麦洼牦牛肺脏比较转录组研究

发布时间：2018-04-14 18:25

本文选题：牦牛 + 肺脏　；参考：《西南民族大学》2015年硕士论文

【摘要】：本研究以四川阿坝地区麦洼品种牦牛及当地黄牛肺脏组织为研究对象,应用第二代高通量测序RNA-Seq技术经Illumina HiSeqTM2000平台对牦牛及当地黄牛肺脏进行了转录组深度测序并开展了相关的比较转录组学研究。将获得的clean reads与牦牛基因组及相关参考基因进行了比对分析,结构优化分析、可变剪接分析、新转录本预测、SNP位点预测同时将牦牛与黄牛转录组比对所筛选出的差异基因进行了进一步的GO和KEGG Pathway富集分析。1.深度测序后,去除接头序列、空读序列以及低质量序列后在牦牛肺脏组织的总mRNA中各获得51641282条clean reads。2.比对分析显示,共有31898650条比对到牦牛参考基因组上,其中唯一比对的序列数(unique match)的序列有30021903条,占产出序列的58.14%。比对到参考基因的序列数(Total Mapped Reads)有18409161,其中唯一比对的序列数(unique match)的序列分别有17626475条,占产出序列的34.13%。3.结构优化分析结果表明,牦牛基因组上共有8123个基因在原有牦牛基因组位置的基础上发生了延伸,其中包括的4719个基因的5′端延伸和,3404个基因的3′端延伸。4.新转录本预测和注释结果显示,牦牛肺脏转录组共发现7059个新转录本,长度分布为180~14884 bp,此结果为进一步挖掘注释牦牛潜在的新基因特别是与高原低氧适应性相关新基因提供了数据。5.可变剪接分析及SNP分析结果显示,牦牛共有4097条已比对上的基因涉及可变剪接。其中内含子保留性剪接方式(intron retention)占据最大比例,其次为外显子跳跃剪接(exon skipping)及3′端可变剪接(alternative 3′splice site).使用SOAPsnp(Li,2009)检测样品间的单核苷酸多态性(Single Nucleotide Polymorphism,SNP),SNP分析显示,牦牛基因组上70601个位点存在单核苷酸多态性。6.差异显著表达基因筛选及GO和KEGG Pathway富集分析结果显示,牦牛肺脏组织共有16815个表达基因,与黄牛肺脏转录组相比较,在牦牛肺脏组织中共筛选出差异显著表达的基因数量为1618个,其中有1037个基因表现为上调,581个基因表现为下调。对差异表达基因进一步的GO富集分析表明,细胞组分(cellular components)部分共涉及418个分类条目,对其Top10进行重点分析发现,细胞质膜部分最为富集占重要比例(4/10),其次为胞外区部分(3/10)和细胞内脂蛋白运输相关条目(3/10)。KEGG注释结果表明,共1412个基因涉及247个通路(pathways),其中富集前10通路(top 10 pathways)中补体和凝血级联反应(Complement and coagulation cascades)最为富集,其次为代谢细胞色素P450的外源性物质(Metabolism of xenobiotics by cytochrome P450)及药物代谢,细胞色素P450(Drug metabolism-cytochrome P450)。本研究通过RNA-Seq转录组测序技术获得了牦牛肺脏正常转录组数据库,描绘出了牦牛肺脏正常转录组图谱。同时通过与黄牛转录组比对筛选出差异基因的手段,首次从转录组学角度探讨牦牛与普通黄牛在高原低氧适应性等方面的差异,并从分子水平揭示牦牛高原低氧适应性的独特的进化过程及遗传分子机制。本研究成果为今后牦牛及高原动物低氧适应性的相关研究提供了基础和平台,为低氧造成的人及动物肺脏相关高原疾病尤其是高原缺氧引起的低氧损伤类疾病的预防和治疗提供了依据。与此同时,本研究成果也为进一步的完善牦牛基因组数据库提供了有价值的数据。
[Abstract]:In this study, Sichuan ABA area of Maiwa Yak breeds and local cattle lung tissue as the research object, using the second generation high-throughput sequencing technology of RNA-Seq through the Illumina HiSeqTM2000 platform for yak and local cattle lung transcriptome deep sequencing and carried out comparative study of transcriptomics related. Clean and reads will get the yak genome and the relevant reference gene by comparison analysis, structure optimization analysis, alternative splicing analysis, new gene prediction, the prediction SNP loci genetic differences compared with cattle yak transcriptome selected for further GO and KEGG Pathway enrichment analysis of.1. deep sequencing after removal of the joint sequence and empty read sequences and low quality sequences after the total mRNA in the yak lung tissue in each 51641282 clean reads.2. comparison analysis showed that a total of 31898650 compared to the reference genome of Yak The sequence alignment, the only number (unique match) sequence 30021903, sequence alignment output accounted for 58.14%. sequences to the reference gene number (Total Mapped Reads) 18409161, the number of unique sequence alignment (unique match) sequences were 17626475, accounting for the output sequence of 34.13%.3. structure optimization analysis results show that the yak genome consists of 8123 genes were extended in the original position of the yak genome, the 