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中华猕猴桃基因组可变剪接事件鉴定及分析

DOI: 10.1360/N052014-00275, PP. 289-300

Keywords: 中华猕猴桃,可变剪接,基因组,维生素

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Abstract:

可变剪接使一个基因能产生多种mRNA成熟体,极大地增加蛋白多样性.采用中华猕猴桃基因组数据做参考数据,利用中华猕猴桃叶片和果实3个不同发育时期(未成熟、半成熟和成熟期)的转录组数据,从中华猕猴桃基因组(39040个基因)中共鉴定出11651个基因(占总基因数的29%)对应的32180个可变剪接事件.在可变剪接不同类型中,内含子保留类型的发生频率最高,占50%以上;3'可变位点类型频率约为5'端可变类型的2倍.GO富集分析结果表明,可变剪接的基因主要富集于酶调控及核苷酸结合相关功能的GO类别中,而组织特有可变剪接基因功能富集热点与组织的重要功能关联,叶片多为肌动蛋白及微管相关;未成熟果实与双组分信号系统相关;半成熟果实多与磷脂合成过程相关;成熟果实多与信号传递过程相关.另外,55.6%的维生素合成相关基因发生可变剪接事件,显著高于基因组水平的29.6%,暗示着可变剪接参与维生素合成相关基因代谢过程中的重要作用.通过对中华猕猴桃全基因组可变剪接的分析,为解析中华猕猴桃基因组及进一步开展相关分子育种工作提供依据.

