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

doi:10.6048/j.issn.1001-4330.2023.11.004

Abstract

Abstract:

【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.

Key words: upland cotton; TCP gene; family identification; bioinformatics; specific expression

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Class Ⅱ亚族;Class Ⅱ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。

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

CLC Number:

S188
S562

HU Wenran, ZHAO Zhun, SHAO Wukui, HUANG Quansheng. Identification of TCP family and analysis of tissue expression in upland cotton[J]. Xinjiang Agricultural Sciences, 2023, 60(11): 2627-2637.

胡文冉, 赵准, 邵武奎, 黄全生. 陆地棉TCP家族基因鉴定及组织表达分析[J]. 新疆农业科学, 2023, 60(11): 2627-2637.

Figures/Tables 7

Fig.1 Phylogenetic analysis of members of TCP family in Arabidopsis, rice and upland cotton

Tab.1 Comparison of TCP proteins number in Arabidopsis, rice and upland cotton

蛋白质类型 Type of protein	亚家族 Subfamilies	拟南芥 Arabido- psis	水稻 Rice	陆地棉 Upland cotton
Class I		13	10	39
Class Ⅱ	CYC/TB1	3	3	7
Class Ⅱ	CIN	8	9	17

Tab.2 The number of exons and protein length of TCP genes in upland cotton

基因类型 Gene type		外显子数量 Number of exons	基因数量 Number of gene	蛋白质大小 Protein length(aa)
Class I		1	38	150-550
Class I		2	1	353
Class Ⅱ	CYC/TB1	1	3	367-501
	CYC/TB1	2	4	325-414
	CIN	1	14	285-463
	CIN	2	3	266-451

Fig.2 Chromosomal distribution of TCP genes in upland cotton

Fig.3 Phylogenetic tree, motif prediction, protein domain and gene structure of Class I TCP genes in upland cotton Note:a.Phylogenetic tree of TCP Class I genes; b.Motif prediction results of TCP Class I proteins; c.Protein domain of TCP Class I; d.Gene structure of Class I TCP

Fig.4 Phylogenetic tree, motif prediction, protein domain and gene structure of Class Ⅱ TCP genes in upland cotton Note:A.Phylogenetic tree, motif prediction, protein domain and gene structure of CIN genes in upland cotton; B.Phylogenetic tree, motif prediction, protein domain and gene structure of CYC/TB1 genes in upland cotton.a.Phylogenetic tree of CIN genes; b.Motif prediction results of CIN proteins; c.Protein domain of CIN; d.Gene structure of CIN; e.Phylogenetic tree of CYC/TB1 genes; f.Motif prediction results of CYC/TB1 proteins; g.Protein domain of CYC/TB1; h.Gene structure of CYC/TB1

Fig.5 Expression analysis of TCP genes from different tissues in upland cotton Note:A: Expression analysis of Class I genes from different tissues in upland cotton; B: Expression analysis of Class Ⅱ genes from different tissues in upland cotton; The numerical range of the right scale represents the variation range of the expression level after normalization, with red as high expression level, blue as low expression level and white as missing value

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