4719 genes including the 5 'end and extending, 3404 genes of the 3' end of the new extension of the.4. transcript prediction and annotation results showed that the yak lung transcriptome were found 7059 new transcripts the length, the distribution of the 180~14884 BP, this result for further mining new gene annotation yak potential especially new genes associated with adaptation to hypobaric hypoxia provides data.5. alternative splicing analysis and SNP analysis results A total of 4097 yak shows, the ratio has genes involved in alternative splicing. The intron retention of splicing (intron retention) occupy the largest proportion, followed by exon skipping splicing (exon skipping) and 3 'splice (3' alternative splice site). The use of SOAPsnp (Li, 2009) single nucleotide polymorphism was detected among the samples (Single Nucleotide, Polymorphism, SNP), SNP analysis showed that the significant expression of GO and KEGG genes and Pathway enrichment analysis showed that single nucleotide polymorphism.6. differences between the 70601 sites on the genome of yak, yak lung tissue has a total of 16815 genes, compared with cattle lung transcriptome, a significant number of the expression in the lung tissues of yak were screened out of 1618 genes, including 1037 genes up-regulated and 581 genes showed down-regulation of differentially expressed genes. Further GO rich Set analysis showed that cell components (cellular components) part involving a total of 418 entries, carries on the key analysis found on the Top10 cell membrane, some of the most concentrated large proportion (4/10), followed by the extracellular domain (3/10) and lipoprotein transport related items within the cell (3/10).KEGG annotation results show that a total of 1412 genes involved in 247 pathways (pathways), of which 10 pathways enrichment before (top 10 pathways) in the complement and coagulation cascades (Complement and coagulation cascades) for the enrichment, followed by exogenous metabolism of cytochrome P450 (Metabolism of xenobiotics by cytochrome P450) and cytochrome P450 (drug metabolism. Drug metabolism-cytochrome P450). This research has obtained the normal yak lung transcriptome database through RNA-Seq sequencing, depicts the yak lung normal transcription pattern. At the same time with yellow Bovine transcriptome comparison genes were screened by means of difference for the first time from the perspective of transcriptome of yak and cattle in the aspects of adaptability to high altitude hypoxia, and reveals the yak plateau hypoxia adaptability unique evolutionary process and molecular genetic mechanisms at the molecular level. The research results provide the foundation and platform for the future research of yak and animal adaptability to plateau hypoxia, hypoxia caused by human and animal lung related diseases especially plateau provides the basis for the prevention and treatment of hypoxic hypoxia injury caused by diseases. At the same time, the results of this study provide valuable data for further improvement of yak genome database.

【学位授予单位】：西南民族大学
【学位级别】：硕士
【学位授予年份】：2015
【分类号】：S823.85

【相似文献】