西瓜 ClKNOX基因家族全基因组鉴定及组织表达分析

Genome-wide identification and expression analysis of ClKNOX gene family in watermelon

摘要

KNOX基因家族是编码同源异型盒蛋白的转录因子，在植物生长发育和胁迫响应中发挥着重要的调控作用。为进一步挖掘西瓜 KNOX转录因子家族成员信息，探究分析其表达模式及基因功能，通过生物信息学方法对西瓜 KNOX基因家族成员进行了鉴定，并对其理化性质、基因结构、系统进化及表达模式进行了分析。结果表明，西瓜基因组中共有12个 KNOX基因，均定位于细胞核中，符合转录因子属性特征；KNOX1、KNOX2、ELK和Homeobox_KN这4类典型结构域均存在于大多数西瓜 KNOX基因中，表明这4类结构域在 KNOX基因功能中具有重要作用；系统发育分析将 ClKNOX基因家族成员分为Class ⅠA、Class ⅠB、Class ⅡA和Class ⅡB 4个亚组，启动子元件分析表明， ClKNOX基因家族含有较多与生长发育和胁迫响应相关的顺式作用调控元件；组织表达分析结果表明， ClKNOX基因具有明显的组织特异表达特性， ClKNOX6和 ClKNOX11在根和茎中高表达，而 ClKNOX3和 ClKNOX10在所有器官中表达量都相对较高，但所有 ClKNOX基因在果肉中的相对表达量都较低。研究结果为进一步深入探究 ClKNOX基因在生长发育中的功能和组织表达特性奠定了基础。

Abstract

KNOTTED-like homeodomain (KNOX) gene family is a class of transcription factors encoding homeobox protein, which plays an important role in plant growth and stress responses. To further investigate the watermelon KNOX transcription factor family members, the bioinformatics methods was utilized to identify and analyze their physical and chemical properties, gene structure, phylogeny, and expression patterns. The study revealed the presence of 12 KNOX genes in the watermelon genome, all of which were identified in the nucleus, the result was consistent with their characteristics as transcription factors. Most KNOX genes in watermelon exhibited the typical domains KNOX1, KNOX2, ELK, and Homeobox_KN, suggesting the significance of these domains in KNOX gene functionality. Phylogenetic analysis categorized ClKNOX gene family members into four subgroups: ClassⅠA, ClassⅠB, ClassⅡA, and ClassⅡB. Analysis of promoter elements indicated that the ClKNOX gene family harbored numerous cis-acting regulatory elements associated with growth, development, and stress response. The results of tissue expression analysis revealed distinct patterns for ClKNOX gene expression. Specifically, ClKNOX6 and ClKNOX11 exhibited high expression levels in roots and stems, whereas ClKNOX3 and ClKNOX10 showed relatively high expression across all organs. However, all ClKNOX genes had low relative expression levels in flesh. These findings provide a basis for future investigations into the functional roles and tissue-specific expression patterns of ClKNOX genes in growth and development.

关键词

西瓜 / KNOX基因家族 / 全基因组鉴定 / 生物信息学分析 / 组织表达

Key words

Watermelon / KNOX gene family / Genome-wide identification / Bioinformatics analysis / Tissue expression

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基金资助

河南省科技攻关项目(222102110124)

河南省农业品种改良联合研究项目(2022010503)