Advance in Transcriptomics and Its Application in Olericulture Research

doi:10.11924/j.issn.1000-6850.casb14100038

Abstract

Abstract: This article not only introduces the main method and principle of transcriptome but also analyzes its application to vegetables and other plants. Genomic data scarcity existing in vegetables can be overcome by the study of transcriptome. What is more, it can clarify the genes structure and its effects in resistance. It was showed that the current method of transcriptome mainly based on hybridization or sequencing technology which consisted of gene chip, SAGE(serial analysis of gene expression), MPSS(massively parallel signature sequencing), and RNA-Seq(RNA-sequencing); research on transcriptome could be used to understand the resistance of vegetables, the molecular mechanism of disease resistance, and demonstrate specific gene expression. But high-speed sequencing and scientific analysis were the bottlenecks restricting its development. Therefore, we believed that caution was needed in the molecular mechanism demonstration when proteomics and bioinformatics were used to provide further evidence; while cutting-edge biological theories like transcriptome should be applied more to the vegetables.

Lian Jie,Zhang Xichun and Gu Jiantian. Advance in Transcriptomics and Its Application in Olericulture Research[J]. Chinese Agricultural Science Bulletin, 2015, 31(8): 118-122.

References

[1] Ansorge W J. Next-generation DNA sequencing techniques[J]. N Biotechnol,2009,25(4):195-203.
[2] 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.
[3] Velcuescu V E, Zhang L, Zhou W. Characterization of the yeast transcriptome[J]. Cell,1997,88:243-251.
[4] 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.
[5] Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics[J]. Nat Rev Genet, 2009,10(1):57-63.
[6] 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(1):51-56.
[7] Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics[J]. Nat Rev Genet,2009,10(1):57-63.
[8] 张骞,盛军.基因芯片技术的发展和应用[J].中国医学科学院学报,2008,30(3):344-347.
[9] 李星,李亚宁,杨文香,等.基因表达系列分析技术及其在植物抗病性研究中的应用[J].农业生物技术学报,2006,14(5):803-808.
[10] 陈杰.大规模平行测序技术(MPSS)研究进展[J].生物化学与生物物理进展,2004,31(8):761-765.
[11] Li X, Chen G H, Zhang W Y, et al. Genome-wide transcriptional analysis of maize endosperm in response to ae wx double mutations[J]. J Genet Genom,2010,37(11):749-762.
[12] 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.
[13] Emrich S J, Barbazuk W B, Li L, et al. Gene discovery and annotation using LCM-454 transcriptome sequencing[J]. Genome Res,2007,17(1):69-73.
[14] Ohtsu K, Smith M B, Emrich S J, et al. Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.)[J]. Plant J,2007,52(3):391-404.
[15] Jones-Rhoades M W, Borevitz J O, Preuss D. Genome-wide expression profiling of the Arabidopsis female gametophyte identifies families of small, secreted proteins[J]. PloS Genet,2007,3(10):1848-1861.
[16] Weber A P M, Weber K L, Carr K, et al. Sampling the arabidopsis transcriptome with massively parallel pyrosequencing[J]. Plant Physiol,2007,144(1):32-42.
[17] 李湘龙,柏斌,吴俊,等.第二代测序技术用于水稻和稻瘟菌互作早期转录组的分析.遗传,2012,34(1):102-112.
[18] Glenn T C. Field guide to next-generation DNA sequencers[J]. Mol Ecol Resour,2011,11(5):759-769.
[19] Huang W, Has an Khatib. Comparison of transcriptiome assembly of RNA-Seq data in a sheep model for delayed hone healing[J]. BMC Genomics,2011,11:711.
[20] Faulconnier Y, Chilliard Y, Torbati M B, et al. The transcriptomic profiles of adipose tissues are modified by feed deprivation in lactating goats[J]. Comparative Biochemistry and Physiology Part D Geomics Proteomics,2011,6(2):139-149.
[21] 李新建.猪脂肪沉积关键基因筛选及TCTP基因功能研究[D].杨凌:西北农林科技大学,2011.
[22] Dai C, Zhang Y M, Zhang Q, et al. A microRNA catalog of swine umbilical vein endothelial cells identified by deep sequencing[J]. Agricultural Sciences in China,2011,10(9):1467-1474.