References

[1]  25 Quevillon E, Silventoinen V, Pillai S, et al. InterProScan: protein domains identifier. Nucleic Acids Res, 2005, 33: W116-W120
[2]  26 Trapnell C, Roberts A, Goff L, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc, 2012, 7: 562-578
[3]  27 Rabbitts T H. Evidence for splicing of interrupted immunoglobulin variable and constant region sequences in nuclear RNA. Nature, 1978, 275: 291-296
[4]  28 Black D L. Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem, 2003, 72: 291-336
[5]  29 Stamm S, Ben-Ari S, Rafalska I, et al. Function of alternative splicing. Gene, 2005, 344: 1-20
[6]  30 Lareau L F, Green R E, Bhatnagar R S, et al. The evolving roles of alternative splicing. Curr Opin Struc Biol, 2004, 14: 273-282
[7]  31 Xu Q, Modrek B, Lee C. Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. Nucleic Acids Res, 2002, 30: 3754-3766
[8]  32 Transcriptome and genome conservation of alternative splicing events in humans and mice. In: Sugnet C W, Kent W J, Haussler D, eds. Proc. 9th Pacific Symposium on Biocomputing. Hawaii. 2004, Singapore: World Scientific, 2004. 66-77
[9]  33 Chacko E, Ranganathan S. Genome-wide analysis of alternative splicing in cow: implications in bovine as a model for human diseases. BMC Genomics, 2009, 10: S11
[10]  34 Babenko V N, Aitnazarov R B, Goncharov F A, et al. Alternative splicing landscape of the Drosophila melanogaster genome. Russ J Genet, 2010, 46: 1036-1038
[11]  35 Labadorf A, Link A, Rogers M F, et al. Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii. BMC Genomics, 2010, 11: 114
[12]  36 Ramani A K, Calarco J A, Pan Q, et al. Genome-wide analysis of alternative splicing in Caenorhabditis elegans. Genome Res, 2011, 21: 342-348
[13]  37 Sablok G, Gupta P K, Baek J M, et al. Genome-wide survey of alternative splicing in the grass Brachypodium distachyon: a emerging model biosystem for plant functional genomics. Biotechnol Lett, 2011, 33: 629-636
[14]  38 Bao H, Li E Y, Mansfield S D, et al. The developing xylem transcriptome and genome-wide analysis of alternative splicing in Populus trichocarpa (black cottonwood) populations. BMC Genomics, 2013, 14: 359
[15]  39 Panahi B, Abbaszadeh B, Taghizadeghan M, et al. Genome-wide survey of alternative splicing in Sorghum Bicolor. Physiol Mol Biol Plants, 2014, 20: 323-329
[16]  40 Wu H P, Su Y S, Chen H C, et al. Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens. Genome Biol, 2014, 15: R10
[17]  41 Shen Y, Zhou Z, Wang Z, et al. Global dissection of alternative splicing in paleopolyploid soybean. Plant Cell, 2014, 26: 996-1008
[18]  42 Li P, Ponnala L, Gandotra N, et al. The developmental dynamics of the maize leaf transcriptome. Nat Genet, 2010, 42: 1060-1067
[19]  43 Marquez Y, Brown J W, Simpson C, et al. Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res, 2012, 22: 1184-1195
[20]  44 Pan Q, Shai O, Lee L J, et al. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet, 2008, 40: 1413-1415
[21]  45 Walters B, Lum G, Sablok G, et al. Genome-wide landscape of alternative splicing events in Brachypodium distachyon. DNA Res, 2013, 20: 163-171
[22]  46 Baek J M, Han P, Iandolino A, et al. Characterization and comparison of intron structure and alternative splicing between Medicago truncatula, Populus trichocarpa, Arabidopsis and rice. Plant Mol Biol, 2008, 67: 499-510
[23]  47 Staiger C J. Signaling to the actin cytoskeleton in plants. Annu Rev Plant Physiol Plant Mol Biol, 2000, 51: 257-288
[24]  48 Kadota A, Wada M. Photoorientation of chloroplasts in protonemal cells of the fernAdiantum as analyzed by use of a video-tracking system. Bot Mag, 1992, 105: 265-279
[25]  49 Wada M, Kagawa T, Sato Y. Chloroplast movement. Annu Rev Plant Biol, 2003, 54: 455-468
[26]  50 Stock A M, Robinson V L, Goudreau P N. Two-component signal transduction. Annu Rev Biochem, 2000, 69: 183-215
[27]  51 吴家森, 管剑峰. 秦美猕猴桃果实生育及营养量变的若干特点. 浙江林学院学报, 2002, 19: 244-246
[28]  52 安华明, 樊卫国, 刘进平. 生育期猕猴桃果实中营养元素积累规律研究. 种子, 2003, 4: 24-25
[29]  53 陈昆松. ABA和IAA对猕猴桃果实成熟进程的调控. 园艺学报, 1999, 26: 81-86
[30]  54 张玉, 陈昆松, 张上隆, 等. 猕猴桃果实采后成熟过程中糖代谢及其调节. 植物生理与分子生物学学报, 2004, 30: 317-324
[31]  55 涂正顺, 李华, 王华, 等. 猕猴桃果实采后香气成分的变化. 园艺学报, 2001, 28: 512-516
[32]  56 殷学仁, 张波, 李鲜, 等. 乙烯信号转导与果实成熟衰老的研究进展. 园艺学报, 2009, 36: 133-140
[33]  1 Arcus A C. Proteolytic enzyme of Actinidia chinensis. Biochim Biophys Acta, 1959, 33: 242-244
[34]  2 Cheng C H, Seal A G, Boldingh H L, et al. Inheritance of taste characters and fruit size and number in a diploid Actinidia chinensis (kiwifruit) population. Euphytica, 2004, 138: 185-195
[35]  3 Skinner M A, Loh J M S, Hunter D C, et al. Gold kiwifruit (Actinidia chinensis ‘Hort16A'') for immune support. Proc Nutr Soc, 2011, 70: 276-280
[36]  4 张菊明, 林佩芳. 中华猕猴桃多糖对巨噬细胞-T细胞免疫介质的作用. 科技通报, 1990, 6: 284-286
[37]  5 宋文瑛, 许冠华, 张光霁. 猕猴桃根多糖对人胃癌SGC-7901细胞增殖, 凋亡及p-p38表达的影响. 中国中西医结合杂志, 2014, 34: 329-333
[38]  6 Wang B B, Brendel V. Genomewide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci USA, 2006, 103: 7175-7180
[39]  7 Huang S, Ding J, Deng D, et al. Draft genome of the kiwifruit Actinidia chinensis. Nat Commun, 2013, 4: 2640
[40]  8 Berget S M, Moore C, Sharp P A. Spliced segments at the 5'' terminus of adenovirus 2 late mRNA. Proc Natl Acad Sci USA, 1977, 74: 3171-3175
[41]  9 Tong C, Wang X, Yu J, et al. Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa. BMC Genomics, 2013, 14: 689
[42]  10 Reddy A S. Alternative splicing of pre-messenger RNAs in plants in the genomic era. Annu Rev Plant Biol, 2007, 58: 267-294
[43]  11 Zhang G, Guo G, Hu X, et al. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res, 2010, 20: 646-654
[44]  12 Reddy A S, Marquez Y, Kalyna M, et al. Complexity of the alternative splicing landscape in plants. Plant Cell, 2013, 25: 3657-3683
[45]  13 Zhang X N, Mount S M. Two alternatively spliced isoforms of the Arabidopsis SR45 protein have distinct roles during normal plant development. Plant Physiol, 2009, 150: 1450-1458
[46]  14 Wang Q, Silver P A. Genome-wide RNAi screen discovers functional coupling of alternative splicing and cell cycle control to apoptosis regulation. Cell Cycle, 2010, 9: 4419-4421
[47]  15 Gu L, Guo R. Genome-wide detection and analysis of alternative splicing for nucleotide binding site-leucine-rich repeats sequences in rice. J genet genomics, 2007, 34: 247-257
[48]  16 Leviatan N, Alkan N, Leshkowitz D, et al. Genome-wide survey of cold stress regulated alternative splicing in Arabidopsis thaliana with tiling microarray. PLoS One, 2013, 8: e66511
[49]  17 Staiger D, Brown J W. Alternative splicing at the intersection of biological timing, development, and stress responses. Plant Cell, 2013, 25: 3640-3656
[50]  18 Quesada V, Macknight R, Dean C, et al. Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time. EMBO J, 2003, 22: 3142-3152
[51]  19 Ding F, Cui P, Wang Z Y, et al. Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis. BMC Genomics, 2014, 15: 431
[52]  20 Wang E T, Sandberg R, Luo S, et al. Alternative isoform regulation in human tissue transcriptomes. Nature, 2008, 456: 470-476
[53]  21 Filichkin S A, Priest H D, Givan S A, et al. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res, 2010, 20: 45-58
[54]  22 Goldberg D H, Victor J D, Gardner E P, et al. Spike train analysis toolkit: enabling wider application of information-theoretic techniques to neurophysiology. Neuroinformatics, 2009, 7: 165-178
[55]  23 Patel R K, Jain M. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One, 2012, 7: e30619
[56]  24 Trapnell C, Pachter L, Salzberg S L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 2009, 25: 1105-1111

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