Genome-wide identification and characterization of the kinesin gene family in upland cotton (Gossypium hirsutum L.)

IF 5.6 1区 农林科学 Q1 AGRICULTURAL ENGINEERING Industrial Crops and Products Pub Date : 2023-08-04 DOI:10.1016/j.indcrop.2023.117246
Lijiao Gu , Fei Wei , Pengyun Chen , Minsheng Yang , Zhi Liu
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Abstract

Kinesin (KIN) genes play vital functions in plant development and the stress response. However, no comprehensive analysis of this gene family has been reported for cotton. In the present study, we performed a genome-wide investigation and comprehensive analysis of KIN genes in Gossypium hirsutum. A total of 172 putative GhKIN genes were identified in the cotton genome, classified into eight subfamilies (KIN1-KIN8) according to a phylogenetic tree. The GhKINs showed an uneven distribution on chromosomes. Gene duplication analysis indicated that segmental duplication was the only driving force for the expansion of the GhKIN gene family. Segmental duplication gene pairs all have undergone purification selection in the process of evolution. Different subfamily genes had differences in gene structure and motif composition, but the same subfamily showed some similarity. The promoter regions of GhKIN genes contained abundant stress- and hormone-related cis-elements. Based on the published RNA-seq data, 56 common potential candidate genes among these 172 GhKINs were used to identify the spatiotemporal expression patterns in different tissues and abiotic stress response patterns under different treatments (drought, salt, heat and cold). Real-time fluorescence quantitative PCR (RTqPCR) analysis further revealed the expression patterns of 15 GhKINs under drought and salt stress. GhKIN14 and 27 were downregulated under both stress conditions, while GhKIN18, 65, 101, 106, and 137 were upregulated at certain time points. Weighted gene coexpression network analysis (WGCNA) showed that five GhKIN genes, GhKIN13, GhKIN14, GhKIN27, GhKIN140 and GhKIN152, may be important genes regulating the salt stress response. Our study comprehensively analyzes the GhKIN genes in Gossypium hirsutum, providing a new perspective on the functional roles of GhKINs in cotton development and stress adaptation.

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陆地棉(Gossypium hirsutum L.)基因家族的全基因组鉴定与特征分析
Kinesin(KIN)基因在植物发育和胁迫反应中发挥着至关重要的作用。然而,目前还没有对棉花的该基因家族进行全面分析的报道。在本研究中,我们对陆地棉的KIN基因进行了全基因组调查和综合分析。在棉花基因组中共鉴定出172个推定的GhKIN基因,根据系统发育树将其分为8个亚科(KIN1-KIN8)。GhKIN在染色体上的分布不均匀。基因重复分析表明,节段重复是GhKIN基因家族扩张的唯一驱动力。节段重复基因对在进化过程中都经过了纯化选择。不同的亚科基因在基因结构和基序组成上存在差异,但同一亚科基因具有一定的相似性。GhKIN基因的启动子区含有丰富的应激和激素相关的顺式元件。基于已发表的RNA-seq数据,使用这172个GhKIN中的56个共同潜在候选基因来鉴定不同组织中的时空表达模式和不同处理(干旱、盐、热和冷)下的非生物胁迫反应模式。实时荧光定量PCR(RTqPCR)分析进一步揭示了干旱和盐胁迫下15个GhKIN的表达模式。GhKIN14和27在两种应激条件下都下调,而GhKIN18、65101106和137在某些时间点上调。加权基因共表达网络分析(WGCNA)表明,5个GhKIN基因,即GhKIN13、GhKIN14、GhKIN27、GhKIR140和GhKIN152,可能是调节盐胁迫反应的重要基因。我们的研究全面分析了陆地棉中的GhKIN基因,为GhKIN在棉花发育和胁迫适应中的功能作用提供了新的视角。
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来源期刊
Industrial Crops and Products
Industrial Crops and Products 农林科学-农业工程
CiteScore
9.50
自引率
8.50%
发文量
1518
审稿时长
43 days
期刊介绍: Industrial Crops and Products is an International Journal publishing academic and industrial research on industrial (defined as non-food/non-feed) crops and products. Papers concern both crop-oriented and bio-based materials from crops-oriented research, and should be of interest to an international audience, hypothesis driven, and where comparisons are made statistics performed.
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