Subtropical Plant Science >

2025 , Vol. 54 >Issue 3: 249 - 260

DOI: https://doi.org/10.3969/j.issn.1009-7791.2025.03.002

Research articles

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

  • 王安邦，叶兴状，杨巧莹，刘美利，陈志云，张国防
Expand
  • (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 date: 2025-01-02

  Accepted date: 2025-04-09

  Online published: 2025-09-08

Fold

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

Cite this article

王安邦，叶兴状，杨巧莹，刘美利，陈志云，张国防 . Genome-wide Identification and Tissue Expression Analysis of the TCP gene Family in Altingia chinensis[J]. Subtropical Plant Science, 2025 , 54(3) : 249 -260 . DOI: 10.3969/j.issn.1009-7791.2025.03.002

References

[1] 魏娜, 李艳鹏, 马艺桐, 刘文献. 全基因组水平紫花苜蓿TCP基因家族的鉴定及其在干旱胁迫下表达模式分析[J]. 草业学报, 2022, 31(1): 118–130.
[2] Shang X W, Han Z L, Zhang D Y, Wang Y, Qin H, Zou Z W, Zhou L, Zhu X J, Fang W P, Ma Y C. Genome-wide analysis of the TCP gene family and their expression pattern analysis in tea plant (Camellia sinensis) [J]. Frontiers in Plant Science, 2022, 13: 840350.
[3] 王建, 邱丽氚, 李雅丽. 中国金缕梅科植物属分布区特点的定量研究[J]. 西北植物学报, 2021, 41(8): 1425–1433.
[4] 王安邦, 叶兴状, 赵金涛, 陈志云, 翁慧莹, 林茂, 张国防.蕈树KNOX基因家族鉴定及组织表达分析[J]. 亚热带植物科学, 2025, 54(1): 1–10.
[5] 吴玲, 李珊珊, 黄玉娟, 郭微, 李永泉, 吴伟, 张晖. 6种金缕梅科植物挥发性成分动态变化及抑菌效果研究[J]. 林业与环境科学, 2023, 39(3): 67–79.
[6] 周云, 韦妍妍. 基于叶绿体基因组解析半枫荷系统位置和进化[J]. 广西植物, 2024, 44(4): 670–681.
[7] 赵金涛, 叶兴状, 王安邦, 陈志云, 翁慧莹, 张国防. 枫香树TCP基因家族鉴定与表达分析[J]. 亚热带植物科学, 2025, 54(2): 109–120.
[8] Wen Y F, Raza A, Chu W, Zou X L, Cheng H T, Hu Q, Liu J, Wei W J. Comprehensive in silico characterization and expression profiling of TCP gene family in rapeseed [J]. Frontiers in Genetics, 2021, 12: 794297.
[9] Wen H F, Chen Y, Du H, Zhang L Y, Zhang K Y, He H L, Pan J S, Cai R, Wang G. Genome-wide identification and characterization of the TCP gene family in cucumber (Cucumis sativus L.) and their transcriptional responses to different treatments [J]. Genes, 2020, 11(11): 1379.
[10] 王桁杰, 梁君, 李梦, 李文渊, 周宁. 全基因组水平鹅掌楸TCP基因家族的鉴定及盐胁迫下表达模式分析[J/OL]. 西南农业学报, 2025, 38: 1–20.
[11] 魏璐, 朱凯凯, 赵娟, 牛牧歌, 马文娟, 谭鹏鹏, 彭方仁. 薄壳山核桃TCP基因家族鉴定及表达模式分析[J]. 植物资源与环境学报, 2025, 34(4): 9–22.
[12] Zhang L, Li C, Yang D N, Wang Y H, Yang Y P, Sun X D. Genome-wide analysis of the TCP transcription factor genes in Dendrobium catenatum Lindl [J]. International Journal of Molecular Sciences, 2021, 22(19): 10269.
[13] Viola I L, Alem A L, Jure R M, Gonzalez D H. Physiological roles and mechanisms of action of class I TCP transcription factors [J]. International Journal of Molecular Sciences, 2023, 24(6): 5437.
[14] Gao Y S, Regad F, Li Z G, Pirrello J L, Bouzayen M, Van Der Rest B. Class I TCP in fruit development: much more than growth [J]. Frontiers in Plant Science, 2024, 15: 1411341.
[15] Dong Z Y, Hao Y P, Zhao Y Y, Tang W C, Wang X Q, Li J, Wang L Y, Hu Y, Guan X Y, Gu F L, Liu Z J, Zhang Z Y. Genome-wide analysis of the TCP transcription factor gene family in Pepper (Capsicum annuum L.) [J]. Plants, 2024, 13(5): 641.
[16] Chen, C Q, Zhang Y, Chen Y F, Chen H X, Gong R G. Sweet cherry TCP gene family analysis reveals potential functions of PavTCP1, PavTCP2 and PavTCP3 in fruit light responses [J]. BMC genomics, 2024, 25(1): 3.
[17] Lucero L E, Manavella P A, Gras D E, Ariel F D, Gonzalez D H. Class I and class Ⅱ TCP transcription factors modulate SOC1-dependent flowering at multiple levels [J]. Molecular plant, 2017, 10(12): 1571–1574.
[18] Tian C, Zhai L S, Zhu W J, Qi X Y, Yu Z Y, Wang H B, Chen F D, Wang L K, Chen S M. Characterization of the TCP gene family in Chrysanthemum nankingense and the role of CnTCP4 in cold tolerance [J]. Plants, 2022, 11(7): 936.
