黄瓜DIR家族基因的全基因组鉴定及其表达分析  

Genome-Wide Identification and Expression Analysis of DIR Gene Family in Cucumber

作　　者：张开京 何帅帅 贾利[2] 胡玉超 杨德坤 陆晓民 张其安[2] 严从生[2] ZHANG KaiJing;HE ShuaiShuai;JIA Li;HU YuChao;YANG DeKun;LU XiaoMin;ZHANG QiAn;YAN CongSheng(College of Agriculture,Anhui Science and Technology University,Fengyang 233100,Anhui;Institute of Horticulture,Anhui Academy of Agricultural Sciences/Key Laboratory of Horticultural Crop Germplasm Innovation and Utilization(Co-construction by Ministry and Province)/Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crop,Anhui Province,Hefei 230031)

机构地区：[1]安徽科技学院农学院,安徽凤阳233100 [2]安徽省农业科学院园艺研究所/农业农村部园艺作物种质创制与利用重点实验室(部省共建)/园艺作物种质创制及生理生态安徽省重点实验室,合肥230031

出　　处：《中国农业科学》2023年第4期711-728,共18页Scientia Agricultura Sinica

基　　金：国家自然科学基金(32002061);国家级大学生创新创业训练计划项目(202010879108);安徽省蔬菜产业技术体系专项经费资助项目(皖农科函(2021)711号);安徽省农业科学院青年英才经费资助项目(QNYC-201906);安徽科技学院人才引进项目(NXYJ202103)。

摘　　要：【目的】基于黄瓜基因组信息和转录组测序大数据,利用生物信息学手段,对黄瓜中DIR基因家族进行鉴定,并分析其在不同组织器官和胁迫响应过程中的表达模式,为后续深入研究黄瓜DIR基因的生物学功能奠定重要基础。【方法】基于已报道的DIR基因HMM模型文件,利用HMMER软件包的hmmsearch程序从黄瓜蛋白数据库中筛选出可能的DIR基因ID,并利用在线工具Pfam和SMART进行验证,最终确定黄瓜DIR家族基因。利用ExPASy、TBtools、GSDS、MEME、MEGA、MCScanX和Circos等工具分析黄瓜DIR基因家族成员的理化特征、染色体定位、基因结构、系统进化树和共线性。基于黄瓜在不同组织和胁迫响应下的转录组测序大数据,利用黄瓜V3版本基因组信息进行转录组分析,检索黄瓜DIR基因在不同转录组测序分析中的表达情况,利用TBtools软件绘制表达热图,分析黄瓜DIR基因在不同组织和胁迫响应过程中的表达模式。【结果】在黄瓜中鉴定到23个DIR家族基因,分布于7条染色体上,编码氨基酸个数在78—684,分子量8.70—73.82 kD;系统进化分析将黄瓜DIR基因家族划分为3个亚族,每个亚族中的基因结构和motif基本一致;共线性分析发现黄瓜中有12个DIR基因与拟南芥中的19个DIR基因存在27种线性关系,黄瓜中有12个DIR基因与水稻中的11个DIR基因存在19种线性关系,而黄瓜中另外8个DIR基因比较保守,既不与拟南芥中的DIR基因存在共线性,也不与水稻中的DIR基因存在共线性;组织特异性表达分析发现有些黄瓜DIR基因在根、茎、花、果实、叶片等所有组织器官中的表达量均较低或不表达,有些黄瓜DIR基因在所有组织器官中的表达量均较高,而有些黄瓜DIR基因只在特定组织中表达,但在其他组织中不表达或低表达,表明不同的黄瓜DIR基因具有组织特异性表达模式;黄瓜DIR家族基因在胁迫响应过程中的表达模式分析发现CsaV3_4G023490【Objective】Based on the cucumber(Cucumis sativus L.)genome information and transcriptome sequencing big-data,the DIR gene family in cucumber was identified with bioinformatics methods,and the expression pattern analysis of DIR family genes in different tissues and stresses response were analyzed.It would lay an important foundation for further study on the biological function of cucumber DIR genes.【Method】With the reported HMM model file of DIR gene,the probable DIR genes ID from the cucumber protein database was firstly identified using HMMSearch program in the HMMER software package.The cucumber DIR genes were ultimately verified using online tools Pfam and SMART.The tools of ExPASy,TBtools,GSDS,MEME,MEGA,MCScanX and Circos were used to analyze the physicochemical characteristics,chromosomal distributions,gene structure,phylogenetic tree and synteny of cucumber DIR genes.Based on cucumber transcriptome sequencing big-data of different tissues and under different stresses,transcriptome sequencing analysis was re-analyzed using cucumber V3 version genome information.The data of cucumber DIR genes in different transcriptome sequencing analysis were retrieved.The expression heatmaps of DIR gene family were drawn using TBtools software,and the expression patterns of cucumber DIR genes in different tissues and stresses response were analyzed.【Result】Total of 23 DIR genes were identified from cucumber genome,which distributed to 7chromosomes.The number of amino acids of these DIR genes ranged from 78 to 684,and the molecular weight ranged from 8.70 to 73.82 kD.Phylogenetic analysis divided the cucumber DIR genes into 3 subgroups,the structure and motif of the genes in each subgroup were similar.Synteny analysis showed that the 12 cucumber DIR genes were collinearity with 19 Arabidopsis DIR genes and with 27 kinds of linear relationships,and 12 cucumber DIR genes were collinearity and with 11 rice DIR genes with 19 kinds of linear relationships.While only 8 cucumber DIR genes were conservative,which were no

关 键 词：黄瓜 DIR 基因家族 生物信息学 表达分析 

分 类 号：S642.2[农业科学—蔬菜学]