陆地棉KFB基因家族全基因组鉴定与表达分析

doi:10.11963/1002-7807.cpyzj.20170322

摘要/Abstract

摘要： 目的 KFB（Kelch containing F-box protein）是普遍存在于各种生物体中含有F-box结构域的一类家族蛋白,参与众多生物过程。本研究旨在开展陆地棉KFB家族基因鉴定和表达分析。方法利用生物信息学方法从陆地棉（TM-1）基因组中鉴定KFB家族成员,与已知的拟南芥、水稻、大豆等KFB蛋白序列构建系统进化树;进一步针对第Ⅱ亚族进行基因结构、染色体定位和表达分析。结果从陆地棉基因组共鉴定出150个KFB家族成员,进化分析表明这些基因可分为7个亚族。陆地棉KFB第Ⅱ亚族24个基因分布在14条染色体上,有9对直系同源基因;该亚族基因结构简单,半数基因只有1个外显子;qRT-PCR结果表明,该亚族基因具有较为广泛的组织表达模式,但在不同组织的表达存在差异。结论这些结果显示陆地棉KFB第Ⅱ亚族基因在进化过程中出现了功能分化。

关键词: 陆地棉; KFB基因家族; 生物信息学; 基因表达

Abstract:

[Objective] The KFB (Kelch containing F-box protein) family, involving in many physiological pathways, is a subfamily of the biggest F-box protein family in all organisms. In the study, we aims to identify the KFB family members in the upland cotton genome and analyze their expression patterns. [Method] The KFB genes were identified from the whole genome of upland cotton (Gossypium hirsutum L. acc. TM-1) by bioinformatics methods. A phylogenetic analysis was conducted based on the alignment of the KFB proteins from upland cotton, Arabidopsis, rice and soybean, and the gene structure, chromosomal localization, and expression of subgroup Ⅱ in this family. [Result] A total of 150 KFB genes were identified from the whole genome of upland cotton and were then divided into seven subgroups based on phylogenetic analyses. In subgroup Ⅱ, 24 genes distributed on fourteen chromosomes, and nine pairs were orthologous genes. Structures of half genes in this subfamily were simple, including only one exon, respectively. According to the results of qRT-PCR, this subfamily had a wide range of tissue expression patterns, but the expression level of these genes varied from different tissues. [Conclusion] The results indicate that the functions of subgroup Ⅱ in KFB family have been differentiated during the process of evolution.

Key words: Gossypium hirsutum; KFB gene family; bioinformatics; gene expression

陈鹏云, 张景霞, 陈煜, 刘国栋, 张传云, 王芙蓉, 刘志, 张军. 陆地棉KFB基因家族全基因组鉴定与表达分析[J]. 棉花学报, 2017, 29(3): 222-232.

Pengyun Chen, Jingxia Zhang, Yu Chen, Guodong Liu, Chuanyun Zhang, Furong Wang, Zhi Liu, Jun Zhang. Genome-Wide Identification and Expression Analysis of the KFB Gene Family in Gossypium hirsutum L.[J]. Cotton Science, 2017, 29(3): 222-232.

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链接本文: https://journal.cricaas.com.cn/Jweb_mhxb/CN/10.11963/1002-7807.cpyzj.20170322

https://journal.cricaas.com.cn/Jweb_mhxb/CN/Y2017/V29/I3/222

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