[19] Yu L, Chen Q W, Zheng J R, Xu F, Ye J B, Zhang W W,Liao Y L, Yang, X Y. Genome-wide identification and expression pattern analysis of the TCP transcription factor family in Ginkgo biloba [J]. Plant Signaling & Behavior, 2022, 17(1): 1994248.
[20] 董炫克, 李映旸, 马豫皖, 蔡艳芳, 丁启涵, 陈海霞, 李玉帆, 陈己任. 月季‘月月红’RcTCP9基因在盐和干旱胁迫中的功能分析[J]. 园艺学报, 2025, 52(7): 1789–1802.
[21] Ding S C, Cai Z Z, Du H W, Wang H W. Genome-wide analysis of TCP family genes in Zea mays L. identified a role for ZmTCP42 in drought tolerance [J]. International Journal of Molecular Sciences, 2019, 20(11): 2762.
[22] Zhao M L, Peng X J, Chen N Z, Shen S H. Genome-wide identification of the TCP gene family in Broussonetia papyrifera and functional analysis of BpTCP8, 14 and 19 in shoot branching [J]. Plants, 2020, 9(10): 1301.
[23] Ma J K, Mei G G, Liu H H, Li H G. Overexpression of a novel LcKNOX transcription factor from Liriodendron chinense induces lobed leaves in Arabidopsis thaliana [J]. Forests, 2019, 11(1): 33.
[24] 张雪莹, 尹一歌, 姜晶, 刘欣. 参与番茄叶形发育的TCP转录因子的表达及生物信息分析[J]. 中国蔬菜, 2021(10): 45–56.
[25] Wang M X, Tu Z H, Wang J, Zhang Y, Hu Q H, Li H G. Genomic survey, bioinformatics analysis, and expression profiles of TCP genes in Liriodendron chinense and functional characterization of LcTCP4 [J]. Trees, 2024, 38(2): 287–302.
[26] Zou R, Peng Y, Zhao Y, Wang X R. Genome-wide identification and expression analysis of the TCP genes in Jatropha curcas L. reveals its roles in involvement of leaf shape [J]. Forests, 2023, 14(4): 780.
[27] 谷玉风, 刘欣欣, 胡尔西旦·吐尔逊, 葛风伟. 扭果花旗杆TCP转录因子家族成员鉴定及表达分析[J]. 农业生物技术学报, 2025, 33(6): 1259–1269.
[28] 王培育, 张春柳, 李尊文, 颜沛沛, 江金兰, 罗维鸿, 叶炜. 铁皮石斛TCP基因家族鉴定及其在不同色系铁皮石斛中对光照的响应[J]. 江苏农业科学, 2025, 53(6): 48–56.
[29] 马琦洋, 宋歌. 黄花蒿TCP转录因子鉴定及其在MeJA处理下的表达模式分析[J]. 河南农业科学, 2024, 53(12): 62–74.
[30] Liu C, Lv T T, Shen Y H, Liu T, Liu M M, Hu J, Liu S Z, Jiang Y, Zhang, M P, Zhao M Z, Wang K Y, Wang Y. Genome-wide identification and integrated analysis of TCP genes controlling ginsenoside biosynthesis in Panax ginseng [J]. BMC Plant Biology, 2024, 24(1): 47.
[31] 谭政委, 郭水柱, 苏小雨, 孙瑶, 余永亮, 李磊, 张利超, 许兰杰, 鲁丹丹, 安素妨, 李春明, 梁慧珍, 王子君. 全基因组水平金银花TCP基因家族的鉴定及表达模式分析[J]. 中草药, 2024, 55(5): 1665–1676.
[32] Zou Q C, Dong Q, Tian D Q, Mao L H, Cao X R, Zhu K Y. Genome-wide analysis of TCP transcription factors and their expression pattern analysis of rose plants (Rosa chinensis) [J]. Current Issues in Molecular Biology, 2023, 45(8): 6352–6364.
[33] 宋姝熠, 蒋开秀, 刘欢艳, 黄亚成, 刘林娅. ‘红阳’猕猴桃TCP基因家族鉴定及其在果实中的表达分析[J]. 生物技术通报, 2025, 41(3): 190–201.
[34] 李栋成, 李魁印, 韦兴启, 段丽丽, 莫泽君, 刘仁祥. 烟草Trihelix转录因子家族鉴定及表达分析[J]. 亚热带植物科学, 2022, 51(1): 1–12.
[35] 王珊珊, 王瑞, 樊二勤, 付鹏跃, 曲冠证, 王楠. 楸树DELLA基因家族生信分析及CbuGRAS9的功能分析[J]. 植物研究, 2024, 44(1): 139–151.
[36] Jiu S T, Xu Y, Wang J Y, Wang L, Wang S P, Ma C, Guan L, Abdullah M, Zhao M X, Xu W P, Ma W L, Zhang C X. Genome-wide identification, characterization, and transcript analysis of the TCP transcription factors in Vitis vinifera [J]. Frontiers in Genetics, 2019, 10: 1276.
[37] Kieffer M, Master V, Waites R, Davies B. TCP14 and TCP15 affect internode length and leaf shape in Arabidopsis [J]. The Plant Journal, 2011, 68(1): 147–158.
[38] Qin W Q, Wang N, Yin Q, Li H L, Wu A M, Qin G J. Activation tagging identifies WRKY14 as a repressor of plant thermomorpho genesis in Arabidopsis [J]. Molecular Plant, 2022, 15(11): 1725–1743.
Options
Outlines

/

〈 〉

Copyright © Editorial office of Subtropical Plant Science
Tel: 0592-5654157　E-mail: yrdzwkx@126.com
Supported by Beijing Magtech Co., Ltd.