期刊文献+

基于RNA-Seq高通量测序技术的牦牛卵巢转录组研究:进一步完善牦牛基因结构及挖掘与繁殖相关新基因 被引量:20

分享 导出
摘要 RNA—Seq作为近年来新发展起来的高通量转录组测序技术,为大规模转录组学研究提供了一种全新的且更为有效的方法.目前该技术已广泛应用于转录组学中多方面的研究,尤其近年来,该技术在进一步完善基因结构信息及挖掘新转录本及新基因方面的功能也逐渐受到关注.本研究以牦牛卵巢组织作为研究对象,应用RNA.Seq技术对其进行高通量转录组测序分析,经测序后得到了一个包含26826516条过滤后测序读数,4828772880bp的卵巢测序文库,比对分析显示,有16992条牦牛基因发生表达,其中3734条基因存在不同类型的可变剪接.功能分析表明,这些表达基因涉及多种GO分类及KEGG通路.进一步分析转录组数据发现,共有7340个基因的5’或3’端在原有基因组的位置基础上发生了延伸,同时还发现了6321个新转录本,定位回基因组预测显示,外显子数量为1~84个,其中2267个新转录本预测具有编码蛋白的能力.比对分析显示,共有1200~4993条新转录本分别与Nt数据库、Nr数据库及SwissProt数据库中的基因比对上,其中与牛相似性基因最多(41.4%),其次为野牦牛(33.0%)、绵羊(6.3%)、人类(2.8%)及小鼠(1.6%)等其他物种.进一步对新转录本进行GO分类注释,结果显示,与繁殖发育相关的GO分类占有较大比例,其中繁殖类别(reproduction)所涉及的新转录本最多.本研究结果为描绘牦牛卵巢正常转录组图谱及进一步探析牦牛繁殖性能提供了基础,同时证实RNA.Seq高通量转录组技术在完善基因结构及挖掘新转录本及新基因方面的具有强大的优势,为进一步完善牦牛基因组结构信息及挖掘潜在的新基因提供了丰富数据.
出处 《中国科学:生命科学》 CSCD 北大核心 2014年第3期307-317,共11页 SCIENTIA SINICA Vitae
基金 国家科技支撑计划(批准号:2012BAD13806)和国家公益性行业(农业)科研专项(批准号:201203009)资助
作者简介 联系人.E—mail:lijian@swun.cn
  • 相关文献

参考文献46

  • 1Suzuki Y, Sugano S. Transcriptome analyses of human genes and applications for proteome analyses. Curr Protein Pept Sci, 2006, 7: 147-163. 被引量:1
  • 2Gustincich S, Sandelin A, Plessy C, et al. The complexity of the mammalian transcriptome. J Physiol, 2006, 575:321-332. 被引量:1
  • 3Sangwan R S, Tripathi S, Singh J, et al. De novo sequencing and assembly of Centella asiatica leaf transcriptome for mapping of structural, functional and regulatory genes with special reference to secondary metabolism. Gene, 2013, 525:58-76. 被引量:1
  • 4Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet, 2009, 10:57-63. 被引量:1
  • 5Tariq M A, Kim H J, Jejelowo O, et al. Whole-transcriptome RNAseq analysis from minute amount of total RNA. Nucleic Acids Res, 2011, 39:e120. 被引量:1
  • 6Richard H, Schulz M H, Sultan M, et al. Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Res, 2010, 38:e112. 被引量:1
  • 7Chert C, Ai H, Ren J, et al. A global view of porcine transcriptome in three tissues from a full-sib pair with extreme phenotypes in growth and fat deposition by paired-end RNA sequencing. BMC Genomics, 2011, 12:448. 被引量:1
  • 8Lu T, Lu G, Fan D, et al. Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-Seq. Genome Res, 2010, 20:1238-1249. 被引量:1
  • 9Jaiger M, Ott C E, Grunhagen J, et al. Composite transcriptome assembly of RNA-Seq data in a sheep model for delayed bone healing. BMC Genomics, 2011, 12:158. 被引量:1
  • 10Huang W, Khatib H. Comparison of transcriptomic landscapes of bovine embryos using RNA-Seq. BMC Genomics, 2010, 11:711. 被引量:1

