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 TypeⅡAlveolar Epithelial Cells in Tibetan Pigs

作　　者：柳烜博 杨雅楠[1] 袁浩楠 柳思奇 王正文 赵生国[1] LIU Xuanbo;YANG Ya'nan;YUAN Haonan;LIU Siqi;WANG Zhengwen;ZHAO Shengguo(College of Animal Science and Technology,Gansu Agricultural University,Lanzhou,730070)

机构地区：[1]甘肃农业大学动物科学技术学院,兰州730070

出　　处：《基因组学与应用生物学》2024年第4期685-696,共12页Genomics and Applied Biology

基　　金：国家自然科学基金地区资助项目(32060730);甘肃农业大学青年导师扶持基金资助项目(GAU-QDFC-2018-03)共同资助。

摘　　要：利用已获得的藏猪(Tibetan pig)Ⅱ型肺泡上皮细胞(typeⅡalveolar epithelial cells,ATⅡ)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)ATⅡ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4245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1646个和3263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4047 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ATⅡ的常氧(21%O_(2))组和低氧(2%O_(2))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ATⅡ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。The annotated Sus scrofa genome information and the new transcript were refined and identified using RNA-seq data,which obtained from typeⅡalveolar epithelial cells(ATⅡ)of Tibetan pig.Stringtie was used to reconstruct transcripts and identify novel genes based on published ATⅡlong-read sequencing data of Tibetan and Landrace pigs.4245 transcripts had their non-translational regions(UTR)lengthened,comprising 1646 genes with 5′UTR and 3263 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 filtered length of 4047 bp.GO enrichment analysis results showed that 14 novel transcripts of ATⅡamong normoxic(21%O_(2))and hypoxic(2%O_(2))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 ATⅡof 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 advancement 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 

分 类 号：S828.2[农业科学—畜牧学]