藏猪Ⅱ型肺泡上皮细胞新转录本及其功能解析
Novel Transcripts and Their Functional Analysis of Type Ⅱ Alveolar Epithelial Cells in Tibetan Pigs
柳烜博 1杨雅楠 1袁浩楠 1柳思奇 1王正文 1赵生国1
作者信息
- 1. 甘肃农业大学动物科学技术学院,兰州,730070
- 折叠
摘要
利用已获得的藏猪(Tibetan pig)Ⅱ型肺泡上皮细胞(type Ⅱ alveolar epithelial cells,AT Ⅱ)的RNA-seq数据完善已注释的猪(Sus scrofa)基因组信息,鉴定并分析新转录本的功能.基于已发表的藏猪和长白猪(Landrace pig)AT Ⅱ的长读段测序数据,使用Stringtie重构转录本并鉴定新转录本.共对4 245个转录本的非翻译区(non-translational region,UTR)进行了延长,其中5'UTR和3'UTR延伸的转录本分别有1 646个和3 263个,5'和3'端共延伸的转录本有648个.发掘出54个新转录本,其经过滤后的平均长度为4 047 bp,且在NC_010448.4染色体上的分布最多.GO富集分析结果表明,藏猪AT Ⅱ的常氧(21％O2)组和低氧(2％O2)组的14个差异新转录本显著富集于细胞器膜、限制性脱氧核糖核酸内切酶活性和转座;KEGG分析结果表明,动物细胞因子-细胞因子受体交互作用、淀粉和蔗糖代谢以及丝裂原活化蛋白激酶(mitogen-activated protein kinase,MAPK)信号通路有大量差异新转录本显著富集.藏猪AT Ⅱ的新转录本可能通过淀粉和蔗糖代谢以及MAPK信号通路与已注释基因共同参与ATⅡ的低氧应答反应.研究结果较好地完善了现有的猪基因组注释,并为相关组学和分子生物学研究的深入开展提供了基础.
Abstract
The annotated Sus scrofa genome information and the new transcript were refined and identified using RNA-seq data,which obtained from type Ⅱ alveolar epithelial cells(AT Ⅱ)of Tibetan pig.Stringtie was used to reconstruct transcripts and identify novel genes based on published AT Ⅱ long-read sequencing data of Tibetan and Landrace pigs.4 245 transcripts had their non-translational regions(UTR)lengthened,comprising 1 646 genes with 5'UTR and 3 263 transcripts with 3'UTR,as well as 648 transcripts with 5'and 3'ends,respectively.The majority of 54 novel transcripts were found on the NC 010448.4 chromosome and had an average fil-tered length of 4 047 bp.GO enrichment analysis results showed that 14 novel transcripts of AT Ⅱ among normoxic(21％O2)and hy-poxic(2％O2)groups of Tibetan pigs were significantly enriched in organelle membrane,restriction of deoxyribonuclease activity and transposition.Numerous divergent novel transcripts were considerably enriched in animal cytokine-cytokine receptor interactions,starch and sucrose metabolism,and mitogen-activated protein kinase(MAPK)signaling pathways by KEGG analysis.Novel transcripts and annotated genes may be involved in the hypoxia response of AT Ⅱ of Tibetan pigs through the starch and sucrose metabolism and MAPK signaling pathway.The results of this research enhance the current annotation of the pig genome and provide a foundation for the ad-vancement of omics and molecular biology in this area.
关键词
Ⅱ型肺泡上皮细胞/藏猪/新转录本Key words
Type Ⅱ alveolar epithelial cells/Tibetan pig/Novel transcript引用本文复制引用
基金项目
国家自然科学基金地区科学基金(32060730)
甘肃农业大学青年导师基金(GAU-QDFC-2018-03)
出版年
2024
NETL
NSTL
万方数据