YAO Na,LIU Xiuming,DONG Yuanyuan,et al.Advances in Application and Seguencing Methods of Transcriptome[J].Northern Horticulture,2017,41(12):192-198.[doi:10.11937/bfyy.201712043]
转录组的测序方法及应用研究概述
- Title:
- Advances in Application and Seguencing Methods of Transcriptome
- Keywords:
- transcriptome; sequencing; 454 sequencing; Solexa; SOLiD
- 文献标志码:
- A
- 摘要:
- 转录组研究是基因的结构和功能研究的基础,转录组测序技术在近年来取得了很大的进展,被应用到多种动植物中。利用其能够获得大量未知序列的优势,已经被广泛应用到未知基因挖掘、分子调控及相关代谢途径中。该研究主要介绍了转录组研究的方法、转录组测序技术的发展及其在动植物中的重要应用,并讨论其存在的问题及发展趋势。
- Abstract:
- Transcriptome is the basis of the research of structure and function of genes,transcriptome sequencing technology has made great progress in recent years and been applied to many plants and animals species.It has been widely applied to unknown gene mining,molecular regulation and related metabolic pathways for its lots of known sequence.This study reviewed methods of transcriptome,development of transcriptome sequencing and its application in plants and animals,we discussed the problem of tanscriptome and the development trend in the future.
参考文献/References:
[1]VELCULESCU V E,ZHANG L,ZHOU W,et al.Characterization of the yeast transcriptome[J].Cell,1997,88(2):243-251. [2]周华,张新,刘腾云,等.高通量转录组测序的数据分析与基因发掘[J].江西科学,2012,30(5):607-611. [3]吴琼,孙超,陈士林,等.转录组学在药用植物研究中的应用[J].世界科学技术(中医药现代化),2010,12(3):457-461. [4]薛建江,邱景富.病原菌感染宿主的转录组学研究进展[J].河北北方学院学报(医学版),2007,24(5):63-66. [5]COSTA V,ANGELINI C,de FEIS I,et al.Uncovering the complexity of transcriptomes with RNA-Seq[J].J Biomed Biotechnol,2010,6(27):853-916. [6]RUAN Y,LE BER P,NG H H,et al.Interrogating the transcriptome[J].Trends Biotechnol,2004(22):23-30. [7]WANG Z,GERSTEIN M,SNYDER M.RNA-Seq:A revolutionary tool for transcriptomics[J].Nat Rev Genet,2009(10):57-63. [8]VELCULESCU V E,ZHANG L,VOGELSTEIN B,et al.Serial analysis of gene expression[J].Science,1995,270(5235):484-487. [9]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. [10]刘思言,沈铖武,王丕武.基因芯片技术在植物中的应用研究进展[J].广东农业科学,2013(8):136-138. [11]RAMSAY G.DNA chips:State of the art[J].Nature Biotechnology,1998,16(1):40-44. [12]张骞,盛军.基因芯片技术的发展和应用[J].中国医学科学学报,2008,30(3):344-347. [13]姜庆利.检测柯萨奇病毒、副流感病毒基因芯片的建立[D].长春:吉林大学,2013. [14]MARK D.Serial analysis of gene expression:ESTs get smaller[J].Bioessays,1996,18(4):261-262. [15]NIELSEN K L,HGH A L,EMMERSEN J.Deep SAGE-digital transcriptomics with high sensitivity,simple experimental protocol and multiplexing of samples[J].Nucleic Acids Res,2006,34:133. [16]MOLINA C,ZAMAN-ALLAH M,KHAN F.The salt-responsive transcriptome of chickpea roots and nodules via deep Super SAGE[J].BMC Plant Biol,2011(11):31. [17]CHUM W W,KWAN H S,AU C H,et al.Cataloging and profiling genes expressed in Lentinula edodes fruiting body by massive cDNA pyrosequencing and Long SAGE[J].Fungal Genet Biol,2011,48:359-369. [18]王大力,黄大鹏.基因表达系列分析技术研究进展[J].动物医学进展,2009,30(4):69-72. [19]鲍忠赞,张彩霞,徐世清,等.