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单分子实时测序技术的原理与应用

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  • 1. 云南大学,云南省生物资源保护与利用重点实验室,昆明 650091; 2. 云南大学,云南省高校动物遗传多样性与进化重点实验室,昆明 650091
柳延虎,博士研究生,研究方向:基因组学。E-mail: liuyanhu005@163.com

收稿日期: 2014-09-25

  修回日期: 2014-12-01

  网络出版日期: 2015-02-10

基金资助

国家自然科学基金重大研究计划项目(编号:91131904)和中国科学院昆明动物研究所遗传资源与进化国家重点实验室开放课题(编号:GREKF14-04)资助

The principle and application of the single-molecule real-time sequencing technology

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  • 1. Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091,China;
    2. Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, Yunnan University, Kunming 650091, China

Received date: 2014-09-25

  Revised date: 2014-12-01

  Online published: 2015-02-10

摘要

单分子DNA测序技术是近10年发展起来的新一代测序技术,也称为第三代测序技术,包括单分子实时测序、真正单分子测序、单分子纳米孔测序等技术。文章介绍了单分子实时(Single-molecule real-time,SMRT)测序技术的基本原理、性能以及应用。与Sanger测序法和下一代测序技术相比,SMRT测序具有超长读长、测序周期短、无需模板扩增和直接检测表观修饰位点等特点,为研究人员提供了新选择。同时,SMRT测序的低准确率备受争议(约85%),其中约93%的错误是插入缺失,因此,其数据应用于基因组组装前需先对数据进行纠错处理。目前,SMRT测序在小型基因组从头测序和完整组装中已有良好应用,并且已经或将在表观遗传学、转录组学、大型基因组组装等领域发挥其优势,促进基因组学的研究。

本文引用格式

柳延虎, 王璐, 于黎 . 单分子实时测序技术的原理与应用[J]. 遗传, 2015 , 37(3) : 259 -268 . DOI: 10.16288/j.yczz.14-323

Abstract

Last decade witnessed the explosive development of the third-generation sequencing strategy, including single-molecule real-time sequencing (SMRT), true single-molecule sequencing (tSMSTM) and the single-molecule nanopore DNA sequencing. In this review, we summarize the principle, performance and application of the SMRT sequencing technology. Compared with the traditional Sanger method and the next-generation sequencing (NGS) technologies, the SMRT approach has several advantages, including long read length, high speed, PCR-free and the capability of direct detection of epigenetic modifications. However, the disadvantage of its low accuracy, most of which resulted from insertions and deletions, is also notable. So, the raw sequence data need to be corrected before assembly. Up to now, the SMRT is a good fit for applications in the de novo genomic sequencing and the high-quality assemblies of small genomes. In the future, it is expected to play an important role in epigenetics, transcriptomic sequencing, and assemblies of large genomes.

参考文献

[1] Maxam AM, Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci USA , 1977, 74(2): 560-564.
[2] Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA , 1977, 74(12): 5463-5467.
[3] Liu L, Li YH, Li SL, Hu N, He YM, Pong R, Lin DN, Lu LH, Law M. Comparison of next-generation sequencing systems. J Biomed Biotechnol , 2012, 2012: Article ID 251364.
[4] Gilles A, Meglécz E, Pech N, Ferreira S, Malausa T, Martin JF. Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genom , 2011, 12(1): 245.
[5] Chin CS, Sorenson J, Harris JB, Robins WP, Charles RC, Jean-Charles RR, Bullard J, Webster DR, Kasarskis A, Peluso P, Paxinos EE, Yamaichi Y, Calderwood SB, Mekalanos JJ, Schadt EE, Waldor MK. The origin of the Haitian cholera outbreak strain. N Engl J Med , 2011, 364(1): 33-42.
[6] Rasko DA, Webster DR, Sahl JW, Bashir A, Boisen N, Scheutz F, Paxinos EE, Sebra R, Chin CS, Iliopoulos D, Klammer A, Peluso P, Lee L, Kislyuk AO, Bullard J, Kasarskis A, Wang S, Eid J, Rank D, Redman JC, Steyert SR, Frimodt-Møller J, Struve C, Petersen AM, Krogfelt KA, Nataro JP, Schadt EE, Waldor MK. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med , 2011, 365(8): 709-717.
[7] Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen ZT, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu PG, Begley RF, Rothberg JM. Genome sequencing in microfabricated high-density picolitre reactors. Nature , 2005, 437(7057): 376-380.
[8] Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu XH, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu XL, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo SJ, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning ZM, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Ste
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