藏猪肺组织新转录本注释及功能解析

doi:10.3969/j.issn.1674-7968.2022.03.007

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摘要藏猪(Sus scrofa)是高原生境中的代表性非模式动物,对其高原反应机制的研究可为其他动物低氧适应机制的探索提供参考依据。为了完善和优化藏猪基因组注释信息,解析藏猪肺组织在转录水平上对低氧环境的响应特征,本研究对不同海拔藏猪的肺脏组织进行RNA-seq测序,构建cDNA文库,将重新组装的测序数据与藏猪参考基因组进行比对分析。结果显示,本研究延伸了334个基因的5'端和3'端,并对1 313个基因的5'端和2 734个基因的3'端分别实现了延伸;挖掘新转录本809个,其中95个新转录本在不同海拔间的表达差异显著(P<0.05)。GO分析显示差异新转录本在细胞代谢、酶催化活性和细胞组分等过程被显著富集(P<0.05);KEGG富集发现差异新转录本显著富集在程序性细胞坏死和核因子κB (nuclear factor-κB, NF-κB)炎症信号等通路(P<0.05)。随机挑选9个显著差异的新转录本进行qPCR验证,结果与RNA-seq一致。本研究为完善藏猪基因组注释信息提供了有益补充和借鉴,为进一步研究藏猪适应不同海拔环境的遗传机制提供参考依据。

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	袁浩楠
	杨雅楠
	杨天良
	权金强
	赵生国

关键词 ：藏猪, 新转录本, 基因结构优化, 低氧适应性

Abstract：Tibetan pig (Sus scrofa) is a representative non model animal in plateau habitat. The study of its plateau response mechanism can provide a reference basis for the exploration of hypoxia adaptation mechanism of other animals. In order to improve and optimize the annotation information of Tibetan pig genome, analyze the characteristics of Tibetan pig lung tissue response to hypoxic environment at transcription level, this study performed RNA-seq sequencing of lung tissues in Tibetan pigs at different altitudes to construct cDNA library, and the reassembled sequencing data was compared and analyzed with the reference genome of Tibetan pigs. The results showed that the 5' end and 3' end of 334 genes were extended, and the 5' end of 1 313 genes and the 3' end of 2 734 genes were extended respectively; 809 new transcripts were excavated and 95 new transcripts at different altitudes were differentially expressed (P<0.05). GO analysis results showed that the differential new transcripts were significantly enriched in the process of cell metabolism, enzyme catalytic activity and cellular components (P<0.05); KEGG pathway enrichment results found that the differential new transcripts were significantly enriched (P<0.05) in the pathways such as programmed cell necrosis and nuclear factor-κB (NF-κB) signaling pathway. Nine new transcripts with significant differences were randomly selected for qPCR verification, and the results were consistent with that of RNA-seq. This study provides a useful supplement and reference for improving the annotation information of Tibetan pig genome and a reference basis for further studying the genetic mechanism of Tibetan pig adapting to different altitude environment.

Key words： Tibetan pig New transcript Gene structure optimization Hypoxic adaptability

收稿日期: 2021-06-29

ZTFLH:

S828.2

基金资助:国家自然科学基金(31760644; 32060730)

通讯作者: *zhaosg@gsau.edu.cn

引用本文:

袁浩楠, 杨雅楠, 杨天良, 权金强, 赵生国. 藏猪肺组织新转录本注释及功能解析[J]. 农业生物技术学报, 2022, 30(3): 485-495.
YUAN Hao-Nan, YANG Ya-Nan, YANG Tian-Liang, QUAN Jin-Qiang, ZHAO Sheng-Guo. Annotations and Functional Analysis of New Transcripts from Tibetan Pig (Sus scrofa) Lung Tissue. 农业生物技术学报, 2022, 30(3): 485-495.

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http://journal05.magtech.org.cn/Jwk_ny/CN/10.3969/j.issn.1674-7968.2022.03.007 或 http://journal05.magtech.org.cn/Jwk_ny/CN/Y2022/V30/I3/485

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