南瓜生长素响应因子(ARF)基因家族的全基因组分析及表达分析

Genome-wide and expressional analyses of auxin response factor (ARF) gene family in pumpkin (Cucurbita moschata)

为研究南瓜(Cucurbita moschata)生长素响应因子(ARF)基因家族,利用生物信息学工具分析南瓜ARF(CmARF)基因数目、在染色体上的分布、结构以及编码蛋白保守结构、基序、顺式作用元件,并利用实时荧光定量PCR (qRT-PCR)技术分析CmARF的组织表达模式。共鉴定出32个CmARF成员,根据其氨基酸序列的一致性将其分为7个亚族(Ⅰ~Ⅶ),同一亚族的ARF通常表现出相似的基因结构(外显子-内含子分布)和保守结构域。染色体定位分析表明, 32个CmARF在21条染色体中的15条存在不均匀分布;其中16个CmARF形成8个重复的基因对,且都经历了片段复制事件。CmARF在根、茎、子叶和真叶中的表达特征表明,其具有组织特异性。顺式作用元件分析表明,一些关键CmARF可能参与对脱落酸、茉莉酸甲酯、生长素、水杨酸等的响应。所有CmARF均含有保守的DBD和MR结构域,部分CmARF还含有CTD结构域。CmARF基因的结构与进化时间相关,且CmARF的扩张是由于基因的片段复制事件造成的。本研究为阐明CmARF的功能和作用机理提供理论基础。

To study auxin response factor(ARF) gene family in pumpkin(Cucurbita moschata), the amount, chromosomal location and structure of CmARF genes, and conserved structure, motifs and cis-acting elements of CmARF proteins were analyzed by bioinformatic tools, and the tissue expression pattern of CmARFs was analyzed by quantitative real-time PCR(qRT-PCR). In this study, 32 CmARF members were identified and divided into seven subfamilies(Ⅰ–Ⅶ) according to their amino acid sequence identity. CmARFs from the same subfamily usually have similar gene structure(intron-exon distribution) and conserved domains. Chromosomal location analysis showed that 32 CmARFs were unevenly distributed in 15 of 21 chromosomes, and 16 of the CmARFs formed 8 duplicate gene pairs, all of which experienced segmental duplication events. The expression characteristics of CmARFs in roots, stems, cotyledons and true leaves showed that they have tissue specificity. Cis-acting element analysis showed that some key genes of CmARFs may be involved in the response to abscisic acid, methyl jasmonate, auxin and salicylic acid. It was shown that all CmARFs contain conserved DBD and MR domains, and some CmARFs contain CTD domain. The structure of the CmARFs was related to the evolution time, and the expansion of CmARFs was caused by the gene segmental duplication event. This study would provide a theoretical basis for elucidating the function and mechanism of CmARFs.