[23] Li T T, Wang S Y, Wu R M, et al. Identification of long non-protei coding RNAs in chicken skeletal muscle using next generation sequencing[J]. Genomics,2012,99(5):292-298.
[24] Peng Z Y, Cheng Y B, Tan B C, et al. Comprehensive analysis of RNA-Esq. data reveals extensive RNA editing in a human transcriptome[J]. Nature Biotechnology,2012,30(3):253-262.
[25] Filichkin S A, Priest H D, Givan S A, et al. Genome-wide mapping of alternative splicing in Arabidops thaliana[J]. Genome Research,2010,20(1):45-58.
[26] Wang L K, Wang X W, Wang X, et al. Observations on novel splice junctions from RNA sequencing data[J]. Biochem Biophys Res Commun,2011,409(2):299-303.
[27] Maher C A, Kumar-Sinha C, Cao X H, et al. Transcriptome Sequencing to detect gene fusions in cancer.Nature,2009,458(7234):97-101.
[28] Ren S C, Peng Z Y, Mao J H, et al. RNA-Seqanalysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noneoding RNAs and aberrant alternative splicing[J]. Cell Res,2012,22(5):806-821.
[29] Montgomery S B, Sammeth M, Gutierrez-Arcelus M, et al. Transcriptome genetics using second generation sequencing in a Caucasian population[J]. Nature,2010,464(7289):773-777.
[30] 付畅,黄宇.转录组学平台技术及其在植物抗逆分子生物学中的应用[J].生物技术通报,2011,6.
[31] Van Vliet A. Next generation sequencing of microbial transcriptomes: challenges and opportunities[J]. Fems Microbiology Letters,2010,302(1):1-7.
[32] 王艳,陶向.比较转录组学研究ABA对番茄抗病基因的影响[A].中国遗传学会第九次全国会员代表大会暨学术研讨会论文摘要汇编[C].2009-2013.
[33] 王晓峰,何卫龙,蔡卫佳,等.马尾松转录组测序和分析[J].分子植物育种,2013,11(3):385-392.
[34] 孙业鹏.盐碱胁迫下羊草转录组测序及分析[D].长春:吉林农业大学,2012.
[35] Cheung F, Haas B J, Goldberg S, et al. Sequencing Medicago truncatula expressed sequenced tags using 454. Life Sciences technology[J]. Bmc Genomics,2006,7:272-282.
[36] Weber A, Weber K L, Carr K, et al. Sampling the arabidopsis transcriptome with massively parallel pyrosequencing[J]. Plant Physiology,2007,144:32-42.
[37] Vera J C, Wheat C W, Fescemyer H W, et al. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing[J]. Mol Ecol,2008,17(7):1636-1647.
[38] Trick M, Long Y, Meng J L, et al. Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing[J]. Plant Biotechnology J,2009,7(4):334-346.
[39] Guo S G, Zheng Y, Joung J G, et al. Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types[J]. BMC Genomics,2010,11(1):384.
[40] Wang Z, Fang B, Chen J, et al. De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas)[J]. BMC Genomics,2010,11(1):726.
[41] Sun X D, Zhou S M, Meng F L, et al. De novo assembly and characterization of the garlic (Allium sativum) bud transcriptome by Illumina sequencing[J]. Plant Cell Rep,2012,31(10):1823-1828.
[42] Wang W, Wang Y J, Zhang Q, et al. Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing[J]. BMC Genomics,2009,10(1):465.
[43] Sun C, Li Y, Wu Q, et al. De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis[J]. BMC Genomics,2010,11(1):262.
[44] Birzele F, Schaub J, Rust W, et al. Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing[J]. Nucleic Acids Research,2010,38(12):3999-4010.
[45] 刘长虹,蔡路昀,韩晓旭,等.UV-C照射后番茄差异表达基因的基因芯片检测[J].农业机械学报,2012,24(1):134-140.
[46] 王晓光,马远征,王晓辉,等.破色期番茄果实均一化cDNA沉默文库的构建和功能基因筛选模型的初步建立[J].生物化学与生物物理进展,2009,36(8):1079-1083.
[47] Deyholos M K. Making the most of drought and salinity transcriptomics[J]. Plant Cell and Enviromment,2010,33:648-654.
[48] Logacheva M D, Kasianov A S, Vinogradov D V, et al. De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum)[J]. BMC Genomics,2011,12(1):30.
[49] Blanca J, Canizares J, Roig C, et al. Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbit a pepo (Cucurbitaceae)[J]. BMC Genomics,2011,12(1):104.
[50] Coppe A, Pujolar J M, Maes G E, et al. Sequencing, de novo annotation and analysis of the first Anguilla transcriptome: EeelBase opens new perspectives for the study of the critically endangered European eel[J]. BMC Genomics,2010,11(1):635.