全长转录组测序技术在非模式植物转录组学研究中的应用
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摘要
转录组连接基因组遗传信息与蛋白质组,也是基因功能研究的基础和出发点。单分子测序技术是近年逐渐成熟的新一代测序技术,也称为第三代测序技术,在转录组学研究方面较前代测序技术具有独到优势,应用前景广阔。在非模式植物的功能基因组学研究中,全长转录本的获得可有力地推进相应基础研究水平,而第三代测序技术为此提供了较好的解决方案。本研究就目前技术较为成熟且应用较广泛的SMRT等单分子测序技术原理进行了介绍,综述了该技术在非模式植物转录组学研究中的应用现状,对其应用前景进行了展望。
Transcriptome, connecting the genomic genetic information with proteome, is the fundament and starting point of gene function analysis. Single-molecule sequencing technology is a new generation of sequencing technology, also known as the third-generation sequencing technology, which has unique advantages over previous sequencing technology in transcriptome research and broad application prospects. In the functional genomics research of non-model plants, the acquisition of full-length transcripts can effectively promote the corresponding basic research level, and the third generation sequencing technology provides a better solution for this. In this paper, we introduced the single-molecule real-time DNA sequencing(SMRT), summarized the present application of full-length transcriptome sequences in non-model plants transcriptome research, and made prospect for the technology in further studies.
Transcriptome, connecting the genomic genetic information with proteome, is the fundament and starting point of gene function analysis. Single-molecule sequencing technology is a new generation of sequencing technology, also known as the third-generation sequencing technology, which has unique advantages over previous sequencing technology in transcriptome research and broad application prospects. In the functional genomics research of non-model plants, the acquisition of full-length transcripts can effectively promote the corresponding basic research level, and the third generation sequencing technology provides a better solution for this. In this paper, we introduced the single-molecule real-time DNA sequencing(SMRT), summarized the present application of full-length transcriptome sequences in non-model plants transcriptome research, and made prospect for the technology in further studies.
引文
Abdel-Ghany S.E.,Hamilton M.,Jacobi J.L.,Ngam P.,Devitt N.,Schilkey F.,Ben-Hur A.,and Reddy A.S.,2016,A survey of the sorghum transcriptome using single-molecule long reads,Nat.Commun.,7:11706
Clavijo B.J.,Venturi ni L.,Schudoma C.,Accinelli G.G.,Kaithakottil G.,Wright J.,Borrill P.,Kettleborough G.,Heavens D.,Chapman H.,Lipscombe J.,Barker T.,Lu F.H.,McKenzie N.,Raats D.,Ramirez-Gonzalez R.H.,Coince A.,Peel N.,Percival-Alwyn L.,Duncan O.,Trsch J.,Yu G.,Bolser D.M.,Namaati G.,Kerhornou A.,Spannagl M.,Gundlach H.,Haberer G.,Davey R.P.,Fosker C.,Palma F.D.,Phillips A.L.,Millar A.H.,Kersey P.J.,Uauy C.,Krasileva K.V.,Swarbreck D.,Bevan M.W.,and Clark M.D.,2017,An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations,Genome Res.,27(5):885-896
