牦牛肺转录组图谱绘制及特有正选择遗传进化基因探究

发布时间：2018-03-11 06:15

本文选题：牦牛　切入点：肺　出处：《畜牧兽医学报》2017年07期 　论文类型：期刊论文

【摘要】：旨在利用RNA-Seq的高通量测序技术从基因组转录水平解析牦牛低氧适应及相关遗传机制。本研究以牦牛和黄牛肺为样本,经Illumina HiSeq2 500平台测序并进行生物信息学分析。结果表明,在黄牛转录测序文库中共获得了54 720 968条序列,包含4 924 882 170bp,在牦牛中共获得了51 641 282条序列,包含4 647 715 380bp。牦牛基本转录组分析发现,8 123条mRNA的5′-或3′-末端在原有基础上发生了延伸,同时还发现了7 059个新转录本,预测其中2 795个新转录本具有编码蛋白的能力;GO分析表明,共有14 764个基因得到分类注释,涉及细胞组分、生物学过程及分子功能3个大类59个小类,其中细胞、细胞过程及绑定类别最为富集;KEGG分析表明,14 485个基因涉及到258个通路,代谢途径通路最为富集,其次为粘着斑通路及阿米巴病通路。将牦牛肺转录组与黄牛进行比较,Ka/Ks分析筛选出39个正选择基因,这些基因的GO分类注释结果显示,在细胞组分TOP10中与核糖体相关的类别所占比例最大(4/10),生物学过程TOP10中与免疫细胞相关的类别所占比例最大(7/10),分子功能TOP10中与酶活性相关的类别所占比例最大(5/10);KEGG注释结果表明,这些基因共涉及56个通路,最为富集的前10个通路中涉及糖类能量、维生素、核酸等相关代谢的通路占到了7/10。同时发现,最为富集前10个通路中有3个涉及到疾病,推测这与牦牛的自我保护机制有关。本研究通过RNA-Seq转录组测序技术获得了牦牛肺正常转录组数据库,描绘出了牦牛肺正常转录组图谱,为进一步的完善牦牛基因组数据库提供了有价值的数据。同时通过与黄牛转录组的比较,筛选出了相关的正选择基因,为进一步在分子水平揭示牦牛高原低氧适应的独特进化过程及遗传分子机制提供了参考依据。
[Abstract]:The aim of this study was to analyze hypoxia adaptation and related genetic mechanisms of yaks at genomic transcription level by using RNA-Seq high-throughput sequencing technique. In this study, yak and yellow cattle lungs were selected as samples, sequenced on Illumina HiSeq2 500 platform and analyzed by bioinformatics. A total of 54 720,968 sequences including 4 924 882 170 BP and 51 641,282 sequences were obtained from the yellow cattle transcription sequencing library. The basic transcriptome analysis of 4 647,715 380bp. found that the 5- or 3H-terminal of 8,123 mRNA were extended on the original basis, and 7 059 new transcripts were also found. It was predicted that 2 795 new transcripts had the ability to encode proteins. The results of go analysis showed that 14 764 genes were classified and annotated, involving 59 subclasses, including cell components, biological processes and molecular functions. KEGG analysis of cell processes and binding types showed that 14 485 genes were involved in 258 pathways, while metabolic pathways were most abundant. 39 genes were selected by comparing the lung transcriptome of yak with that of yellow cattle. The go taxonomy of these genes showed that, The largest proportion of ribosomal related classes in cellular component TOP10 is 4 / 10%, the largest proportion of immunocyte-related classes in biological process TOP10 is 7 / 10%, and the largest proportion of TOP10 classes related to enzyme activity in molecular functional TOP10 is 5 / 10% KEGG. These genes are involved in 56 pathways, and the first 10 most enriched pathways involve carbohydrate energy, vitamins, nucleic acid and other related metabolic pathways that account for 7 / 10. At the same time, it was found that 3 of the top 10 most enriched pathways were related to disease. In this study, the RNA-Seq transcriptional sequencing technique was used to obtain the normal transcriptome database of yak lung, and the map of normal transcriptome of yak lung was obtained. It provides valuable data for further improvement of the yak genome database. At the same time, the positive selection genes are screened by comparison with the yellow cattle transcriptome. It provides a reference basis for further revealing the unique evolutionary process and genetic molecular mechanism of hypoxia adaptation in yak plateau at molecular level.
【作者单位】：西南民族大学生命科学与技术学院;西南民族大学青藏高原研究院;金川畜牧兽医局;
【基金】：西南民族大学中央高校基本科研业务费专项资金(2015NZYTD01)
【分类号】：S823.85

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