应用基因表达系列分析 (SAGE) 技术研究高温处理前后家蚕的基因表达差异[J].蚕业科学,2012,38(3):456-467. [20]邓永键,郝飞.基因表达系列分析及其应用前景[J].免疫学杂志,2003,19(4):315-321. [21]刘红亮,郑丽明,刘青青,等.非模式生物转录组研究[J].遗传,2013,35(8):955-970. [22]井赵斌,魏琳,俞靓,等.转录组测序及其在牧草基因资源发掘中的应用前景[J].草业科学,2011,28(7):1364-1369. [23]祁云霞,刘永斌,荣威恒.转录组研究新技术:RNA-Seq 及其应用[J].遗传,2011,33(11):1191-1202. [24]张春兰,秦孜娟,王桂芝,等.转录组与RNA-Seq技术[J].生物技术通报,2012(12):51-56. [25]WALL P K,LEEBENS-MACK J,CHANDERBALI A S,et al.Comparison of next generation sequencing technologies for transcriptome characterization[J].BMC Genomics,2009(10):347. [26]ADAMS M D,KELLEY J M,GOCAYNE J D,et al.Complementary DNA sequencing:expressed sequence tags and human genome project[J].Science,1991,252(5013):1651-1656. [27]BOUCK A,VISION T.The molecular ecologist′s guide to expressed sequence tags[J].Mol Ecol,2007,16(5):907-924. [28]MARGULIES M,EGHOLM M,ALTMAN W E,et al.Genome sequencing in microfabricated high-density picolitre reactors[J].Nature,2005,437(7057):376-380. [29]PORRECA G J,ZHANG K,LI J B,et al.Multiplex amplification of large sets of human exons[J].Nat Methods,2007,4(11):931-936. [30]张全芳,李军,范仲学,等.高通量测序技术在农业研究中的应用[J].山东农业科学,2013,45(1):137-140. [31]WANG Z W,JIANG C,WEN Q,et al.Deep sequencing of the Camellia chekiangoleosa transcriptome revealed candidate genes for anthocyan in biosynthesis[J].Gene,2014,538(1):1-7. [32]李滢,孙超,罗红梅,等.基于高通量测序454 GS FLX 的丹参转录组学研究[J].药学学报,2010,45(4):524-529. [33]ALAGNA F,AGOSTINO N D,TORCHIA L,et al.Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development[J].BMC Genomics,2009(10):399. [34]HE L,XU X,LI Y,et al.Transcriptome analysis of buds and leaves using 454 pyrosequencing to discover genes associated with the biosynthesis of active ingredients in Lonicera japonica Thunb.[J].PLoS One,2013,8(4):e62922. [35]BHATTACHARYYA D,SINHA R,HAZRA S,et al.De novo transcriptome analysis using 454 pyrosequencing of the Himalayan Mayapple,Podophyllum hexandrum[J].BMC Genomics,2013(14):748. [36]DUARTE J,RIVIERE N,BARANGER A,et al.Transcriptome sequencing for high throughput SNP development and genetic mapping in pea[J].BMC Genomics,2014,15(1):126. [37]WANG XL,LI Y,LIAO L,et al.Isolation and characterization of microsatellite markers for Axonopus compressus(Sw.) Beauv.(Poaceae) using 454 sequencing technology[J].Genet Mol Res,2015,14(2):4696-4702. [38]WANG F,CHEN H,LI X,et al.Mining and identification of polyunsaturated fatty acid synthesis genes active during camelina seed development using 454 pyrosequencing[J].BMC Plant Biol,2015(15):147. [39]ZHU G,YANG F,SHI S,et al.Transcriptome characterization of cymbidium sinense ‘Dharma’ using 454 pyrosequencing and its application in the identification of genes associated with leaf color variation[J].PLoS One,2015,10(6):e0128592. [40]MOELLER S,WHRMANN T,HUETTEL B,et al.Development of 18 polymorphic microsatellite markers for Vinca minor (Apocynaceae) via 454 pyrosequencing[J].Appl Plant Sci,2015,3(5):1500015. [41]陈新.