三代测序PacBio在转录组研究中的应用
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摘要
本文介绍了PacBio测序在转录组学研究中的一些应用及PacBio测序数据分析常用的方法流程,根据PacBio测序的发展综述了PacBio测序经常遇到的一些问题及相应解决方案,并就PacBio测序技术所面临的挑战和未来的发展进行讨论.
Some applications of PacBio sequencing in transcriptome study and the commonly used methods of PacBio sequencing data analysis are introduced. According to the development of PacBio sequencing,the problems and corresponding solutions of PacBio sequencing are reviewed. The challenges and future development of PacBio sequencing technology are also discussed.
Some applications of PacBio sequencing in transcriptome study and the commonly used methods of PacBio sequencing data analysis are introduced. According to the development of PacBio sequencing,the problems and corresponding solutions of PacBio sequencing are reviewed. The challenges and future development of PacBio sequencing technology are also discussed.
引文
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[9]WANG B,TSENG E,REGULSKI M,et al. Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing[J]. Nature Communications,2016,7:11 708.
[10]ABDEL-GHANY S E,MICHAEL H,JACOBI J L,et al. A survey of the sorghum transcriptome using single-molecule long reads[J]. Nature Communications,2016,7:11 706.
[11]HOANG N V,FURTADO A,MASON P J,et al. A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing[J]. BMC Genomics,2017,18(1):395-416.
[12]NING G,CHENG X,LUO P,et al. Hybrid sequencing and map finding(Hy Se MaFi):optional strategies for extensively deciphering gene splicing and expression in organisms without reference genome[J]. Scientific Reports,2017,7:43 793.
[13]WANG T,WANG H,CAI D,et al. Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation in moso bamboo(Phyllostachys edulis)[J]. Plant Journal for Cell&Molecular Biology,2017,91(4):684-699
[14]GAO S,REN Y,SUN Y,et al. PacBio full-length transcriptome profiling of insect mitochondrial gene expression[J]. RNA Biology,2016,13(9):820-825.
[15]BARBAZUK W B,FU Y,MCGINNIS K M. Genome-wide analyses of alternative splicing in plants:opportunities and challenges[J]. Genome Research,2008,18(9):1 381-1 392.
[16]CHEN L,AL E. Alternative splicing:a potential source of functional innovation in the eukaryotic genome[J/OL]. International Journal of Evolutionary Biology,(2012-07-2)[2012-04-19].http://dx.doi.org/10.1155/2012/596274.
[17]KORNBLIHTT A R,SCHOR I E,ALLO M,et al. Alternative splicing:a pivotal step between eukaryotic transcription and translation[J]. Nature Reviews Molecular Cell Biology,2013,14(3):153-165.
[18]KALSOTRA A,COOPER T A. Functional consequences of developmentally regulated alternative splicing[J]. Nature Reviews Genetics,2011,12(10):715-729.
[19]SEO P J,PARK M J,PARK C M. Alternative splicing of transcription factors in plant responses to low temperature stress:mechanisms and functions[J]. Planta,2013,237(6):1 415-1 424.
[20]SCHMUCKER D,CLEMENS J C,SHU H,et al. Drosophila dscam is an axon guidance receptor exhibiting extraordinary molecular diversity[J]. Cell,2000,101(6):671-684.
[21]SHERSTNEV A,DUC C,COLE C,et al. Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation[J]. Nature Structural&Molecular Biology,2012,19(8):845-852.
[22]NAM D K,LEE S,ZHOU G,et al. Oligo(d T)primer generates a high frequency of truncated c DNAs through internal poly(A)priming during reverse transcription[J]. Proceedings of the National Academy of Sciences of the United States of America,2002,99(9):6 152-6 156.
[23]AU K F,JIANG H,LIN L,et al. Detection of splice junctions from paired-end RNA-seq data by Splice Map[J]. Nucleic Acids Research,2010,38(14):4 570-4 578.
[24]AU K F,UNDERWOOD J G,LEE L,et al. Improving PacBio long read accuracy by short read alignment[J]. Plos One,2012,7(10):e46 679.
[2]WANG Z,GERSTEIN M,SNYDER M. RNA-Seq:a revolutionary tool for transcriptomics[J]. Nat Rev Genet,2009,10(1):57-63.
[3]MCCARTHY A. Third generation DNA sequencing:pacific biosciences'single molecule real time technology[J]. Chemistry&Biology,2010,17(7):675-676.
