番茄LBD转录因子家族的鉴定与分析

Identification and analysis of the LBD transcription factor family in tomato

摘要

侧生器官边界域(lateral organ boundaries domain,LBD)基因家族是一类植物特有的转录因子,参与植物生长、营养代谢和逆境胁迫响应的调控.在基因组水平对番茄LBD基因家族进行了系统鉴定和分析.共鉴定出53个番茄LBD基因,根据系统发育树及进化关系将其划分为ClassⅠ和ClassⅡ这2大类,并进一步细分为7个亚家族.其中,ClassⅠ的LBD蛋白质结构域具备完整的亮氨酸拉链基序,而ClassⅡ的LBD蛋白结构域缺少该基序.染色体定位分析表明,在番茄的12条染色体中有10条含有LBD基因.番茄与马铃薯2个茄科物种的LBD基因呈现出高度的基因共线性,共存在19对LBD直系同源基因对.收缩与扩张分析显示,LBD基因家族在番茄、马铃薯、辣椒、葡萄、拟南芥和中果咖啡中并没有明显的扩张,数目趋于稳定.此外,密码子分析显示番茄LBD基因的密码子偏好性较弱.表达分析表明,渗透胁迫可引起多个LBD基因在番茄根和叶中的表达量上调.为后续深入研究番茄LBD基因功能奠定了基础.

Abstract

The lateral organ boundaries domain (LBD) gene family is a class of plant-specific transcription factors involved in the regulation of plant growth,nutrient metabolism,and stress response.In this study,a systematic identification and analysis of the LBD gene family in tomato were conducted at the genomic level.A total of 53 LBD genes were identified in tomato.Based on phylogenetic and evolutionary relationship analysis,they were divided into two major categories(Class I and Class Ⅱ),which were further subdivided into seven subfamilies.Among them,Class I LBD proteins possess a complete leucine zipper motif within their domain structure,whereas Class Ⅱ LBD proteins lack this motif.Chromosomal localization analysis showed that LBD genes are distributed across 10 of the 12 tomato chromosomes.Notably,a high degree of gene collinearity was observed for LBD genes between tomato and potato,two solanaceous species,with 19 orthologous gene pairs identified.Contraction and expansion analysis showed that the LBD gene family does not exhibit obvious expansion and showed stable gene numbers across the species analyzed,including tomato,potato,pepper,grape,arabidopsis,and robusta coffee.Furthermore,weak codon usage bias was observed in tomato LBD genes.Expression analysis revealed that osmotic stress could induce the upregulation of the expression levels of multiple LBD genes in both roots and leaves of tomato plants.These findings lay an important theoretical foundation for further investigations into the functions of tomato LBD genes.

关键词

番茄 / LBD转录因子 / 基因家族 / 生物信息学分析

Key words

Solanum lycopersicum / LBD transcription factor / gene family / bioinformatics analysis

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基金资助

河北省自然科学基金(C2024209006)