番茄DIR基因家族鉴定及其对非生物胁迫响应的分析  

Genome-Wide Identification of DIR Family Genes in Tomato and Response to Abiotic Stress

作　　者：陈凤琼 陈秋森 林佳昕 王雅亭 刘汉林 梁冰若诗 邓艺茹 任春元[1] 张玉先[1] 杨凤军[1] 于高波[1] 魏金鹏[1] 王孟雪[1] CHEN FengQiong;CHEN QiuSen;LIN JiaXin;WANG YaTing;LIU HanLin;LIANG BingRuoShi;DENG YiRu;REN ChunYuan;ZHANG YuXian;YANG FengJun;YU GaoBo;WEI JinPeng;WANG MengXue(College of Horticulture and Landscape Architecture,Heilongjiang Bayi Agricultural University,Daqing 163319,Heilongjiang)

机构地区：[1]黑龙江八一农垦大学园艺园林学院,黑龙江大庆163319

出　　处：《中国农业科学》2022年第19期3807-3821,I0001-I0003,共18页Scientia Agricultura Sinica

基　　金：黑龙江省博士后科研启动项目(LBH-Q20052);黑龙江八一农垦大学博士科研启动项目;黑龙江省“揭榜挂帅”科技攻关项目(2021ZXJ05B02);黑龙江省留学归国项目;国家自然科学基金(31301769);黑龙江省自然科学基金(QC2018023)。

摘　　要：【目的】鉴定番茄DIR基因家族所有成员,并对其基因结构、编码蛋白的理化性质、系统进化、染色体定位、共线性、启动子元件、表达模式、互作转录因子及内源竞争RNA预测等进行了解析,为探究DIR在番茄生长发育和逆境胁迫中的作用提供参考。【方法】采用生物信息学方法,基于全基因组数据对番茄DIR基因家族成员进行鉴定,运用Phytozome、MEME、PlantCARE、opsRNATarget和plantcircnet等在线网站获取染色体位置、保守基序、顺式作用元件、存在互作的转录因子、miRNA和circRNA等信息。利用Mapteace、TBtools、Cytoscape、OmicShare等作图软件及工具绘制染色体定位图、进化树、DIR与转录因子关系图、ceRNA网络等。采用NCBI的基因数据库结合转录组测序及qRT-PCR试验研究DIR基因家族在逆境下的表达情况。【结果】共鉴定到番茄中27个DIR基因,将其命名为SlDIR1—SlDIR27,分别位于12条染色体上,且大部分基因位于染色体末端,其基因结构、基序和结构域相对保守,其中22个SlDIR具有一个外显子的经典结构。番茄DIR基因家族同拟南芥的共线性关系远高于水稻和大豆。基于系统进化关系将27个番茄DIR成员分为3个不同的亚家族。转录组数据表明大部分DIR基因在番茄根部具有较高的表达量。此外,DIR基因的启动子区域含有多个与干旱、低温等非生物胁迫,以及MeJA、ABA、SA等激素诱导相关的顺式作用元件,且预测到与激素、生长发育、非生物胁迫相关的ERF、E2F/DP、MYB等互作转录因子。结合转录组数据分析,分别有5、10、10和13个SlDIR在农药、干旱、盐和冷胁迫后显著上调表达,其中,SlDIR23受到以上4种胁迫的诱导表达,而SlDIR8、SlDIR13和SlDIR20特异性响应冷胁迫的诱导,SlDIR17特异性响应盐胁迫。番茄DIR的ceRNA调控表明,miR-156与靶基因SlDIR8可能共同作用调控番茄的逆境胁迫。【结论】共鉴定出番茄DIR家�【Objective】The aim of this study was to identify all members of tomato DIR gene family, and to predict and analyze their gene structures, physicochemical properties of proteins, phylogenetic relationship, chromosome location, collinearity analysis,promoter elements, expression pattern, prediction of interacting transcription factors and endogenous competitive RNA, so as to provide a reference for exploring the role of DIR in tomato growth and development and response to environmental stresses.【Method】The family members of DIR were identified in the whole genome level by bioinformatics methods. The chromosome location, conserved motif, cis-acting element, transcription factors, miRNA and circRNA were analyzed with Phytozome, MEME,PlantCARE, opsRNATarget and plantcircnet, respectively. Chromosome location map, evolutionary tree, relationship map between DIR and transcription factors, ceRNA network, and etc., were drown using Maptea, TBtools, Cytoscape and Omicshare. The expression level of DIR under environmental stresses was studied by NCBI gene database, transcriptome sequencing and qRT-PCR.【Result】27 members of DIR family were identified from the whole genome of the tomato, which were named SlDIR1-SlDIR27, and DIR genes of the tomato were located on 12 chromosomes, most of which were located at the end of chromosomes. The gene structures, motifs and domains were relatively conservative, and the classical structure of one exon existed in 22 SlDIR genes. The collinear relationship of DIR genes between tomato and Arabidopsis was much higher than that of rice and soybean. Based on the phylogenetic relationship, 27 DIR members of tomato were divided into three different subfamilies. The tissue specific expression analysis revealed that transcription levels of DIR members of tomato were higher in root. In addition, the promoter region of these genes contained multiple cis-acting elements related to abiotic stress, including drought, low temperature, and hormone induction,such as MeJA, ABA and SA. Hormone,

关 键 词：DIR蛋白 番茄 基因家族 生物信息学 

分 类 号：S641.2[农业科学—蔬菜学]