陆地棉TCP家族基因鉴定及组织表达分析  

Identification of TCP family and analysis of tissue expression in upland cotton

作　　者：胡文冉[1] 赵准 邵武奎 黄全生[1] HU Wenran;ZHAO Zhun;SHAO Wukui;HUANG Quansheng(Xinjiang Key Laboratory of Crop Biotechnology/Institute of Nuclear and Biological Technologies,Xinjiang Academy of Agricultural Sciences,Urumqi 830091,China)

机构地区：[1]新疆农业科学院核技术生物技术研究所/新疆农作物生物技术重点实验室,乌鲁木齐830091

出　　处：《新疆农业科学》2023年第11期2627-2637,共11页Xinjiang Agricultural Sciences

基　　金：新疆维吾尔自治区自然科学基金面上项目(2022D01A88);新疆维吾尔自治区重点实验室开放课题(2021D04002)。

摘　　要：【目的】鉴定、分析陆地棉TCP家族基因,为进一步研究TCP基因在棉花植株内的生物学功能奠定基础。【方法】基于2019年最新组装的陆地棉TM-1参考基因组,通过Pfam网站获取TCP家族HMM模型文件,使用HMMER网站鉴定陆地棉TCP基因,CottonFGD网站获取陆地棉TCP基因组蛋白序列。利用MapInspect进行染色体定位、MEGA 7.0进行多序列比对聚类分析、MEME网站motif预测、TBtools软件鉴定基因结构以及陆地棉TCP基因组织特异性表达分析。【结果】共鉴定出63个陆地棉TCP基因,其中39个Class I亚族,24个ClassⅡ亚族;ClassⅡ亚族中包括17个CIN亚类,7个CYC/TB1亚类。染色体定位发现该63个TCP基因在陆地棉22条染色体上均有分布,其中A组染色体上分布有33个基因、D组上分布有30个基因。所有TCP蛋白均包含TCP结构域。TCP基因外显子、内含子结构及长度在同一亚家族内具有相似性。TCP家族基因中有12个基因在陆地棉纤维中优势表达,32个基因在花器官中优势表达,16个基因在营养器官:根、茎和叶中优势表达。【结论】获得了与陆地棉生长发育相关的TCP基因。【Objective】Identification and analysis of TCP family genes in upland cotton can lay a foundation for studying the biological functions of TCP genes.【Methods】Based on the newly assembled upland cotton TM-1 reference genome in 2019,the TCP family HMM model file was obtained from Pfam website,the upland cotton TCP gene was identified using Hmmer website,and the upland cotton TCP genome protein sequence was obtained from Cotton FGD website.MapInspect software was used for chromosome location,MEGA 7.0 was used for multiple sequence alignment cluster analysis,MEME website was used for motif prediction,TBtools software was used for gene structure identification and tissue-specific expression analysis of upland cotton.【Results】Sixty-three TCP genes of upland cotton were identified from the whole genome level,including 39 subclasses of Class I and 24 subclasses of Class II.The Class II subfamilies included 17 CIN subclasses and 7 CYC/TB1 subclasses.The 63 genes were distributed on 22 chromosomes of upland cotton,including 33 genes in group A and 30 genes in Group D.All TCP proteins contained TCP domains.The gene structure analysis results showed that the structures and lengths of exon and introns were similar in the same subfamily.12 of the TCP family genes were preferentially expressed in fibrous tissue,32 in flower organs,and 16 in roots,stems and leaves.【Conclusion】In this study,TCP genes related to flowering regulation and fiber development in upland cotton are identified and obtained by bioinformatics method.

关 键 词：陆地棉 TCP基因 基因家族鉴定 生物信息学 特异性表达 

分 类 号：S188[农业科学—农业基础科学] S562