榛子花芽转录组文库的Solexa测序及冷调节基因的表达谱分析[D].北京:中国林业科学研究院,2011. [42]XU Q,ZHANG Y,CHEN Y,et al.Identification and differential expression of microRNAs in ovaries of laying and broody geese (Anser cygnoides) by Solexa sequencing[J].PLoS One,2014,9(2):e87920. [43]MI X,WEI Z,ZHOU Z,et al.dentification and profiling of sex-biased microRNAs from sea urchin Strongylocentrotus nudus gonad by Solexadeep sequencing[J].Comp Biochem Physiol Part D Genomics Proteomics,2014,10C:1-8. [44]XIAO J,ZHONG H,ZHOU Y,et al.Identification and characterization of microRNAs in ovary and testis of Nile tilapia (Oreochromis niloticus) by using solexa sequencing technology[J].PLoS One,2014,9(1):e86821. [45]ZHOU Y,CHEN L,FAN X,et al.De novo assembly of auricularia polytricha transcriptome using illumina sequencing for gene discovery and ssr marker identification[J].PLoS One,2014,9(3):e91740. [46]WU Q,XU L,GUO J,et al.Transcriptome profile analysis of sugarcane responses to Sporisorium scitaminea infection using Solexa sequencing technology[J].Biomed Res Int,2013:298920. [47]ZHAO Z,WU G,WANG J,et al.Next-generation sequencing-based transcriptome analysis of Helicoverpa armigera larvae immune-primed with Photorhabdus luminescens TT01[J].PLoS One,2013,8(11):e80146. [48]YI S,GAO Z X,ZHAO H,et al.Identification and characterization of microRNAs involved in growth of blunt snout bream (Megalobrama amblycephala) by Solexa sequencing[J].BMC Genomics,2013(14):754. [49]KANG K,ZHONG J,JIANG L,et al.Identification of microRNA-Like RNAs in the filamentous fungus Trichoderma reesei by Solexa sequencing[J].PLoS One,2013,8(10):e76288. [50]WANG F,LI H,ZHANG Y,et al.MicroRNA expression analysis of rosette and folding leaves in Chinese cabbage using high-throughput Solexasequencing[J].Gene,2013,32(2):222-229. [51]PAN Y Z,WU S G,DAI H C,et al.Solexa sequencing of microRNAs on chromium metabolism in broiler chicks[J].Nutrigenet Nutrigenomics,2013,6(3):137-153. [52]YUAN C,WANG X,GENG R,et al.Discovery of cashmere goat (Capra hircus) microRNAs in skin and hair follicles by Solexa sequencing[J].BMC Genomics,2013(14):511. [53]张绍鹏,金健,胡炳雄,等.珍稀药用植物珠子参的转录组测序及分析[J].中国中药杂志,2015,40(1):2084-2089. [54]RAVEENDAR S,NA Y W,LEE J R,et al.The complete chloroplast genome of Capsicum annuum var.glabriusculum using illumina sequencing[J].Molecules,2015,20(7):13080-13088. [55]MITRA S,FRSTER-FROMME K,DAMMS-MACHADO A,et al.Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing[J].BMC Genomics,2013,5:S16. [56]李小白,向林,罗洁,等.转录组测序(RNA-seq)策略及其数据在分子标记开发上的应用[J].