nature Methods , vol.5 , pp. 247-252
    • Van Tassel, C.P.1    Smith, T.P.L.2    Matukumalli, L.K.3    Taylor, J.F.4    Schnabel, R.D.5
  • 35
    • 34547781750 scopus 로고    scopus 로고
    • MEGA 4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4
    • Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA 4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4. Molecular Biology and Evolution 24: 1596-1599.
    • (2007) Molecular Biology and Evolution , vol.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 36
    • 0005604114 scopus 로고    scopus 로고
    • Determining the species status of one of the world's rarest frogs: a conservation dilemma
    • Holyoake A, Waldman B, Gemmell NJ, (2001) Determining the species status of one of the world's rarest frogs: a conservation dilemma. Animal Conservation 4: 29-35.
    • (2001) Animal Conservation , vol.4 , pp. 29-35
    • Holyoake, A.1    Waldman, B.2    Gemmell, N.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.