{"title":"Identification and expression analysis of TALE superfamily genes explore their key roles in response to abiotic stress in Brassica napus.","authors":"Meili Xie, Xiaojuan Zhang, Kexin Liu, Zhixian Qiao, Xiaohui Cheng","doi":"10.1186/s12870-024-05953-1","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>The three-amino-acid-loop-extension (TALE) superfamily genes are broadly present in plants and play important roles in plant growth, development, and abiotic stress responses. So far, the TALE family in B.napus have not been systematically studied, especially their potential roles in response to abiotic stress.</p><p><strong>Results: </strong>In this study, we identified 74 TALE family genes distributed on 19 chromosomes in the B. napus genome using bioinformatics methods. Phylogenetic analysis divided the BnTALE superfamily into two subfamilies, the BEL1-like (BLH/BELL homeodomain) and the KNOX (KNOTTED-like homeodomain) subfamilies. Moreover, the KNOX subfamily could be further categorized into three clades (KNOX Class I, KNOX Class II, and KNOX Class III). BnTALE members in the same subclass or branch of the phylogenetic tree generally showed similar gene structures and conserved domain compositions, which may indicate that they have similar biological functions. The BnTALE promoter regions contained many hormone-related elements and stress response elements. Duplication events identification analysis showed that WGD/segmental duplications were the main drivers of amplification during the evolution of TALE genes, and most of the duplicated BnTALE genes underwent purifying selection pressures during evolution. Potential protein interaction network analysis showed that a total of 12,615 proteins might interact with TALE proteins in B. napus. RNA-seq and qRT-PCR analyses showed that the expression of BnTALE was tissue-differentiated and can be induced by abiotic stresses such as dehydration, cold, and NaCl stress. In addition, weighted gene co-expression network analysis (WGCNA) identified four co-expression modules containing the most BnTALE genes, which would be notably related to dehydration and cold stresses.</p><p><strong>Conclusions: </strong>Our study paves the way for future gene functional research of BnTALE and facilitate their applications in the genetic improvement of B. napus in response to abiotic stresses.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"24 1","pages":"1238"},"PeriodicalIF":4.3000,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11665101/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"BMC Plant Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s12870-024-05953-1","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"PLANT SCIENCES","Score":null,"Total":0}
引用次数: 0
Abstract
Background: The three-amino-acid-loop-extension (TALE) superfamily genes are broadly present in plants and play important roles in plant growth, development, and abiotic stress responses. So far, the TALE family in B.napus have not been systematically studied, especially their potential roles in response to abiotic stress.
Results: In this study, we identified 74 TALE family genes distributed on 19 chromosomes in the B. napus genome using bioinformatics methods. Phylogenetic analysis divided the BnTALE superfamily into two subfamilies, the BEL1-like (BLH/BELL homeodomain) and the KNOX (KNOTTED-like homeodomain) subfamilies. Moreover, the KNOX subfamily could be further categorized into three clades (KNOX Class I, KNOX Class II, and KNOX Class III). BnTALE members in the same subclass or branch of the phylogenetic tree generally showed similar gene structures and conserved domain compositions, which may indicate that they have similar biological functions. The BnTALE promoter regions contained many hormone-related elements and stress response elements. Duplication events identification analysis showed that WGD/segmental duplications were the main drivers of amplification during the evolution of TALE genes, and most of the duplicated BnTALE genes underwent purifying selection pressures during evolution. Potential protein interaction network analysis showed that a total of 12,615 proteins might interact with TALE proteins in B. napus. RNA-seq and qRT-PCR analyses showed that the expression of BnTALE was tissue-differentiated and can be induced by abiotic stresses such as dehydration, cold, and NaCl stress. In addition, weighted gene co-expression network analysis (WGCNA) identified four co-expression modules containing the most BnTALE genes, which would be notably related to dehydration and cold stresses.
Conclusions: Our study paves the way for future gene functional research of BnTALE and facilitate their applications in the genetic improvement of B. napus in response to abiotic stresses.
背景:TALE (three-amino-acid-loop-extension)超家族基因广泛存在于植物中,在植物生长发育和非生物胁迫响应中发挥重要作用。迄今为止,对甘蓝型油菜的TALE家族尚未进行系统的研究,特别是它们在应对非生物胁迫中的潜在作用。结果:本研究利用生物信息学方法鉴定了分布在油菜基因组19条染色体上的74个TALE家族基因。系统发育分析将BnTALE超家族分为两个亚家族,BEL1-like (BLH/BELL同源结构域)和KNOX (knot -like同源结构域)亚家族。此外,KNOX亚家族可进一步划分为3个分支(KNOX Class I、KNOX Class II和KNOX Class III)。在系统发育树的同一亚类或分支的BnTALE成员普遍表现出相似的基因结构和保守的结构域组成,这可能表明它们具有相似的生物学功能。BnTALE启动子区域包含许多激素相关元件和应激反应元件。重复事件鉴定分析表明,WGD/片段重复是TALE基因进化过程中扩增的主要驱动因素,大多数复制的BnTALE基因在进化过程中都经历了纯化选择压力。潜在蛋白相互作用网络分析表明,甘蓝型油菜中有12615个蛋白可能与TALE蛋白相互作用。RNA-seq和qRT-PCR分析表明,BnTALE的表达是组织分化的,可以受到脱水、低温和NaCl胁迫等非生物胁迫的诱导。此外,加权基因共表达网络分析(WGCNA)鉴定出4个含有最多BnTALE基因的共表达模块,这些共表达模块与脱水和冷胁迫密切相关。结论:本研究为进一步研究BnTALE基因功能奠定了基础,并为其在甘蓝型油菜非生物胁迫遗传改良中的应用奠定了基础。
期刊介绍:
BMC Plant Biology is an open access, peer-reviewed journal that considers articles on all aspects of plant biology, including molecular, cellular, tissue, organ and whole organism research.