中国细胞生物学学报,2013,35(5):720-726. [57]WANG L,LI P,BRUTNELL T P.Exploring plant transcriptomes using ultra high-throughput sequencing[J].Brief Funct Genomics,2010,9(2):118-128. [58]YAN H,ZHANG H,CHEN M,et al.Transcriptome and gene expression analysis during flower blooming in Rosa chinensis ‘Pallida’[J].Gene,2013,540(1):96-103. [59]GIORDANO A,COGAN NO,KAUR S,et al.Gene discovery and molecular marker development,based on high-throughput transcript sequencing of paspalum dilatatum poir[J].PLoS One,2014,9(2):e85050. [60]CHE R,SUN Y,WANG R,et al.Transcriptomic analysis of endangered chinese salamander:identification of immune,sex and reproduction-related genes and genetic markers[J].PLoS One,2014,9(1):e87940. [61]NG D W,SHI X,NAH G,et al.High-throughput RNA-seq for allelic or locus-specific expression analysis in Arabidopsis-related species,hybrids,and allotetraploids[J].Methods Mol Biol,2014,1112:33-48. [62]LIU R,DONG Y,FAN G,et al.Discovery of genes related to witches broom disease in Paulownia tomentosa×Paulownia fortunei by a de novo assembled transcriptome[J].PLoS One,2013,8(11):e80238. [63]HSU J C,CHIEN T Y,HU C C,et al.Discovery of genes related to insecticide resistance in Bactrocera dorsalis by functional genomic analysis of a de novo assembled transcriptome[J].PLoS One,2012,7(8):e40950. [64]KAYA H B,CETIN O,KAYA H,et al.SNP discovery by illumina-based transcriptome sequencing of the olive and the genetic characterization of Turkish olive genotypes revealed by AFLP,SSR and SNP markers[J].PLoS One,2013,8(9):e73674. [65]ZOU D,CHEN X,ZOU D.Sequencing,de novo assembly,annotation and SSR and SNP detection of sabaigrass (Eulaliopsis binata)transcriptome[J].Genomics,2013,102(1):57-62. [66]NICOLA M,PISANI C,BOUCHET J P,et al.Discovery of a large set of SNP and SSR genetic markers by high-throughput sequencing of pepper (Capsicum annuum)[J].Net Mol Res,2012,11(3):2295-2300. [67]WEI L,LI S,LIU S,et al.Transcriptome analysis of Houttuynia cordata Thunb.by Illumina paired-end RNA sequencing and SSR marker discovery[J].PLoS One,2014,9(1):e84105. [68]LIU Z,CHEN T,MA L,et al.Global transcriptome sequencing using the illumina platform and the development of EST-SSR markers in autotetraploid alfalfa[J].PLoS One,2013,8(12):e83549. [69]李满堂,张仕林,邓鹏,等.洋葱转录组 SSR 信息分析及其多态性研究,园艺学报,2015,42(6):1103-1111. [70]WANG Y,PAN Y,LIU Z,et al.De novo transcriptome sequencing of radish (Raphanus sativus L.) and analysis of major genes involved in glucosinolate metabolism[J].BMC Genomics,2013,14:836. [71]LI E,WANG S,LI C,et al.Transcriptome sequencing revealed the genes and pathways involved in salinity stress of Chinese mitten crab,Eriocheir sinensis[J].Physiol Genomics,2014,46(5):177-190. [72]刘英华,陈瑛.高通量测序技术的最新研究进展[J].中国妇幼保健,2013,28(13):1990-1992.
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备注/Memo
第一作者简介:姚娜(1980-),女,硕士,实验师,现主要从事生物反应器等研究工作。E-mail:52730603@qq.com.责任作者:李海燕(1971-),女,博士,教授,现主要从事植物抗逆工程与分子生物学等研究工作。E-mail:hyli99@163.com.基金项目:国家自然科学基金资助项目(31501366,31101172);国家“863”高技术研究发展计划资助项目(2011AA100606);吉林省科技厅资助项目(20150623024TC-11);大学生创新创业训练计划资助项目(201510193033)。