高通量测序技术的发展及其在生命科学中的应用

摘要/Abstract

摘要： DNA测序技术从以Sanger法为代表的第一代测序技术到如今的高通量测序(HTS)技术,经历了漫长而曲折的发展过程,如今该技术在动植物基因组的研究中获得了很大的成功,它的问世可以使人们以更低廉的价格,更全面、更深入地对全基因组进行分析.作者阐述了几种关于HTS的测序技术平台:Roche/454测序技术、ABI/SOLID测序技术、Illumina/Solexa测序技术、单分子测序技术及Ion Torrent测序技术,并且还归纳了HTS在基因组学、转录组学及表观基因组学等方面的应用.

关键词: 高通量测序技术; 基因组学; 转录组学; 应用

Abstract: The DNA sequencing technology, developing from the first generation to high-throughput sequencing (HTS) technology, has experienced a long and tortuous process amazing progress now. The technology has been used widely in the animal and plant genome with a great success. In addition, its also makes us to investigate the whole genome with lower cost, more in-depth. In this study, we had elaborated sequencing plaforms of HTS, such as Roche/454 sequencing, ABI/SOLID sequencing, Illumina/Solexa sequencing, single molecule sequencing and Ion Torrent sequencing technology. And we also had summarized the application of HTS in the genomics, transcriptomes, and epigenetics.

Key words: high-throughput sequencing; genomics; transcriptomes; application

中图分类号:

杜玲, 刘刚, 陆健, 刘丑生, 哈福. 高通量测序技术的发展及其在生命科学中的应用[J]. , 2014, 41(12): 109-116.

DU Ling, LIU Gang, LU Jian, LIU Chou-sheng, HA Fu. Development of High-throughput Sequencing Technology and its Application in Bioscience[J]. , 2014, 41(12): 109-116.