Dong L.L.,Liu H.F.,Zhang J.C.,Yang S.J.,Kong G.Y.,Chu J.S.C.,Chen N.S.,and Wang D.W.,2015,Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research,BMCGenomics,16:1039
Eid J.,Fehr A.,Gray J.,Luong K.,Lyle J.,Otto G.,Peluso P.,Rank D.,Baybayan P.,Bettman B.,Bibillo A.,Bjornson K.,Chaudhuri B.,Christians F.,Cicero R.,Clark S.,Dalal R.,Dewinter A.,Dixon J.,Foquet M.,Gaertner A.,Hardenbol P.,Heiner C.,Hester K.,Holden D.,Kearns G.,Kong X.,Kuse R.,Lacroix Y.,Lin S.,Lundquist P.,Ma C.,Marks P.,Maxham M.,Murphy D.,Park I.,Pham T.,Phillips M.,Roy J.,Sebra R.,Shen G.,Sorenson J.,Tomaney A.,Travers K.,Trulson M.,Vieceli J.,Wegener J.,Wu D.,Yang A.,Zaccarin D.,Zhao P.,Zhong F.,Korlach J.,and Turner S.,2009,Real-time DNA sequencing from single polymerase molecules,Science,323(5910):133-138
Ge Y.J.,and Chen S.,2017,Single molecule real time sequencing and its applications in microbial epigenetics,Weishengwuxue Tongbao(Microbiology China),44(1):186-199(葛元洁,陈实,2017,单分子实时测序及其在微生物表观遗传学中的应用,微生物学通报,44(1):186-199)
Gonzalez-Ibeas D.,Martinez-Garcia P.J.,Famula R.A.,Delfino-Mix A.,Stevens K.A.,Loopstra C.A.,Langley C.H.,Neale D.B.,and Wegrzyn J.L.,2016,Assessing the gene content of the megagenome:sugar pine(Pinus lambertiana),G3(Bethesda),6(12):3787-3802
Goodwin S.,McPherson J.D.,and McCombie W.R.,2016,Coming of age:ten years of next-generation sequencing technologies,Nat.Rev.Genet.,17(6):333-351
Gross S.M.,Martin J.A.,Simpson J.,Abraham-Juarez M.J.,Wang Z.,and Visel A.,2013,De novo transcriptome assembly of drought tolerant CAM plants,Agave deserti and A-gave tequilana,BMC Genomics,14:563
Hoang N.V.,Furtado A.,Mason P.J.,Marquardt A.,Kasirajan L.,Thirugnanasambandam P.P.,Botha F.C.,and Henry R.J.,2017,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,BMC Genomics,18(1):395
Larsen P.A.,and Smith T.P.,2012,Application of circular consensus sequencing and network analysis to characterize the bovine Ig G repertoire,BMC Immunol.,13:52
Larsen P.A.,Campbell C.R.,and Yoder A.D.,2014,Next-generation approaches to advancing eco-immunogenomic research in critically endangered primates,Mol.Ecol.Resour.,14(6):1198-1209
Li Y.P.,Dai C.,Hu C.G.,Liu Z.C.,and Kang C.Y.,2017,Global identification of alternative splicing via comparative analysis of SMRT-and Illumina-based RNA-seq in strawberry,Plant J.,90(1):164-176
Liu X.,Mei W.,Soltis P.S.,Soltis D.E.,and Barbazuk W.B.,2017,Detecting alternatively spliced transcript isoforms from single-molecule long-read aequences without a reference genome,Mol.Ecol.Resour.,17(6):1243-1256
Mace E.S.,Tai S.,Gilding E.K.,Li Y.,Prentis P.J.,Bian L.,Campbell B.C.,Hu W.,Innes D.J.,Han X.,Cruickshank A.,Dai C.,Frère C.,Zhang H.,Hunt C.H.,Wang X.,Shatte T.,Wang M.,Su Z.,Li J.,Lin X.,Godwin I.D.,Jordan D.R.,and Wang J.,2013,Whole-genome sequencing reveals untapped genetic potential in Africa's indigenous cereal crop sorghum,Nat.Commun.,4:2320
Minoche A.E.,Dohm J.C.,Schneider J.,Holtgrawe D.,Viehover P.,Montfort M.,Sorensen T.R.,Weisshaar B.,and Himmelbauer H.,2015,Exploiting single-molecule transcript sequencing for eukaryotic gene prediction,Genome Biol.,16:184
