陆地棉(Gossypium hirsutum L.)基因家族的全基因组鉴定与特征分析

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
{"title":"陆地棉(Gossypium hirsutum L.)基因家族的全基因组鉴定与特征分析","authors":"Lijiao Gu ,&nbsp;Fei Wei ,&nbsp;Pengyun Chen ,&nbsp;Minsheng Yang ,&nbsp;Zhi Liu","doi":"10.1016/j.indcrop.2023.117246","DOIUrl":null,"url":null,"abstract":"<div><p><span><em>Kinesin</em></span> (<em>KIN</em>) 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 <em>KIN</em> genes in <span><em>Gossypium hirsutum</em></span>. A total of 172 putative <em>GhKIN</em> genes were identified in the cotton genome, classified into eight subfamilies (KIN1-KIN8) according to a phylogenetic tree. The <em>GhKINs</em><span> showed an uneven distribution on chromosomes. Gene duplication<span> analysis indicated that segmental duplication was the only driving force for the expansion of the </span></span><em>GhKIN</em><span> 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 </span><em>GhKIN</em> genes contained abundant stress- and hormone-related <em>cis</em>-elements. Based on the published RNA-seq data, 56 common potential candidate genes among these 172 <em>GhKINs</em><span> 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 (RT</span><img>qPCR) analysis further revealed the expression patterns of 15 <em>GhKINs</em> under drought and salt stress. <em>GhKIN14</em> and <em>27</em> were downregulated under both stress conditions, while <em>GhKIN18</em>, <em>65</em>, <em>101</em>, <em>106</em>, and <em>137</em> were upregulated at certain time points. Weighted gene coexpression network analysis (WGCNA) showed that five <em>GhKIN</em> genes, <em>GhKIN13</em>, <em>GhKIN14</em>, <em>GhKIN27</em>, <em>GhKIN140</em> and <em>GhKIN152</em>, may be important genes regulating the salt stress response. Our study comprehensively analyzes the <em>GhKIN</em> genes in <em>Gossypium hirsutum</em>, providing a new perspective on the functional roles of <em>GhKINs</em> in cotton development and stress adaptation.</p></div>","PeriodicalId":13581,"journal":{"name":"Industrial Crops and Products","volume":null,"pages":null},"PeriodicalIF":5.6000,"publicationDate":"2023-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Genome-wide identification and characterization of the kinesin gene family in upland cotton (Gossypium hirsutum L.)\",\"authors\":\"Lijiao Gu ,&nbsp;Fei Wei ,&nbsp;Pengyun Chen ,&nbsp;Minsheng Yang ,&nbsp;Zhi Liu\",\"doi\":\"10.1016/j.indcrop.2023.117246\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p><span><em>Kinesin</em></span> (<em>KIN</em>) 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 <em>KIN</em> genes in <span><em>Gossypium hirsutum</em></span>. A total of 172 putative <em>GhKIN</em> genes were identified in the cotton genome, classified into eight subfamilies (KIN1-KIN8) according to a phylogenetic tree. The <em>GhKINs</em><span> showed an uneven distribution on chromosomes. Gene duplication<span> analysis indicated that segmental duplication was the only driving force for the expansion of the </span></span><em>GhKIN</em><span> 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 </span><em>GhKIN</em> genes contained abundant stress- and hormone-related <em>cis</em>-elements. Based on the published RNA-seq data, 56 common potential candidate genes among these 172 <em>GhKINs</em><span> 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 (RT</span><img>qPCR) analysis further revealed the expression patterns of 15 <em>GhKINs</em> under drought and salt stress. <em>GhKIN14</em> and <em>27</em> were downregulated under both stress conditions, while <em>GhKIN18</em>, <em>65</em>, <em>101</em>, <em>106</em>, and <em>137</em> were upregulated at certain time points. Weighted gene coexpression network analysis (WGCNA) showed that five <em>GhKIN</em> genes, <em>GhKIN13</em>, <em>GhKIN14</em>, <em>GhKIN27</em>, <em>GhKIN140</em> and <em>GhKIN152</em>, may be important genes regulating the salt stress response. Our study comprehensively analyzes the <em>GhKIN</em> genes in <em>Gossypium hirsutum</em>, providing a new perspective on the functional roles of <em>GhKINs</em> in cotton development and stress adaptation.</p></div>\",\"PeriodicalId\":13581,\"journal\":{\"name\":\"Industrial Crops and Products\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":5.6000,\"publicationDate\":\"2023-08-04\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Industrial Crops and Products\",\"FirstCategoryId\":\"97\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S0926669023010117\",\"RegionNum\":1,\"RegionCategory\":\"农林科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"AGRICULTURAL ENGINEERING\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Industrial Crops and Products","FirstCategoryId":"97","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0926669023010117","RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"AGRICULTURAL ENGINEERING","Score":null,"Total":0}
引用次数: 0

摘要

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。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
Genome-wide identification and characterization of the kinesin gene family in upland cotton (Gossypium hirsutum L.)

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.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
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.
期刊最新文献
Microwave-assisted pyrolysis of biomass and electrode materials from spent lithium-ion batteries: Characteristics and product compositions Metal-organic framework and rice husk derived NiCo2O4@SiO2-RH composites for catalytic degradation Water-soluble and environmentally friendly polyvinyl alcohol/straw aerogel for sustainable packaging Assessment of two-stage hyper- and thermophilic anaerobic co-digestion of briquetted wheat straw and liquid fraction of digestate Profiling volatile organic compounds of different grape seed oil genotypes using gas chromatography-mass spectrometry and chemometric methods
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1