葡萄HB基因家族全基因组鉴定及表达分析

Genome-wide identification and expression analysis of HB gene family in Vitis vinifera

[目的]本文旨在利用生物信息学方法鉴定葡萄同源异型盒(homeobox,HB)基因家族,对其序列和结构特征,进化特征和表达特性进行系统分析,筛选响应芽休眠及多种胁迫的候选葡萄HB基因。[方法]利用本地BLAST程序,以拟南芥HB基因为靶序列与葡萄全基因组蛋白序列进行比对。利用ExPASy预测葡萄HB基因家族蛋白理化性质,并使用MapGene2Chro定位染色体。基于邻近法,利用MEGA X软件构建葡萄和拟南芥HB基因家族成员系统进化树。同时使用TBtools软件分析HB家族成员基因结构、保守结构域及启动子顺式作用元件特征。采用MCScanX分析HB基因家族成员在葡萄与拟南芥之间的基因组共线性。基于已有的转录组数据,分析HB基因在芽休眠、果实发育和不同非生物胁迫下的表达情况。[结果]在葡萄基因组中共鉴定出80个HB基因家族成员,分布在18条染色体上,根据进化分析将其分为9个亚族。家族成员氨基酸数量为66~1772,相对分子质量为(8.28~198.55)×103,等电点为4.60~10.03,亚细胞定位预测其主要定位于叶绿体之中。基因结构分析发现,葡萄HB基因家族成员均包含外显子,数量为1~20个。葡萄HB基因家族存在2对串联重复基因和23对共线性基因,在拟南芥和葡萄间存在82对共线性基因对。启动子顺式作用元件分析表明,HB家族含有光响应元件、多种激素响应元件、逆境胁迫响应元件和组织特异性响应元件等。葡萄HB家族蛋白中KNOX与BEL亚家族成员间互作关系最为密切。通过葡萄HB基因家族的表达谱分析发现,绝大部分HB家族成员在芽休眠和干旱胁迫下有显著差异表达,并且还发现了7个HB家族成员可能参与芽休眠调控,其中VvHB9和VvHB34可参与多种非生物胁迫。[结论]本研究鉴定并分析了葡萄HB家族成员的基本信息,基于转录组数据,筛选了多个参与芽休眠调控和能够响应多种非生物胁迫的关键基因。

[Objectives]The paper aimed to identify the grape homeobox(HB)gene family using bioinformatics methods,systematically analyze their sequence and structural characteristics,evolutionary features and expression characteristics,and screen candidate grape HB genes in response to bud dormancy and various stresses.[Methods]Using the local BLAST program,the HB gene in Arabidopsis thaliana was used as the target sequence for comparison with the grape whole genome protein sequence.ExPASy was used to predict the physical and chemical properties of grape HB gene family proteins,and MapGene2Chro was used to locate chromosomes.Based on Neighbour-joining method,the MEGA X software was used to perform phylogenetic tree of these HB genes in grape and A.thaliana.Meanwhile,TBtools software was used to analyze the gene structure,conserved domain and promoter cis-elements characteristics of HB family members.Genomic collinearity of HB gene family members between grape and A.thaliana was analyzed by MCScanX.Based on known transcriptomic data,the expression of HB genes was analyzed under bud dormancy,fruit development and different abiotic stresses.[Results]Eighty HB genes were identified in the grape genome,distributed on 18 chromosomes,which were divided into 9 subfamilies based on evolutionary analysis.The amino acid quantity was 66-1772,molecular weight was(8.28-198.55)×103 and isoelectric point was 4.60-10.03.The prediction of subcellular localization indicated that the family members were mainly located in chloroplasts.Gene structure analysis revealed that all grape HB members contain exons ranging from 1 to 20 in number.There were 2 pairs of tandem duplicated genes and 23 co-linear pairs in the grape HB gene family,and 82 co-linear pairs between A.thaliana and grape.Promoter cis-elements analysis showed that the HB family contained cis-elements related to light response,plant hormones and stress,and tissue-specific expression.Among grape HB family proteins,KNOX and BEL subfamily members had the closest interaction.Through the analysis of the expression profile of grape HB gene family,it was found that most HB family members were significantly differentially expressed under bud dormancy and drought stress.In addition,seven HB family members were found to be involved in bud dormancy regulation,and VvHB9 and VvHB34 were involved in various abiotic stresses.[Conclusions]In this study,basic information was identified and analyzed on the members of the grape HB family,and several key genes were screened which were involved in the regulation of bud dormancy and response to multiple abiotic stresses based on transcriptomic data.