Ning G.,Cheng X.,Luo P.,Liang F.,Wang Z.,Yu G.,Li X.,Wang D.,and Bao M.,2017,Hybrid sequencing and map finding(HySeMaFi):optional strategies for extensively deciphering gene splicing and expression in organisms without reference genome,Sci.Rep.,7:43793
Ocwieja K.E.,Sherrill-Mix S.,Mukherjee R.,Custers-Allen R.,David P.,Brown M.,Wang S.,Link D.R.,Olson J.,Travers K.,Schadt E.,and Bushman F.D.,2012,Dynamic regulation of HIV-1 m RNA populations analyzed by single-molecule enrichment and long-read sequencing,Nucleic Acids Res.,40(20):10345-10355
Rhoads A.,and Au K.F.,2015,PacBio sequencing and its applications,Genomics Proteom.Bioinf.,13(5):278-289
Tilgner H.,Grubert F.,Sharon D.,and Snyder M.P.,2014,Defining a personal,allele-specific,and single-molecule long-read transcriptome,Proc.Natl.Acad.Sci.USA,111(27):9869-9874
Travers K.J.,Chin C.S.,Rank D.R.,Eid J.S.,and Turner S.W.,2010,A flexible and efficient template format for circular consensus sequencing and SNP detection,Nucleic Acids Res.,38(15):e159
Treutlein B.,Gokce O.,Quake S.R.,and Sudhof T.C.,2014,Cartography of neurexin alternative splicing mapped by single-molecule long-read m RNA sequencing,Proc.Natl.A-cad.Sci.USA,111(13):1291-1299
Wang B.,Tseng E.,Regulski M.,Clark T.A.,Hon T.,Jiao Y.P.,Lu Z.Y.,Olson A.,Stein J.C.,and Ware D.,2016,Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing,Nat.Commun.,7:11708
Wang M.J.,Wang P.C.,Liang F.,Ye Z.X.,Li J.Y.,Shen C.,Pei L.L.,Wang F.,Hu J.,Tu L.L.,Lindsey K.,He D.H.,and Zhang X.L.,2018,A global survey of alternative splicing in allopolyploid cotton:landscape,complexity and regulation,New Phytol.,217(1):163-178
Wang T.T.,Wang H.Y.,Cai D.W.,Gao Y.B.,Zhang H.X.,Wang Y.S.,Lin C.T.,Ma L.Y.,and Gu L.F.,2017,Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation in moso bamboo(Phyllostachys edulis),Plant J.,91(4):684-699
Xu Z.C.,Peters R.J.,Weirather J.,Luo H.M.,Liao B.S.,Zhang X.,Zhu Y.J.,Ji A.J.,Zhang B.,Hu S.N.,Au K.F.,Song J.Y.,and Chen S.L.,2015,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,Plant J.,82(6):951-961
Zhu F.Y.,Chen M.X.,Ye N.H.,Shi L.,Ma K.L.,Yang J.F.,Cao Y.Y.,Zhang Y.,Yoshida T.,Fernie A.R.,Fan G.Y.,Wen B.,Zhou R.,Liu T.Y.,Fan T.,Gao B.,Zhang D.,Hao G.F.,Xiao S.,Liu Y.G.,and Zhang J.,2017,Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings,Plant J.,91(3):518-533
Zulkapli M.M.,Rosli M.A.F.,Salleh F.I.M.,Mohd Noor N.,Aizat W.M.,and Goh H.H.,2017,Iso-Seq analysis of Nepenthes ampullaria,Nepenthes rafflesiana and Nepenthes×hookeriana for hybridisation study in pitcher plants,Genomics Data,12:130-131
Clavijo B.J.,Venturi ni L.,Schudoma C.,Accinelli G.G.,Kaithakottil G.,Wright J.,Borrill P.,Kettleborough G.,Heavens D.,Chapman H.,Lipscombe J.,Barker T.,Lu F.H.,McKenzie N.,Raats D.,Ramirez-Gonzalez R.H.,Coince A.,Peel N.,Percival-Alwyn L.,Duncan O.,Trsch J.,Yu G.,Bolser D.M.,Namaati G.,Kerhornou A.,Spannagl M.,Gundlach H.,Haberer G.,Davey R.P.,Fosker C.,Palma F.D.,Phillips A.L.,Millar A.H.,Kersey P.J.,Uauy C.,Krasileva K.V.,Swarbreck D.,Bevan M.W.,and Clark M.D.,2017,An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations,Genome Res.,27(5):885-896
