Bioinformatics Analysis of TCP Gene Family in Amaranthus hypochondriacus

doi:10.11733/j.issn.1007-0435.2022.04.012

Acta Agrestia Sinica ›› 2022, Vol. 30 ›› Issue (4): 867-878.DOI: 10.11733/j.issn.1007-0435.2022.04.012

Bioinformatics Analysis of TCP Gene Family in Amaranthus hypochondriacus

ZHOU Tao, PENG Hui, YU Wang-chen, LIU Ning-fang, HU Long-xing, XU Qian

Department of Pratacultural Science, College of Agriculture, Hunan Agricultural University, Changsha, Hunan Province 410128, China

Received:2022-01-10 Revised:2022-02-22 Published:2022-04-25

千穗谷TCP基因家族生物信息学分析

周涛, 彭辉, 喻望晨, 刘宁芳, 胡龙兴, 徐倩

湖南农业大学农学院草业科学系, 湖南长沙 410128

通讯作者: 胡龙兴,E-mail:grass@hunau.edu.cn;徐倩,E-mail:xq20052005@126.com
作者简介:周涛(1993-),男,汉族,河南安阳人,硕士研究生,主要从事牧草种质资源评价研究,E-mail:310600587@qq.com
基金资助:
国家自然科学基金项目(32001408);湖南省教育厅项目(20C0934;21A0126)资助

Abstract

Abstract: TCP is a class of transcription factors regulating the plant growth and development.In this study,16 TCP family genes were identified based on the recently published genomic data of Amaranthus hypochondriacus.The TCP gene family of A.hypochondriacus can be divided into two subclasses,Class Ⅰ and Class Ⅱ,which can be further divided into CIN/TB1 and CYC branches.Chromosome mapping results showed that the TCP genes were distributed unevenly on 6 chromosomes,some of which were distributed in clusters.According to the transcriptome data from Phytozome database,we found that the expression patterns of AhTCPs in each tissue were different and correlated to the subclass type.In addition,cis-acting element analysis about the AhTCP promoters suggested a large number of elements related to plant growth and development,hormone signaling and stress response.The element number and types of AhTCPs were conserved with their lineal homologous genes.Many TCP genes were demonstrated to be the target genes of miR319 in previous study,while in A.hypochondriacus,the coding sequence of three CIN subclass members contains the acting site of miR319.This study provides a theoretical basis for the AhTCPs function and regulatory mechanism research.

Key words: Amaranthus hypochondriacus, TCP, Transcription factor, MiR319, Gene family

摘要： TCP是一类与植物生长发育密切相关的转录因子。基于最新发布的千穗谷(Amaranthus hypochondriacus)基因组,本研究鉴定出16个TCP家族基因,并根据序列特征和结构域特点将其分为ClassⅠ和ClassⅡ两个亚类,其中ClassⅡ亚类又可分为CIN/TB1和CYC两个分支。染色体定位结果显示,千穗谷TCP家族成员不均匀地分布在6条染色体上,个别基因呈簇状分布。根据phytozome数据库信息可知,千穗谷TCP家族不同基因在各个组织中的表达模式不同,且与所属亚类相关。此外,顺式作用元件分析结果显示,AhTCP基因启动子中包含大量与生长发育、激素信号和逆境胁迫相关的元件,且不同成员所含元件的数目和类型与其直系同源基因相似。已知TCP基因是miR319的主要靶基因,根据结合位点预测发现千穗谷中CIN分支的3个成员编码区均存在miR319的作用位点。本研究为千穗谷TCP转录因子家族的功能和调控机制研究提供了理论基础。

关键词: 千穗谷, TCP, 转录因子, miR319, 基因家族

CLC Number:

S943.2

ZHOU Tao, PENG Hui, YU Wang-chen, LIU Ning-fang, HU Long-xing, XU Qian. Bioinformatics Analysis of TCP Gene Family in Amaranthus hypochondriacus[J]. Acta Agrestia Sinica, 2022, 30(4): 867-878.

周涛, 彭辉, 喻望晨, 刘宁芳, 胡龙兴, 徐倩. 千穗谷TCP基因家族生物信息学分析[J]. 草地学报, 2022, 30(4): 867-878.

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Bioinformatics Analysis of TCP Gene Family in Amaranthus hypochondriacus

千穗谷TCP基因家族生物信息学分析

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