新疆农业科学 ›› 2023, Vol. 60 ›› Issue (11): 2627-2637.DOI: 10.6048/j.issn.1001-4330.2023.11.004
• 作物遗传育种·种质资源·分子遗传学·土壤肥料 • 上一篇 下一篇
收稿日期:
2023-02-11
出版日期:
2023-11-20
发布日期:
2023-12-07
通信作者:
黄全生(1964-),男,新疆人,研究员,博士,研究方向为农作物生物技术,(E-mail)hquansheng@126.com
作者简介:
胡文冉(1974-),女,河南人,研究员,博士,研究方向为棉花生物技术,(E-mail)huwran@126.com
基金资助:
HU Wenran(), ZHAO Zhun, SHAO Wukui, HUANG Quansheng()
Received:
2023-02-11
Online:
2023-11-20
Published:
2023-12-07
Correspondence author:
Huang Quansheng (1964-), Male, Urumqi, researcher, doctor, research direction: molecular biology of crop resistance, (E-mail) hquansheng@126.com
Supported by:
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。
中图分类号:
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.
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.
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 |
CIN | 8 | 9 | 17 |
表1 拟南芥、水稻和陆地棉TCP蛋白质数目比较
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 |
CIN | 8 | 9 | 17 |
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 | |
2 | 1 | 353 | ||
Class Ⅱ | CYC/TB1 | 1 | 3 | 367-501 |
2 | 4 | 325-414 | ||
CIN | 1 | 14 | 285-463 | |
2 | 3 | 266-451 |
表2 陆地棉TCP基因外显子数量及蛋白质长度
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 | |
2 | 1 | 353 | ||
Class Ⅱ | CYC/TB1 | 1 | 3 | 367-501 |
2 | 4 | 325-414 | ||
CIN | 1 | 14 | 285-463 | |
2 | 3 | 266-451 |
图3 陆地棉TCP Class I型基因进化树、蛋白保守基序预测结果、蛋白结构域及基因结构 注:a.Class I TCP 型基因进化树;b.Class I TCP 型蛋白motif预测结果;c.Class I TCP 型蛋白结构域;d.Class I TCP型基因结构
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
图4 陆地棉Class Ⅱ TCP型基因进化树、蛋白motif 预测结果、蛋白结构域及基因结构 注:A.陆地棉CIN型基因进化树、蛋白motif预测结果、蛋白结构域及基因结构;B.陆地棉CYC/TB1型基因进化树、蛋白motif预测结果、蛋白结构域及基因结构。a.CIN型基因进化树;b.CIN型蛋白motif预测结果;c.CIN型蛋白结构域;d.CIN型基因结构;e.CYC/TB1型基因进化树;f.CYC/TB1型蛋白motif预测结果;g.CYC/TB1型蛋白结构域;h.CYC/TB1型基因结构
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
图5 TCP基因在陆地棉不同组织中的表达 注:A:Class I型TCP基因在陆地棉不同组织中的表达;B:Class Ⅱ型TCP基因在陆地棉不同组织中的表达;右侧标尺数值范围代表均一化后表达量的变化范围;红色为高表达,蓝色为低表达,白色为缺失值
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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