牦牛肺转录组图谱绘制及特有正选择遗传进化基因探究

doi:10.11843/j.issn.0366-6964.2017.07.004

摘要/Abstract

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4 924 882 170 bp，在牦牛中共获得了51 641 282条序列，包含4 647 715 380 bp。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:

In this study, yak hypoxia adaptation and its related genetic molecular mechanism at the whole transcriptome level were analyzed using high-throughput RNA-Seq technology. Lung tissue samples were collected from yak and cattle, and RNA-Seq was performed on an Illumina HiSeq 2500 platform. A total of 54 720 968 filtered sequences containing 4 924 882 170 bp were obtained in the cattle sequencing library while 51 641 282 sequences containing 4 647 715 380 bp were obtained in the yak sequencing library. The basic transcriptome analysis showed that either the 5'-or 3'-ends of 8 123 genes in the yak genome were extended compared to the original yak genome. A total of 7 059 new transcripts were identified, of which 2 795 were predicted to have the ability to encode proteins. The GO analysis showed that a total of 14 764 genes were annotated in the cellular component, biological process and molecular function categories as well as 59 subcategories. Cell process and binding were the most enriched. The KEGG analysis showed that 14 485 genes were involved in 258 pathways. The metabolic pathway was the most enriched, followed by the focal adhesion pathway and then the amoebiasis pathway. A total of 39 positively selected genes were identified by Ka/Ks analysis based on a comparison between yak and cattle lung transcriptomes. The GO classification analysis results showed that, among the top 10 cellular component subcategories, those related to ribosome accounted for the highest proportion (4/10). Among the top 10 biological subcategories, those related to immunological cells accounted for the highest proportion (7/10). Among the top 10 molecular function subcategories, those related to enzymatic activities accounted for the highest proportion (5/10). The KEGG annotation results showed that the positively selected genes were involved in 56 pathways. Among the top 10 enriched pathways, 7 pathways were involved in sugar energy, vitamin and nucleic acid related metabolic pathways. Three of the top 10 enriched pathways were related to diseases, which might be attributed to the self-protective mechanism of yak. In conclusion, the normal transcriptome profile of yak lungs was successfully established by using RNA-Seq technology. It provided valuable data for further improving the yak genome database. Furthermore, the unique evolutionary process of yak hypoxia adaptation and its related genetic molecular mechanism were revealed by the positively selected genes identified in this study.

中图分类号:

杨琦玥, 陈通, 兰道亮, 熊显荣, 候定超, 李键. 牦牛肺转录组图谱绘制及特有正选择遗传进化基因探究[J]. 畜牧兽医学报, 2017, 48(7): 1202-1211.

YANG Qi-yue, CHEN Tong, LAN Dao-liang, XIONG Xian-rong, HOU Ding-chao, LI Jian. Mapping of Transcriptome and Identification of Positively Selected Genes in Lung in Yak[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2017, 48(7): 1202-1211.

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