메뉴 건너뛰기




Volumn 12, Issue 5, 2012, Pages 834-845

Reference-free transcriptome assembly in non-model animals from next-generation sequencing data

Author keywords

Alleles; Next generation sequencing; Paralogues; Transcriptomics

Indexed keywords

TRANSCRIPTOME;

EID: 84865300368     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2012.03148.x     Document Type: Article
Times cited : (117)

References (38)
  • 1
    • 78349238864 scopus 로고    scopus 로고
    • Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies
    • Boisvert S, Laviolette F, Corbeil J (2010) Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. Journal of Computational Biology, 17, 1519-1533.
    • (2010) Journal of Computational Biology , vol.17 , pp. 1519-1533
    • Boisvert, S.1    Laviolette, F.2    Corbeil, J.3
  • 3
    • 78649997118 scopus 로고    scopus 로고
    • Speciation in the European rabbit (Oryctolagus cuniculus): islands of differentiation on the X chromosome and autosomes
    • Carneiro M, Blanco-Aguiar JA, Villafuerte R, Ferrand N, Nachman MW (2010) Speciation in the European rabbit (Oryctolagus cuniculus): islands of differentiation on the X chromosome and autosomes. Evolution, 64, 3443-3460.
    • (2010) Evolution , vol.64 , pp. 3443-3460
    • Carneiro, M.1    Blanco-Aguiar, J.A.2    Villafuerte, R.3    Ferrand, N.4    Nachman, M.W.5
  • 4
    • 78651249577 scopus 로고    scopus 로고
    • De novo analysis of transcriptome dynamics in the migratory locust during the development of phase trait
    • Chen S, Yang P, Jiang F, Wei Y, Ma Z, Kang L (2010) De novo analysis of transcriptome dynamics in the migratory locust during the development of phase trait. PLoS ONE, 5, e15633.
    • (2010) PLoS ONE , vol.5
    • Chen, S.1    Yang, P.2    Jiang, F.3    Wei, Y.4    Ma, Z.5    Kang, L.6
  • 5
    • 3042615882 scopus 로고    scopus 로고
    • Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs
    • Chevreux B, Pfisterer T, Drescher B et al. (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Research, 14, 1147-1159.
    • (2004) Genome Research , vol.14 , pp. 1147-1159
    • Chevreux, B.1    Pfisterer, T.2    Drescher, B.3
  • 6
    • 78650911200 scopus 로고    scopus 로고
    • RNA extraction from sauropsids blood: evaluation and improvement of methods
    • Chiari Y, Galtier N (2011) RNA extraction from sauropsids blood: evaluation and improvement of methods. Amphibia-Reptilia, 32, 136-139.
    • (2011) Amphibia-Reptilia , vol.32 , pp. 136-139
    • Chiari, Y.1    Galtier, N.2
  • 7
    • 77951916371 scopus 로고    scopus 로고
    • Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes
    • Elmer KR, Fan S, Gunter HM et al. (2010) Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes. Molecular Ecology, 19, 197-211.
    • (2010) Molecular Ecology , vol.19 , pp. 197-211
    • Elmer, K.R.1    Fan, S.2    Gunter, H.M.3
  • 9
    • 79960264362 scopus 로고    scopus 로고
    • Full-length transcriptome assembly from RNA-Seq data without a reference genome
    • Grabherr MG, Haas BJ, Yassour M et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29, 644-652.
    • (2011) Nature Biotechnology , vol.29 , pp. 644-652
    • Grabherr, M.G.1    Haas, B.J.2    Yassour, M.3
  • 10
    • 77953600890 scopus 로고    scopus 로고
    • Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types
    • Guo S, Zheng Y, Joung JG et al. (2010) Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genomics, 11, 384.
    • (2010) BMC Genomics , vol.11 , pp. 384
    • Guo, S.1    Zheng, Y.2    Joung, J.G.3
  • 11
    • 0032849859 scopus 로고    scopus 로고
    • CAP3: a DNA sequence assembly program
    • Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Research, 9, 868-877.
    • (1999) Genome Research , vol.9 , pp. 868-877
    • Huang, X.1    Madan, A.2
  • 12
    • 36849073678 scopus 로고    scopus 로고
    • Sequencing breakthroughs for genomic ecology and evolutionary biology
    • Hudson ME (2008) Sequencing breakthroughs for genomic ecology and evolutionary biology. Molecular Ecology Resources, 8, 3-17.
    • (2008) Molecular Ecology Resources , vol.8 , pp. 3-17
    • Hudson, M.E.1
  • 13
    • 34547922775 scopus 로고    scopus 로고
    • Mitogenomics reveals two cryptic species in Ciona intestinalis
    • Iannelli F, Pesole G, Sordino P, Gissi C (2007) Mitogenomics reveals two cryptic species in Ciona intestinalis. Trends in Genetics, 9, 419-422.
    • (2007) Trends in Genetics , vol.9 , pp. 419-422
    • Iannelli, F.1    Pesole, G.2    Sordino, P.3    Gissi, C.4
  • 14
    • 77957926979 scopus 로고    scopus 로고
    • Comparing de novo assemblers for 454 transcriptome data
    • Kumar S, Blaxter ML (2010) Comparing de novo assemblers for 454 transcriptome data. BMC Genomics, 11, 571.
    • (2010) BMC Genomics , vol.11 , pp. 571
    • Kumar, S.1    Blaxter, M.L.2
  • 15
    • 77951918115 scopus 로고    scopus 로고
    • Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species
    • Künstner A, Wolf JB, Backström N et al. (2010) Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Molecular Ecology, 19, 266-276.
    • (2010) Molecular Ecology , vol.19 , pp. 266-276
    • Künstner, A.1    Wolf, J.B.2    Backström, N.3
  • 16
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10, R25.
    • (2009) Genome Biology , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 17
    • 75649124547 scopus 로고    scopus 로고
    • De novo assembly of human genomes with massively parallel short read sequencing
    • Li R, Zhu H, Ruan J et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Research, 20, 265-272.
    • (2010) Genome Research , vol.20 , pp. 265-272
    • Li, R.1    Zhu, H.2    Ruan, J.3
  • 18
    • 76949092432 scopus 로고    scopus 로고
    • Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans
    • Maydan JS, Lorch A, Edgley ML, Flibotte S, Moerman DG (2010) Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans. BMC Genomics, 11, 62.
    • (2010) BMC Genomics , vol.11 , pp. 62
    • Maydan, J.S.1    Lorch, A.2    Edgley, M.L.3    Flibotte, S.4    Moerman, D.G.5
  • 19
    • 0034708758 scopus 로고    scopus 로고
    • A whole-genome assembly of Drosophila
    • Myers EW, Sutton GG, Delcher AL et al. (2000) A whole-genome assembly of Drosophila. Science, 287, 2196-2204.
    • (2000) Science , vol.287 , pp. 2196-2204
    • Myers, E.W.1    Sutton, G.G.2    Delcher, A.L.3
  • 23
    • 77951894310 scopus 로고    scopus 로고
    • Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery
    • Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA (2010) Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics, 11, 180.
    • (2010) BMC Genomics , vol.11 , pp. 180
    • Parchman, T.L.1    Geist, K.S.2    Grahnen, J.A.3    Benkman, C.W.4    Buerkle, C.A.5
  • 25
    • 77951936990 scopus 로고    scopus 로고
    • Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae)
    • Renaut S, Nolte AW, Bernatchez L (2010) Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae). Molecular Ecology, 19, 115-131.
    • (2010) Molecular Ecology , vol.19 , pp. 115-131
    • Renaut, S.1    Nolte, A.W.2    Bernatchez, L.3
  • 26
    • 78049346632 scopus 로고    scopus 로고
    • De novo assembly and analysis of RNA-seq data
    • Robertson G, Schein J, Chiu R et al. (2010) De novo assembly and analysis of RNA-seq data. Nature Methods, 7, 909-912.
