ACTA THERIOLOGICA SINICA ›› 2020, Vol. 40 ›› Issue (5): 475-484.DOI: 10.16829/j.slxb.150414

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Transcriptomics analysis of lungs in yaks breeding at different altitudes

FU Fang 1# , GUAN Jiuqiang 2# ,QU Xiulong1, WANG Li1, LUO Xiaolin2, AN Tianwu2, ZHANG Xiangfei 2#br#   

  1. (1 The Key Laboratory of Qinghai-Tibet Plateau Animal Genetic Resource and Utilization, Ministry of Education and Sichuan Province, Southwest Minzu University, Chengdu 610041, China)(2 Sichuan Academy of Grassland Sciences, Chengdu 611731, China)
  • Online:2020-09-30 Published:2020-09-27


傅芳1# 官久强2# 曲秀龙1 王利1 罗晓林2 安添午2 张翔飞2   

  1. (1 西南民族大学,青藏高原动物遗传资源保护与利用教育部和四川省重点实验室,成都 610041)
    (2 四川省草原科学研究院,成都 611731)
  • 通讯作者: 王 利 E-mail:; 罗晓林 E-mail:
  • 基金资助:

Abstract: This study was aimed to explore the characteristics and regularity of gene expression of yaks adapting to high-altitude hypoxic environment. Transcriptome sequencing was performed in 2.5-3-year-old healthy male Maiwa yaks bred at high and low altitudes for 4 months. The average altitudes were 3 560 m and 478 m, respectively. Lungs of yaks were sequenced by RNA-Seq technology using Illumina II High-throughput Sequencing Platform (HiSeqTM 2500/4000). Then, the expressions of differentially expressed genes in lungs of yaks were verified by qRT-PCR. The results indicated that there were approximately 576, 610 million Clean Reads in lung transcriptome of yaks bred in high and low altitudes, respectively. The numbers of reads mapped to the reference genome accounted for more than 91.74% and 91.28% percentages, respectively. And 2 047 new transcripts were discovered in lung RNA-Seq. There were 199 differentially expressed genes (DEGs) between the two test groups, including 89 up-regulated DEGs and 110 down-regulated DEGs. The differentially expressed genes were enriched in 297 GO terms and 146 KEGG pathways, which contained 62 GO terms and 35 KEGG pathways related to hypoxic adaptation. The cell adhesion, protein complex and calcium ion binding were the largest proportions of biological processes, cellular component and molecular function in hypoxia-related GO terms. Meanwhile, TNF signaling pathway were the largest proportion of KEGG pathways related to hypoxia, followed by HIF-1 signaling pathway. In addition, qRT-PCR results showed that the expressions of HLA-DOA, HLA-DRA, C2 and MASP1 were consistent with those of RNA-Seq. This study will benefit for a global and in-depth understanding of gene expression of yak lung response to high altitude hypoxia.

Key words: Yaks, Hypoxic adaptation, Lung, Transcriptomics

摘要: 为了探讨牦牛适应高海拔低氧环境的基因表达特征与规律,对在高海拔(3 560 m)和低海拔地区(478 m)饲育4个月的2.5~3岁健康雄性麦洼牦牛肺组织进行转录组测序。转录组测序采用Illumina高通量测序平台(HiSeqTM2500/4000)进行,并以qRT-PCR验证差异表达基因的表达量。结果显示,高海拔组牦牛肺脏转录组平均每个测序样本得到约5.76亿条Clean Reads,低海拔组牦牛中得到约6.10亿条Clean Reads,比对到参考基因组上的Reads数分别占91.74%和91.28%以上,共发现了2 047个新转录本。低海拔组与高海拔组牦牛肺脏组织之间共有199个差异表达基因,其中含89个差异上调表达基因和110个差异下调表达基因。所得差异表达基因富集在297个GO条目和146个KEGG通路中,包含62个低氧适应相关的GO条目和35个低氧适应相关代谢通路。其中低氧适应相关GO条目在生物过程、细胞组成和分子功能三种类别中占比最多的分别为细胞粘附、蛋白复合物和钙离子结合。低氧适应相关KEGG通路中占比最多的为肿瘤坏死因子(TNF)信号通路,其次为低氧诱导因子1(HIF-1)信号通路。qRT-PCR验证结果显示,Ⅱ类人类白细胞抗原α链(HLA-DOA、HLA-DRA)、补体因子 (C2)和甘露糖结合凝集素相关丝氨酸蛋白酶1(MASP1)基因的表达量变化与转录组测序结果相符。本研究为全局和深入理解牦牛肺组织转录本表达对高海拔低氧的响应提供了有价值的切入点。

关键词: 牦牛, 低氧适应, 肺脏, 转录组