Dong L.L.,Liu H.F.,Zhang J.C.,Yang S.J.,Kong G.Y.,Chu J.S.C.,Chen N.S.,and Wang D.W.,2015,Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research,BMCGenomics,16:1039
Eid J.,Fehr A.,Gray J.,Luong K.,Lyle J.,Otto G.,Peluso P.,Rank D.,Baybayan P.,Bettman B.,Bibillo A.,Bjornson K.,Chaudhuri B.,Christians F.,Cicero R.,Clark S.,Dalal R.,Dewinter A.,Dixon J.,Foquet M.,Gaertner A.,Hardenbol P.,Heiner C.,Hester K.,Holden D.,Kearns G.,Kong X.,Kuse R.,Lacroix Y.,Lin S.,Lundquist P.,Ma C.,Marks P.,Maxham M.,Murphy D.,Park I.,Pham T.,Phillips M.,Roy J.,Sebra R.,Shen G.,Sorenson J.,Tomaney A.,Travers K.,Trulson M.,Vieceli J.,Wegener J.,Wu D.,Yang A.,Zaccarin D.,Zhao P.,Zhong F.,Korlach J.,and Turner S.,2009,Real-time DNA sequencing from single polymerase molecules,Science,323(5910):133-138
Ge Y.J.,and Chen S.,2017,Single molecule real time sequencing and its applications in microbial epigenetics,Weishengwuxue Tongbao(Microbiology China),44(1):186-199(葛元洁,陈实,2017,单分子实时测序及其在微生物表观遗传学中的应用,微生物学通报,44(1):186-199)
Gonzalez-Ibeas D.,Martinez-Garcia P.J.,Famula R.A.,Delfino-Mix A.,Stevens K.A.,Loopstra C.A.,Langley C.H.,Neale D.B.,and Wegrzyn J.L.,2016,Assessing the gene content of the megagenome:sugar pine(Pinus lambertiana),G3(Bethesda),6(12):3787-3802
Goodwin S.,McPherson J.D.,and McCombie W.R.,2016,Coming of age:ten years of next-generation sequencing technologies,Nat.Rev.Genet.,17(6):333-351
Gross S.M.,Martin J.A.,Simpson J.,Abraham-Juarez M.J.,Wang Z.,and Visel A.,2013,De novo transcriptome assembly of drought tolerant CAM plants,Agave deserti and A-gave tequilana,BMC Genomics,14:563
Hoang N.V.,Furtado A.,Mason P.J.,Marquardt A.,Kasirajan L.,Thirugnanasambandam P.P.,Botha F.C.,and Henry R.J.,2017,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,BMC Genomics,18(1):395
Larsen P.A.,and Smith T.P.,2012,Application of circular consensus sequencing and network analysis to characterize the bovine Ig G repertoire,BMC Immunol.,13:52
Larsen P.A.,Campbell C.R.,and Yoder A.D.,2014,Next-generation approaches to advancing eco-immunogenomic research in critically endangered primates,Mol.Ecol.Resour.,14(6):1198-1209
Li Y.P.,Dai C.,Hu C.G.,Liu Z.C.,and Kang C.Y.,2017,Global identification of alternative splicing via comparative analysis of SMRT-and Illumina-based RNA-seq in strawberry,Plant J.,90(1):164-176
Liu X.,Mei W.,Soltis P.S.,Soltis D.E.,and Barbazuk W.B.,2017,Detecting alternatively spliced transcript isoforms from single-molecule long-read aequences without a reference genome,Mol.Ecol.Resour.,17(6):1243-1256
Mace E.S.,Tai S.,Gilding E.K.,Li Y.,Prentis P.J.,Bian L.,Campbell B.C.,Hu W.,Innes D.J.,Han X.,Cruickshank A.,Dai C.,Frère C.,Zhang H.,Hunt C.H.,Wang X.,Shatte T.,Wang M.,Su Z.,Li J.,Lin X.,Godwin I.D.,Jordan D.R.,and Wang J.,2013,Whole-genome sequencing reveals untapped genetic potential in Africa's indigenous cereal crop sorghum,Nat.Commun.,4:2320