    • (2010) Nature Methods , vol.7 , pp. 909-912
    • Robertson, G.1    Schein, J.2    Chiu, R.3
  • 27
    • 70349208979 scopus 로고    scopus 로고
    • Complete alternative splicing events are bubbles in splicing graphs
    • Sammeth M (2009) Complete alternative splicing events are bubbles in splicing graphs. Journal of Computational Biology, 16, 1117-1140.
    • (2009) Journal of Computational Biology , vol.16 , pp. 1117-1140
    • Sammeth, M.1
  • 28
    • 77954978906 scopus 로고    scopus 로고
    • Copy number changes of CNV regions in intersubspecific crosses of the house mouse
    • Scavetta RJ, Tautz D (2010) Copy number changes of CNV regions in intersubspecific crosses of the house mouse. Molecular Biology and Evolution, 27, 1845-1856.
    • (2010) Molecular Biology and Evolution , vol.27 , pp. 1845-1856
    • Scavetta, R.J.1    Tautz, D.2
  • 29
    • 78649734757 scopus 로고    scopus 로고
    • A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences
    • Schwartz TS, Tae H, Yang Y et al. (2010) A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences. BMC Genomics, 11, 694.
    • (2010) BMC Genomics , vol.11 , pp. 694
    • Schwartz, T.S.1    Tae, H.2    Yang, Y.3
  • 30
    • 74549161429 scopus 로고    scopus 로고
    • Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella
    • Schwarz D, Robertson HM, Feder JL et al. (2009) Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella. BMC Genomics, 10, 633.
    • (2009) BMC Genomics , vol.10 , pp. 633
    • Schwarz, D.1    Robertson, H.M.2    Feder, J.L.3
  • 33
    • 78649294100 scopus 로고    scopus 로고
    • Optimization of de novo transcriptome assembly from next-generation sequencing data
    • Surget-Groba Y, Montoya-Burgos J (2010) Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Research, 20, 1432-1440.
    • (2010) Genome Research , vol.20 , pp. 1432-1440
    • Surget-Groba, Y.1    Montoya-Burgos, J.2
  • 34
    • 41149167170 scopus 로고    scopus 로고
    • Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing
    • Vera JC, Wheat CW, Fescemyer HW et al. (2008) Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Molecular Ecology, 17, 1636-1647.
    • (2008) Molecular Ecology , vol.17 , pp. 1636-1647
    • Vera, J.C.1    Wheat, C.W.2    Fescemyer, H.W.3
  • 35
    • 69449099392 scopus 로고    scopus 로고
    • Comparison of next generation sequencing technologies for transcriptome characterization
    • Wall PK, Leebens-Mack J, Chanderbali AS et al. (2009) Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics, 10, 347.
    • (2009) BMC Genomics , vol.10 , pp. 347
    • Wall, P.K.1    Leebens-Mack, J.2    Chanderbali, A.S.3
  • 36
    • 78449277186 scopus 로고    scopus 로고
    • Extremely high molecular diversity within the East Asian nematode Caenorhabditis sp. 5
    • Wang GX, Ren S, Ren Y, Ai H, Cutter AD (2010a) Extremely high molecular diversity within the East Asian nematode Caenorhabditis sp. 5. Molecular Ecology, 19, 5022-5029.
    • (2010) Molecular Ecology , vol.19 , pp. 5022-5029
    • Wang, G.X.1    Ren, S.2    Ren, Y.3    Ai, H.4    Cutter, A.D.5
  • 38
    • 77951917823 scopus 로고    scopus 로고
    • Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow
    • Wolf JB, Bayer T, Haubold B, Schilhabel M, Rosenstiel P, Tautz D (2010) Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow. Molecular Ecology, 19, 162-175.
    • (2010) Molecular Ecology , vol.19 , pp. 162-175
    • Wolf, J.B.1    Bayer, T.2    Haubold, B.3    Schilhabel, M.4    Rosenstiel, P.5    Tautz, D.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.