二级参考文献27

  • 1Blanchard A D, Page K R, Watkin H, Hayward P, Wong T, Bartholomew M, Quint D J, Daly M, Garcia-Lopez J, Champion B R. Identification and characterization of SKAT-2, a novel Th2-specific zinc finger gene. Eur J Immunol, 2000, 30 (11):3100~3110. 被引量:1
  • 2Lu C C, Brennan J, Robertson E J. From fertilization to gastrulation:axis formation in the mouse embryo. Curr Opin Genet Dev,2001, 11(4):384~392. 被引量:1
  • 3Zawel L, Reinberg D. Common themes in assembly and function of eukaryotic transcription complexes. Annu Rev Biochem,1995, 64:533~561. 被引量:1
  • 4Lander E S, Linton L M, Birren B, Nusbaum C, Zody M C,Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov J P, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M,Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J,Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N,Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I,Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A; International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature, 2001, 409(6822) :860~921. 被引量:1
  • 5McCarty A S, Kleiger G, Eisenberg D, Smale S T. Selective dimerization of a C2 H2 zinc finger subfamily. Mol Cell, 2003, 11(2):459 ~470. 被引量:1
  • 6Wang F, Zhu Y, Huang Y, McAvoy S, Johnson W B, Cheung T H, Chung T K, Lo K W, Yim S F, Yu M M, Ngan H Y, Wong Y F, Smith D I. Transcriptional repression of WEE1 by Kruppellike factor 2 is involved in DNA damage-induced apoptosis. Oncogene, 2005, Feb, 28. 被引量:1
  • 7Williams A J, Khachigian L M, Shows T, Collins T. Isolation and characterization of a novel zinc-finger protein with transcription repressor activity. J Biol Chem, 1995, 270(38) :22143~22152. 被引量:1
  • 8Williams A J, Blacklow S C, Collins T. The zinc finger-associated SCAN box is a conserved oligomerization domain. Mol Cell Biol, 1999, 19(12):8526~8535. 被引量:1
  • 9Rousseau-Merck M F, Hillion J, Jonveaux P, Couillin P, Seite P, Thiesen H J, Berger R. Chromosomal localization of 9 KOX zinc finger genes:physical linkages suggest clustering of KOX genes on chromosomes 12, 16, and 19. Hum Genet, 1993, 92(6) :583~587. 被引量:1
  • 10Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y,Arakawa T, Hara A, Fukunishi Y, Konno H, Adachi J, Fukuda S, Aizawa K, Izawa M, Nishi K, Kiyosawa H, Kondo S, Yamanaka I, Saito T, Okazaki Y, Gojobori T, Bono H, Kasukawa T, Saito R, Kadota K, Matsuda H, Ashburner M, Batalov S,Casavant T, Fleischmann W, Gaasterland T, Gissi C, King B,Kochiwa H, Kuehl P, Lewis S, Matsuo Y, Nikaido I, Pesole G,Quackenbush J, Schriml LM, Staubli F, Suzuki R, Tomita M,Wagner L, Washio T, Sakai K, Okido T, Furuno M, Aono H,Baldarelli R, Barsh G, Blake J, Boffelli D, Bojunga N, Carninci P, de Bonaldo M F, Brownstein M J, Bult C, Fletcher C.Functional annotation of a full-length mouse cDNA collection.Nature, 2001, 409(6821) 685~690. 被引量:1

共引文献3

同被引文献286

引证文献20

二级引证文献30

投稿分析

相关作者

内容加载中请稍等...

相关机构

内容加载中请稍等...

相关主题

内容加载中请稍等...

浏览历史

内容加载中请稍等...
;
使用帮助 返回顶部 意见反馈