Minoche A.E.,Dohm J.C.,Schneider J.,Holtgrawe D.,Viehover P.,Montfort M.,Sorensen T.R.,Weisshaar B.,and Himmelbauer H.,2015,Exploiting single-molecule transcript sequencing for eukaryotic gene prediction,Genome Biol.,16:184
Ning G.,Cheng X.,Luo P.,Liang F.,Wang Z.,Yu G.,Li X.,Wang D.,and Bao M.,2017,Hybrid sequencing and map finding(HySeMaFi):optional strategies for extensively deciphering gene splicing and expression in organisms without reference genome,Sci.Rep.,7:43793
Ocwieja K.E.,Sherrill-Mix S.,Mukherjee R.,Custers-Allen R.,David P.,Brown M.,Wang S.,Link D.R.,Olson J.,Travers K.,Schadt E.,and Bushman F.D.,2012,Dynamic regulation of HIV-1 m RNA populations analyzed by single-molecule enrichment and long-read sequencing,Nucleic Acids Res.,40(20):10345-10355
Rhoads A.,and Au K.F.,2015,PacBio sequencing and its applications,Genomics Proteom.Bioinf.,13(5):278-289
Tilgner H.,Grubert F.,Sharon D.,and Snyder M.P.,2014,Defining a personal,allele-specific,and single-molecule long-read transcriptome,Proc.Natl.Acad.Sci.USA,111(27):9869-9874
Travers K.J.,Chin C.S.,Rank D.R.,Eid J.S.,and Turner S.W.,2010,A flexible and efficient template format for circular consensus sequencing and SNP detection,Nucleic Acids Res.,38(15):e159
Treutlein B.,Gokce O.,Quake S.R.,and Sudhof T.C.,2014,Cartography of neurexin alternative splicing mapped by single-molecule long-read m RNA sequencing,Proc.Natl.A-cad.Sci.USA,111(13):1291-1299
Wang B.,Tseng E.,Regulski M.,Clark T.A.,Hon T.,Jiao Y.P.,Lu Z.Y.,Olson A.,Stein J.C.,and Ware D.,2016,Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing,Nat.Commun.,7:11708
Wang M.J.,Wang P.C.,Liang F.,Ye Z.X.,Li J.Y.,Shen C.,Pei L.L.,Wang F.,Hu J.,Tu L.L.,Lindsey K.,He D.H.,and Zhang X.L.,2018,A global survey of alternative splicing in allopolyploid cotton:landscape,complexity and regulation,New Phytol.,217(1):163-178
Wang T.T.,Wang H.Y.,Cai D.W.,Gao Y.B.,Zhang H.X.,Wang Y.S.,Lin C.T.,Ma L.Y.,and Gu L.F.,2017,Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation in moso bamboo(Phyllostachys edulis),Plant J.,91(4):684-699
Xu Z.C.,Peters R.J.,Weirather J.,Luo H.M.,Liao B.S.,Zhang X.,Zhu Y.J.,Ji A.J.,Zhang B.,Hu S.N.,Au K.F.,Song J.Y.,and Chen S.L.,2015,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,Plant J.,82(6):951-961
Zhu F.Y.,Chen M.X.,Ye N.H.,Shi L.,Ma K.L.,Yang J.F.,Cao Y.Y.,Zhang Y.,Yoshida T.,Fernie A.R.,Fan G.Y.,Wen B.,Zhou R.,Liu T.Y.,Fan T.,Gao B.,Zhang D.,Hao G.F.,Xiao S.,Liu Y.G.,and Zhang J.,2017,Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings,Plant J.,91(3):518-533
Zulkapli M.M.,Rosli M.A.F.,Salleh F.I.M.,Mohd Noor N.,Aizat W.M.,and Goh H.H.,2017,Iso-Seq analysis of Nepenthes ampullaria,Nepenthes rafflesiana and Nepenthes×hookeriana for hybridisation study in pitcher plants,Genomics Data,12:130-131