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柑橘U-box基因家族的鉴定及表达分析 预览

Genome Wide Identification and Expression Analysis of the U-box Gene Family in Citrus
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摘要 【目的】通过生物信息学分析U-box在柑橘基因组中的分布、结构及进化,研究家族成员在不同组织中的表达特异性以及对非生物胁迫和激素的响应,解析柑橘U-box基因家族的生物学功能。【方法】根据已经报道的拟南芥U-box基因,利用Phytozome数据库中的BLASTp工具鉴定柑橘基因组中的U-box基因。采用MEGA6.0、Cello、SMART、GSDS2.0、ExPASy和MapChart等软件构建系统进化树、亚细胞定位预测、预测蛋白的相对分子质量与等电点等理化性质、绘制家族成员Scaffold定位图等,分析U-box基因家族在低温胁迫下表达模式,利用实时荧光定量PCR技术(q RT-PCR)检测柑橘U-box基因家族部分成员在NaCl、PEG6000和不同激素处理下的表达情况。【结果】从柑橘克里曼丁(Citrus clementina)全基因组中鉴定出56个Cc PUBs基因家族成员,可将其分为7类,即U-box only、U-box+ARM-1、U-box+WD40-1、TPR+U-box、Kinase+U-box、U-box+ARM-2和U-box+WD40-2。该家族蛋白理论等电点分布在5.19—9.14,编码的氨基酸数目介于281—1 441;亚细胞定位预测结果显示该基因家族成员位于细胞不同位置,主要位于细胞核或叶绿体,少数位于质膜;聚类分析发现,柑橘U-box与单子叶植物水稻的亲缘关系较远,柑橘中具有相同结构域的成员和拟南芥具有相同结构域的成员聚在一起,表明柑橘U-box成员具有不同生物学功能;Scaffold定位分析发现,56个U-box成员分布在1—9 Scafflod上且呈不均分布。在冷胁迫下的RNA-Seq分析结果表明,U-box基因家族参与植物对冷胁迫的应答,并表现出4种不同的应答模式;从柑橘U-box基因家族的5个不同簇上分别选取1个代表基因进行qRT-PCR,分析结果表明,Cc PUB48在金柑的各个组织中均有表达,CcPUB9和CcPUB4主要在茎和花中表达,Cc PUB10主要在花、茎和幼果中表达,CcPUB41主要在叶和茎中表达,体现了不同U-box成员的组织特异性的表达差异。CcPUB4、CcPUB10和C 【Objective】The objectives of this study were to analyze the distribution,structure and evolution of U-box in citrus genome by bioinformatics,to study the expression specificity of family members in different tissues and their responses to abiotic stress and hormones,and to investigate the biological function of U-box gene family in citrus.【Method】According to the reported U-box gene of Arabidopsis thaliana,the U-box gene in citrus genome was identified by BLASTp tool in Phytozome database.Phylogenetic tree,subcellular localization prediction,relative mass and isoelectric point and other physical and chemical properties,and scaffold location of U-box member were analyzed with MEGA6.0,Cello,SMART,GSDS2.0,ExPASy and MapChart,respectively.The expression pattern of U-box gene family under low temperature stress was analyzed,and the expression of some members of U-box gene family in citrus treated with NaCl,PEG6000 and different hormones was detected by real-time fluorescence quantitative PCR(qRT-PCR).【Result】Fifty-six members of CcPUBs gene family were identified from the whole genome of Citrus clementina,and they could be divided into 7 categories,namely as U-box only,U-box+ARM-1,U-box+WD40-1,TPR+U-box,Kinase+U-box,U-box+ARM-2 and U-box+WD40-2.The theoretical isoelectric point of the family protein was ranged from 5.19 to9.14,and the number of amino acids encoded was 281 to 1 441.The results of subcellular localization prediction showed that the members of the gene family were located in different positions of the cell,mainly in the nucleus or chloroplast,and a few in the plasma membrane.Cluster analysis showed that citrus U-box was closely related to monocotyledonous rice,and members with the same domain in citrus and Arabidopsis thaliana were clustered together.The results showed that U-box members of citrus had different biological functions,and scaffold localization analysis showed that 56 U-box members were unevenly distributed on citrus1-9 scaffold.The results of RNA-Seq analysis under cold stress s
作者 李秋月 张亚飞 彭洁 王旭 张志强 戴祥生 江东 LI QiuYue;ZHANG Yafei;PENG Jie;WANG Xu;ZHANG ZhiQiang;DAI Xiangsheng;JIANG Dong(Citrus Research Institute,Southwest University,Chongqing 400712;Citrus Research Institute of Chinese Academy of Agricultural Sciences,Chongqing 400712;Management Committee of Jinggangshan Agricultural Science and Technology Park,Jinggangshan 343000,Jiangxi)
出处 《中国农业科学》 CAS CSCD 北大核心 2019年第11期1942-1960,共19页 Scientia Agricultura Sinica
基金 国家重点研发计划(2018YFD1000101) 重庆市科委重点项目(cstc2016shms-ztzx80004).
关键词 柑橘 CcPUB基因家族 激素 胁迫 基因表达 citrus Cc PUB gene family hormone stress gene expression
作者简介 李秋月,E-mail:437010037@qq.com;通信作者:江东,E-mail:jiangdong@cric.cn。
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