新一代测序技术的发展和应用

doi:10.13560/j.cnki.biotech.bull.1985.2015.11.003

摘要/Abstract

摘要： DNA测序技术是人类探索生命秘密的重要研究手段。自第一代的Sanger测序技术诞生以来，DNA测序技术经历了三代变革，产生了第二代到第四代测序技术，统称为新一代测序技术。目前，新一代测序技术的数据产出能力呈指数增长，而且这一技术本身也从依赖DNA聚合酶的生化反应转变为面向物理学中纳米技术的新领域。新一代测序对生命科学领域具有里程碑意义，引领了科学研究模式革新和研究思维的转变。科研人员可利用新一代测序技术对基因组、转录组和表观组等诸多领域展深入的研究。分析了新一代测序技术的特点，并对其未来的发展方向以及应用进行了展望。

关键词: 新一代DNA测序, 边合成边测序, 单分子测序, 纳米孔, 应用

Abstract: DNA sequencingtechnology isan important research method inlifescience. Since thebirth of theSanger sequencing technology, DNA sequencingtechnologyhas experienced three generationsof change, resulting the secondgeneration to the fourth generation sequencingtechnology. DNA sequencing not only has been improving its productivity in an exponential growth rate but also been evolving into a new technological territories toward physical disciplines of nanotechnology. Next generation sequencingthat has landmark significance oflife sciences, can improve researches in the genome, transcriptome and epigenome. This review analyzes technical characteristics of the next generation sequencers and provide prospective insights into their future development and applications.

Key words: next generation sequencing, sequence by synthesis, single molecule sequencing, nanopore, applications

田李,张颖, 赵云峰. 新一代测序技术的发展和应用[J]. 生物技术通报, 2015, 31(11): 1-8.

Tian Li, Zhang Ying, Zhao Yunfeng. The Next Generation Sequencing Technology and Its Applications[J]. Biotechnology Bulletin, 2015, 31(11): 1-8.

