Genome-wide Identification and Tissue Expression Analysis of the TCP gene Family in Altingia chinensis

doi:10.3969/j.issn.1009-7791.2025.03.002

Subtropical Plant Science ›› 2025, Vol. 54 ›› Issue (3): 249-260.DOI: 10.3969/j.issn.1009-7791.2025.03.002

• Research articles • Previous Articles

Genome-wide Identification and Tissue Expression Analysis of the TCP gene Family in Altingia chinensis

WANG An-bang1,2, YE Xing-zhuang1,3, YANG Qiao-ying1, LIU Mei-li4, CHEN Zhi-yun5, ZHANG Guo-fang1*

(1. College of Forestry, Fujian Agriculture and Forestry University，Fuzhou 350002, Fujian China; 2. College of Life Sciences, Fujian Agriculture and Forestry University，Fuzhou 350002, Fujian China; 3. Fujian Institute of Subtropical Botany / Fujian Key Laboratory of Physiology and Biochemistry for Subtropical Plant, Xiamen 361006, Fujian China; 4. Fujian Province Taining State-owned Forest Farm, Sanming 354400, Fujian China; 5. Weimin National Forest Farm of Shaowu, Nanping 354000, Fujian China)

Received:2025-01-02 Accepted:2025-04-09 Published:2025-09-08
Contact: ZHANG Guo-fang

蕈树TCP基因家族鉴定及组织表达分析

王安邦1,2，叶兴状1,3，杨巧莹1，刘美利4，陈志云5，张国防1*

(1. 福建农林大学林学院，福建福州 350002；2. 福建农林大学生命科学学院，福建福州 350002；3. 福建省亚热带植物研究所 / 福建省亚热带植物生理生化重点实验室，福建厦门 361006；4. 福建省泰宁国有林场，福建三明 354400；5. 福建省邵武卫闽国有林场，福建南平 354000)

通讯作者: 张国防
基金资助:
福建农林大学林学学科创新团队支持计划(72202200205)；福建省林业科研项目(2023FKJ05)

Abstract

Abstract: The TCP gene family plays a crucial regulatory role in leaf-shape development in plants. This paper aims to identify and analyze the AcTCPs gene family in Altingia chinensis, exploring their tissue expression pattern to provide a reference for understanding the expression and function of TCPs in this species. Utilizing the whole genome data of A. chinensis and bioinformatics methods, we identified the AcTCPs gene family and analyzed theirs gene structure, protein physicochemical properties, chromosome localization, subcellular localization, collinearity, cis-acting elements of promoters, and transcription expression patterns in different tissues. The results showed that 21 AcTCPs were obtained of the A. chinensis genome. All AcTCPs contain the TCP superfamily domain, with only AcTCP3 uniquely possessing the nitrilase superfamily domain. The AcTCPs can be classified into three categories: PCF (AcTCP1/2/3/4/7/8/9/11/12/17/20/21), CIN (AcTCP5/6/13/15/16/19) and CYC/TB1 (AcTCP10/14/18). The AcTCP proteins range from 197 to 554 amino acids in length. Subcellular localization analysis revealed that AcTCP3 is located at the cell membrane, while the others are localized in the nucleus, all of which are unstable hydrophilic proteins. The promoters of AcTCPs genes contain light-responsive elements, hormone-responsive elements, stress-responsive elements and growth and development-related elements. Transcriptomic expression analysis revealed that tissue specificity for AcTCPs, with AcTCP6, AcTCP7, and AcTCP16 showing significantly high expression in leaf-I (March), although most members of the same subfamily exhibited similar expression patterns. This study identified a total of 21 AcTCP members and highlighted three key potential genes–AcTCP16, AcTCP19 and AcTCP20 that are associated with leaf development in A. chinenesis. It is inferred that A. chinenesis TCPs play important roles in light response, plant growth and development, hormone signaling, and stress response. The findings provide a scientific basis for further studies on the genomic characteristics of the TCP gene family.

Key words: Altingia chinensis; TCP gene family; bioinformatics; tissue expression

摘要： TCP基因家族在植物叶形建成方面具有重要调节功能。以蕈树Altingia chinensis全基因组数据为依据，利用生物信息学方法，对AcTCP基因家族进行鉴定，并对其基因结构、蛋白理化性质、染色体和蛋白亚细胞定位、共线性、启动子顺式作用元件和转录组表达模式进行分析。结果表明，从蕈树基因组中鉴定到21个AcTCPs。所有AcTCPs均含有TCP superfamily结构域，只有AcTCP3单独具有nitrilase superfamily结构域。蕈树TCPs分为PCF (AcTCP1/2/3/4/7/8/9/11/12/17/20/21)、CIN (AcTCP5/6/13/15/16/19)和CYC/TB1 (AcTCP10/14/18) 3类。AcTCPs蛋白包含197～554个氨基酸，亚细胞定位除AcTCP3位于细胞膜，其余均位于细胞核，均为不稳定亲水蛋白。AcTCPs基因的启动子含有光、激素、胁迫及生长发育相关元件。转录组表达分析表明，AcTCPs基因存在组织特异性，其中AcTCP6/7/16在叶-Ⅰ (3月取样)中特异高效表达，但同一亚家族大部分成员的表达模式相似。从21个AcTCPs成员中挖掘出AcTCP16、AcTCP19和AcTCP20三个与蕈树叶形发育相关的关键潜在基因，推测蕈树TCPs在光、植物生长发育、激素和胁迫响应中发挥重要作用。

关键词: 蕈树；TCP基因家族；生物信息学；组织表达

CLC Number:

Q943

WANG An-bang, YE Xing-zhuang, YANG Qiao-ying, LIU Mei-li, CHEN Zhi-yun, ZHANG Guo-fang. Genome-wide Identification and Tissue Expression Analysis of the TCP gene Family in Altingia chinensis[J]. Subtropical Plant Science, 2025, 54(3): 249-260.

王安邦，叶兴状，杨巧莹，刘美利，陈志云，张国防. 蕈树TCP基因家族鉴定及组织表达分析[J]. 亚热带植物科学, 2025, 54(3): 249-260.

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Genome-wide Identification and Tissue Expression Analysis of the TCP gene Family in Altingia chinensis

蕈树TCP基因家族鉴定及组织表达分析

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