参考文献

1 王滔. 猪皮下与内脏脂肪组织mRNA转录组鉴定和差异分析[D]. 雅安:四川农业大学, 2013.
2 李敏俐, 王薇, 陆祖宏. ChIP 技术及其在基因组水平上分析DNA与蛋白质相互作用[J]. 遗传, 2010, 32(3): 219～228.
3 李庆岗, 陶立. 高通量测序技术及其在生命科学中的应用[J]. 畜牧与饲料科学, 2012, 33(2): 25～28.
4 朱燕. DNA甲基化的分析与状态检测[J]. 现代预防医学, 2005, 9:1070～1073.
5 朱晓攀. 基于高通量测序的济宁青山羊和莱芜黑山羊卵巢转录组研究[D]. 北京:中国农业科学院, 2013.
6 孙雪莲. 豌豆SSR标记开发及遗传连锁图谱构建[D]. 北京:中国农业科学院, 2013.
7 闫绍鹏, 杨瑞,冷淑华,等. 高通量测序技术及其在农业科学研究中的应用[J]. 中国农学通报, 2012,28(30): 171～176.
8 陈梅丽. 转录组学研究人肿瘤细胞的表达调控机制和大熊猫基因组重注释[D]. 北京:中国科学院, 2013.
9 罗宗刚. 猪不同发育阶段 microRNA 转录组的鉴定[D].雅安:四川农业大学, 2011.
10 张小丽. 猪背部浅层和背部深层脂肪组织全基因组甲基化研究[D]. 雅安:四川农业大学,2013.
11 储成风, 汪存利, 习海涛,等, 亚硫酸氢盐测序法检测小鼠胚胎Oct4启动子区甲基化[J]. 安徽农业大学学报, 2007,34(4): 577～580.
12 Ashelford K, Eriksson M E, Allen C M, et al. Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis[J]. Genome Biol, 2011, 12(3): R28.
13 Bennett S. Solexa Ltd[J]. Pharmacogenomics, 2004, 5(4): 433～438.
14 Bentley D R. Whole-genome re-sequencing[J]. Current Opinion in Genetics & Development, 2006, 16(6): 545～552.
15 Bibikova M, Lin Z, Zhou L, et al. High-throughput DNA methylation profiling using universal bead arrays[J]. Genome Res, 2006, 16(3): 383～393.
16 Buggs R J, Renny-Byfield S, Chester M, et al. Next-generation sequencing and genome evolution in allopolyploids[J]. Am J Bot, 2012,99(2): 372～382.
17 Canovas A, Rincon G, Islas-Treio A, et al. SNP discovery in the bovine milk transcriptome using RNA-Seq technology[J]. Mammalian Genome, 2010, 21(11～12): 592～598.
18 Chan J Z, Pallen M J, Oppenheim B, et al. Genome sequencing in clinical microbiology[J]. Nat Biotechnol, 2012, 30(11): 1068～1071.
19 Dalloul R A, Long J A, Zimin A V, et al.Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): Genome assembly and analysis[J]. PLoS Biology, 2010, 8(9): e1000475.
20 Edwards D, Batley J. Plant genome sequencing: Applications for crop improvement[J]. Plant Biotechnol J, 2010, 8(1): 2～9.
21 Garg R, Patel R K, Jhanwar S, et al. Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development[J]. Plant Physiology, 2011, 156(4): 1661～1678.
22 Goffeau A, Ramezani R M, Rasmussen S W, et al. The yeast genome directory[J]. Nature, 1997, 387(6632): 5～6.
23 Harris T D, Buzby P R, Babcock H, et al. Single-molecule DNA sequencing of a viral genome[J]. Science, 2008, 320(5872): 106～109.
24 Holt R A, Jones S J. The new paradigm of flow cell sequencing[J]. Genome Res, 2008, 18(6): 839～846.
25 Huang S, Li R, Zhang Z, et al. The genome of the cucumber, Cucumis sativus L.[J]. Nat Genet, 2009, 41(12): 1275～1281.
26 International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome[J]. Nature, 2004, 431(7011): 931～945.
27 Lai J, Li R, Xu X, et al. Genome-wide patterns of genetic variation among elite maize inbred lines[J]. Nat Genet, 2010, 42(11): 1027～1030.
28 Lee R C, Feinbaum R L, Ambros V. The C.elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 [J]. Cell, 1993, 75(5): 843～854.
29 Li R, Fan W, Tian G, et al. The sequence and de novo assembly of the giant panda genome[J]. Nature, 2009, 463(7279): 311～317.
30 Li Z, Zhang Z, Yan P, et al. RNA-Seq improves annotation of protein-coding genes in the cucumber genome[J]. BMC Genomics, 2011a, 12(1): 540.
31 Li Q, Li N, Hu X, et al. Genome-wide mapping of DNA methylation in chicken[J]. PLoS One, 2011b, 6(5): e19428.
32 Li T, Wu R, Zhang D, et al. A systematic analysis of the skeletal muscle miRNA transcriptome of chicken varieties with divergent skeletal muscle growth identifies novel miRNAs and differentially expressed miRNAs[J]. BMC Genomics, 2011c, 12(1): 186.
33 Lister R, Ecker J R. Finding the fifth base: Genome-wide sequencing of cytosine methylation[J]. Genome Res, 2009, 19(6): 959～966.
34 Liu L, Li Y, Li S, et al. Comparison of next-generation sequencing systems[J]. J Biomed Biotechnol, 2012, 2012: 251364.
35 Metzker M L. Sequencing technologies——The next generation[J]. Nature Reviews Genetics, 2010, 11(1): 31～46.
36 Morozova O, Marra M A. Applications of next-generation sequencing technologies in functional genomics[J]. Genomics, 2008, 92(5): 255～264.
37 Margulies M, Eqhoim M, Altman W E, et al. Genome sequencing in microfabricated high-density picolitre reactors[J]. Nature, 2005, 437(7057): 376～380.
38 Mardis E R. Next-generation DNA sequencing methods[J]. Annu Rev Genomics Hum Genet, 2008a, 9: 387～402.
39 Mardis E R. The impact of next-generation sequencing technology on genetics[J]. Trends in Genetics, 2008b, 24(3): 133～141.
40 Nair S S, Coolen M W, Stizaker C, et al. Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias[J]. Epigenetics, 2011, 6(1): 34～44.
41 Pan Q, Shai O, Lee L J, et al. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing[J]. Nat Genet, 2008, 40(12): 1413～1415.
42 Radford A D, Chapman D, Dixon L, et al. Application of next-generation sequencing technologies in virology[J]. J Gen Virol, 2012, 93(9): 1853～1868.
43 Riedmaier I, Benes V, Blake J, et al. RNA-Sequencing as useful screening tool in the combat against the misuse of anabolic agents[J]. Analytical Chemistry, 2012, 84(15): 6863～6868.
44 Rubin C J, Zody M C, Eriksson J, et al.Whole-genome resequencing reveals loci under selection during chicken domestication[J]. Nature, 2010, 464(7288): 587～591.
45 Sanger F, Coulson A R, Friedmann T, et al. The nucleotide sequence of bacteriophage phiX174[J]. J Mol Biol, 1978, 125(2): 225～246.
46 Schuster S C. Next-generation sequencing transforms today's biology[J]. Nat Methods, 2008, 5(1): 16～18.
47 Shendure J, Ji H. Next-generation DNA sequencing[J]. Nat Biotechnol, 2008, 26(10): 1135～1145.
48 Shu Y, Li Y, Zhu Z, et al. SNPs discovery and CAPS marker conversion in soybean[J]. Molecular Biology Reports, 2011, 38(3): 1841～1846.
49 Subbaiyan G K, Waters D L, Katiyar S K, et al. Genome-wide DNA polymorphisms in elite indica rice inbreds discovered by whole-genome sequencing[J]. Plant Biotechnology Journal, 2012, 10(6): 623～634.
50 Sun H, Wu J, Wickramasinghe P, et al.Genome-wide mapping of RNA Pol-Ⅱ promoter usage in mouse tissues by ChIP-Seq[J]. Nucleic Acids Res, 2011, 39(1): 190～201.
51 Tawfik D S, Griffiths A D. Man-made cell-like compartments for molecular evolution[J]. Nat Biotechnol, 1998, 16(7): 652～656.
52 Timp W,Mirsaidov U M, Wang D, et al.Nanopore sequencing: Electrical measurements of the code of life[J]. IEEE Trans Nanotechnol, 2010,9(3): 281～294.
53 Whitington T, Frith M C, Johnson J, et al.Inferring transcription factor complexes from ChIP-Seq data[J]. Nucleic Acids Res, 2011, 39(15): e98.
54 Xi Y, Li W.BSMAP: Whole genome bisulfite sequence MAPping program[J]. BMC Bioinformatics, 2009, 10(1): 232.
55 Zeng S, Xiao G, Guo J, et al. Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim[J]. BMC Genomics, 2010, 11(1): 94.
56 Zhan B, Fadista J,Thomsen B, et al.Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping[J]. BMC Genomics, 2011, 12(1): 557.
57 Zhang H, Wei L, Miao H, et al. Development and validation of genic-SSR markers in sesame by RNA-Seq[J]. BMC Genomics,2012,13: 316.

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