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

Abstract

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.

CLC Number:

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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Mapping of Transcriptome and Identification of Positively Selected Genes in Lung in Yak

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