参考文献

[1]周晓光, 任鲁风, 李运涛, 等. 下一代测序技术: 技术回顾与展望[J]. 中国科学: 生命科学, 2010, 40(1): 23-37.
[2]岳桂东, 高强, 罗龙海, 等. 高通量测序技术在动植物研究领域中的应用[J]. 中国科学: 生命科学, 2012, 42(2): 107-124.
[3]Sanger F. Sequences, sequences, and sequences[J]. Annual Review of Biochemistry, 1988, 57(1): 1-29.
[4]McPherson JD, Marra M, Hillier LD, et al. A physical map of the human genome[J]. Nature, 2001, 409(6822): 934-941.
[5]Fedurco M, Romieu A, Williams S, et al. BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies[J]. Nucleic Acids Research, 2006, 34(3): e22.
[6]Margulies M, Egholm M, Altman WE, et al. Genome sequencing in microfabricated high-density picolitre reactors[J]. Nature, 2005, 437(7057): 376-380.
[7]Ronaghi M, Karamohamed S, Pettersson B, et al. Real-time DNA sequencing using detection of pyrophosphate release[J]. Analytical Biochemistry, 1996, 242(1): 84-89.
[8]Holt RA, Jones SJM. The new paradigm of flow cell sequencing[J]. Genome Research, 2008, 18(6): 839-846.
[9]Pop M, Salzberg SL. Bioinformatics challenges of new sequencing technology[J]. Trends in Genetics, 2008, 24(3): 142-149.
[10]Torres TT, Metta M, Ottenw?lder B, et al. Gene expression profiling by massively parallel sequencing[J]. Genome Research, 2008, 18(1): 172-177.
[11]Eid J, Fehr A, Gray J, et al. Real-time DNA sequencing from single polymerase molecules[J]. Science, 2009, 323(5910): 133-138.
[12]Schadt EE, Turner S, Kasarskis A. A window into third-generation sequencing[J]. Human Molecular Genetics, 2010, 19(R2): R227-R240.
[13] 张得芳, 马秋月, 尹佟明, 夏涛. 第三代测序技术及其应用[J]. 中国生物工程杂志, 2013, 33(5): 125-131
[14]Yang J, Ferranti DC, Stern LA, et al. Rapid and precise scanning helium ion microscope milling of solid-state nanopores for biomolecule detection[J]. Nanotechnology, 2011, 22(28): 285310.
[15]Marshall MM, Yang J, Hall AR. Direct and transmission milling of suspended silicon nitride membranes with a focused helium ion beam[J]. Scanning, 2012, 34(2): 101-106.
[16]陈文辉, 罗军, 赵超. 固态纳米孔: 下一代DNA测序技术——原理、工艺与挑战[J]. 中国科学: 生命科学, 2014, 44(7): 649-662.
[17]任鲁风, 于军. 解读生命密码的基本手段——DNA测序技术的前世今生[J]. 生命科学, 2012, 24(12): 1357-1362.
[18]Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana[J]. Nature, 2000, 408(6814): 796.
[19]Hillier LDW, Marth GT, Quinlan AR, et al. Whole-genome sequencing and variant discovery in C. elegans[J]. Nature Methods, 2008, 5(2): 183-188.
[20]Powell K, Abbott A, Check E. Mouse genome: The real deal[J]. Nature, 2002, 420(6915): 456-456.
[21]Li R, Fan W, Tian G, et al. The sequence and de novo assembly of the giant panda genome[J]. Nature, 2010, 463(7279): 311-317.
[22]Perry GH, Reeves D, Melsted P, et al. A genome sequence resource for the aye-aye(Daubentonia madagascariensis), a nocturnal lemur from Madagascar[J]. Genome Biology and Evolution, 2012, 4(2): 126-135.
[23]Lam HM, Xu X, Liu X, et al. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection[J]. Nature Genetics, 2010, 42(12): 1053-1059.
[24] Zheng LY, Guo XS, He B, et al. Genome-wide patterns of genetic variation in sweet and grain sorghum(Sorghum bicolor)[J]. Genome Biology, 2011, 12(11): R114.
[25]Ashelford K, Eriksson ME, Allen CM, et al. Full genome re-sequen-cing reveals a novel circadian clock mutation in Arabidopsis[J]. Genome Biol, 2011, 12(3): R28.
[26] Chen MX, Ai L, Xu MJ, et al. Identification and characterization of microRNAs in Trichinella spiralis by comparison with Brugia malayi and Caenorhabditis elegans[J]. Parasitology Research, 2011, 109(3): 553-558.
[27]Li P, Ponnala L, Gandotra N, et al. The developmental dynamics of the maize leaf transcriptome[J]. Nature Genetics, 2010, 42(12): 1060-1067.
[28]Wang QQ, Liu F, Chen XS, et al. Transcriptome profiling of early developing cotton fiber by deep-sequencing reveals significantly differential expression of genes in a fuzzless/lintless mutant[J]. Genomics, 2010, 96(6): 369-376.
[29]Hao DC, Ge G, Xiao P, et al. The first insight into the tissue specific taxus transcriptome via Illumina second generation sequencing[J]. PLoS One, 2011, 6(6): e21220.
[30]Guo W, Wu G, Yan F, et al. Identification of novel Oryza sativa miRNAs in deep sequencing-based small RNA libraries of rice infected with Rice stripe virus[J]. PLoS One, 2012, 7(10): e46443.
[31]Zhou M, Gu L, Li P, et al. Degradome sequencing reveals endogen-ous small RNA targets in rice(Oryza sativa L. ssp. indica)[J]. Frontiers in Biology, 2010, 5(1): 67-90.
[32] Uemura S, Aitken CE, Korlach J, et al. Real-time tRNA transit on single translating ribosomes at codon resolution[J]. Nature, 2010, 464(7291): 1012-1017.
[33]Ozsolak F, Platt AR, Jones DR, et al. Direct RNA sequencing[J]. Nature, 2009, 461(7265): 814-818.
[34]Xiang H, Zhu J, Chen Q, et al. Single base-resolution methylome of the silkworm reveals a sparse epigenomic map[J]. Nature Biotechnology, 2010, 28(5): 516-520.
[35]Song CX, Clark TA, Lu XY, et al. Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine[J]. Nature Methods, 2012, 9(1): 75-77.
[36]Wang X, Elling AA, Li X, et al. Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize[J]. The Plant Cell, 2009, 21(4): 1053-1069.