南瓜SWEET蛋白家族的全基因组鉴定与进化分析

Genome-wide identification and phylogenetic analysis of SWEET protein family in pumpkin

关键词:  南瓜, SWEET, 系统发育分析, 共线性, 顺式作用元件, 生物信息学

Key words:  pumpkin, SWEET, phylogenetic analysis, collinearity, cis-acting elements, bioinformatics

摘要:

SWEET(sugar will eventually be exported transporter)家族是一种新型的糖转运体,该家族基因在碳水化合物运输、发育、环境适应性和寄主-病原相互作用等多个过程中发挥着重要作用。为更好地了解南瓜发育的分子机理,该研究基于已知的南瓜基因组数据库,利用生物信息学方法对中国南瓜SWEET基因(CmSWEET)的系统发育树、基因结构、跨膜结构、保守基序、启动子预测、共线性预测和基因复制等进行综合分析。结果表明:共鉴定到21个CmSWEET 基因,通过系统发育分析将21个CmSWEET基因分为4个亚族(I,II,III和IV),分别包含3、5、10和3个基因。此外,通过基因结构、跨膜结构域和保守基序发现CmSWEET在进化过程中是非常保守的。染色体定位结果显示,CmSWEET基因不均匀地分布在21条中国南瓜染色体中的13条染色体上,且在染色体Cm00、Cm01、Cm03、Cm05、Cm07、Cm09、Cm19和Cm20上不存在。启动子顺式作用元件分析显示,CmSWEET基因与植物激素(脱落酸、茉莉酸甲酯、水杨酸和生长素)响应有关,也可能参与各种环境胁迫的响应。从系统进化发育树和基因共线性方面揭示了CmSWEET基因与印度南瓜SWEET(CmaSWEET)之间的进化关系。该研究在全基因组水平上系统地鉴定了中国南瓜中SWEET基因家族,为进一步了解中国南瓜和其他葫芦科作物SWEET基因提供了基础,也为进一步的功能分析提供了重要的候选基因。

Abstract:

SWEET(sugar will eventually be exported transporter)is a new type of sugar transporter, which plays important roles in carbohydrate transport, development, environmental adaptability and host pathogen interaction. In order to better understand the molecular mechanism of pumpkin development, we used bioinformatics methods to comprehensively analyzed the phylogenetic tree, gene structure, transmembrane structure, conserved motif, promoter prediction, collinearity prediction and gene replication of the Cucurbita moschata SWEET gene(CmSWEET), based on the known pumpkin genome database. The results were of follows: 21 CmSWEET genes were identified and divided into four subfamilies(I, Ⅱ, Ⅲ and IV)by phylogenetic analysis, including 3, 5, 10 and 3 genes respectively. In addition, the gene structure, transmembrane domain and conserved motif showed that CmSWEET genes were very conserved in evolution. The results of chromosome mapping showed that CmSWEET genes were unevenly distributed on 13 of 21 chromosomes and did not exist on chromosomes Cm00, Cm01, Cm03, Cm05, Cm07, Cm09, Cm19 and Cm20. Analysis of promoter cis-acting element showed that the CmSWEET genes were related to plant hormone response(abscisic acid, methyl jasmonate, salicylic acid and auxin), and may also participate in response to various environmental stresses. Finally, the phylogenetic relationship was revealed from phylogenetic tree and gene collinearity. This study systematically identified the SWEET genes family in C. moschata at the whole genome level, which provided a basis for further understanding the SWEET gene of C. moschatas and other Cucurbitaceae crops, and also provided an important candidate gene for further functional analysis.