[4]AU K F,SEBASTIANO V,AFSHAR P T,et al. Characterization of the human ESC transcriptome by hybrid sequencing[J].Proceedings of the National Academy of Sciences,2013,110(50):4821-4830.
[5]XU Z,PETERS R J,WEIRATHER J,et al. Full-length transcriptome sequences and splice variants obtained by a combination of sequencing platforms applied to different root tissues of Salvia miltiorrhiza and tanshinone biosynthesis[J]. Plant Journal for Cell&Molecular Biology,2015,82(6):951-961.
[6]LARSEN P A,SMITH T P L. Application of circular consensus sequencing and network analysis to characterize the bovine Ig G repertoire[J/OL]. BMC Immunology,2012,13(1).http://www.biomedcentral.com/1471-2172/13/52.
[7]TREUTEIN B,GOKCE O,QUAKE S R,et al. Cartography of neurexin alternative splicing mapped by single-molecule longread mRNA sequencing[J]. Proceedings of the National Academy of Sciences of the United States of America,2014,111(13):1 291-1 299.
[8]OCWIEJA K E,SHERRILLMIX S,MUKHERJEE R,et al. Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing[J]. Nucleic Acids Research,2012,40(20):10 345-10 355.
[9]WANG B,TSENG E,REGULSKI M,et al. Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing[J]. Nature Communications,2016,7:11 708.
[10]ABDEL-GHANY S E,MICHAEL H,JACOBI J L,et al. A survey of the sorghum transcriptome using single-molecule long reads[J]. Nature Communications,2016,7:11 706.
[11]HOANG N V,FURTADO A,MASON P J,et al. A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing[J]. BMC Genomics,2017,18(1):395-416.
[12]NING G,CHENG X,LUO P,et al. Hybrid sequencing and map finding(Hy Se MaFi):optional strategies for extensively deciphering gene splicing and expression in organisms without reference genome[J]. Scientific Reports,2017,7:43 793.
[13]WANG T,WANG H,CAI D,et al. Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation in moso bamboo(Phyllostachys edulis)[J]. Plant Journal for Cell&Molecular Biology,2017,91(4):684-699
[14]GAO S,REN Y,SUN Y,et al. PacBio full-length transcriptome profiling of insect mitochondrial gene expression[J]. RNA Biology,2016,13(9):820-825.
[15]BARBAZUK W B,FU Y,MCGINNIS K M. Genome-wide analyses of alternative splicing in plants:opportunities and challenges[J]. Genome Research,2008,18(9):1 381-1 392.
[16]CHEN L,AL E. Alternative splicing:a potential source of functional innovation in the eukaryotic genome[J/OL]. International Journal of Evolutionary Biology,(2012-07-2)[2012-04-19].http://dx.doi.org/10.1155/2012/596274.
[17]KORNBLIHTT A R,SCHOR I E,ALLO M,et al. Alternative splicing:a pivotal step between eukaryotic transcription and translation[J]. Nature Reviews Molecular Cell Biology,2013,14(3):153-165.
[18]KALSOTRA A,COOPER T A. Functional consequences of developmentally regulated alternative splicing[J]. Nature Reviews Genetics,2011,12(10):715-729.
[19]SEO P J,PARK M J,PARK C M. Alternative splicing of transcription factors in plant responses to low temperature stress:mechanisms and functions[J]. Planta,2013,237(6):1 415-1 424.
[20]SCHMUCKER D,CLEMENS J C,SHU H,et al. Drosophila dscam is an axon guidance receptor exhibiting extraordinary molecular diversity[J]. Cell,2000,101(6):671-684.
[21]SHERSTNEV A,DUC C,COLE C,et al. Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation[J]. Nature Structural&Molecular Biology,2012,19(8):845-852.
[22]NAM D K,LEE S,ZHOU G,et al. Oligo(d T)primer generates a high frequency of truncated c DNAs through internal poly(A)priming during reverse transcription[J]. Proceedings of the National Academy of Sciences of the United States of America,2002,99(9):6 152-6 156.
[23]AU K F,JIANG H,LIN L,et al. Detection of splice junctions from paired-end RNA-seq data by Splice Map[J]. Nucleic Acids Research,2010,38(14):4 570-4 578.
[24]AU K F,UNDERWOOD J G,LEE L,et al. Improving PacBio long read accuracy by short read alignment[J]. Plos One,2012,7(10):e46 679.