甜菜NBS-LRR家族基因的鉴定与分析

Identification and analysis of NBS-LRR gene family in sugar beet

为明确甜菜中由抗性基因R编码的包含富亮氨酸重复序列(leucine-rich repeat,LRR)和核苷酸结合位点(nucleotide-binding site,NBS)的家族成员及其功能,基于甜菜基因组全长序列,利用HMMER、TBtools、Pfam、NCBI等软件和在线程序对甜菜NBS-LRR家族成员进行筛选和鉴定,采用生物信息学方法对鉴定到的成员进行亚家族分类、染色体定位、结构域分析、进化树构建、顺式元件分析和同源序列筛选。结果显示,从甜菜基因组中最终筛选鉴定到267条NBS-LRR家族基因序列,占甜菜基因组的0.614%,通过对267条基因序列进行结构域预测并进行分类,分属于N型、NL型、CNL型、TNL型和RNL型5个亚家族,分别包含110、25、128、3和1条序列。甜菜NBS-LRR家族基因大多位于2号、3号、4号和7号染色体上,根据基因簇划分原则发现有73.25%的基因以基因簇形式存在。经Clustal Omega和MEME在线程序对CNL型亚家族中具有完整卷曲螺旋(coiled-coil,CC)、NBS和LRR结构域的24条基因序列进行结构域保守性分析,共发现7个保守性较高的基序,基于CNL型亚家族128条基因序列构建的进化树显示CNL型亚家族的系统进化受CC、NBS和LRR结构域的影响较大。甜菜NBS-LRR家族基因含有大量植物激素相关顺式元件和多种胁迫响应元件,部分序列含有植物生理响应元件。甜菜NBS-LRR家族基因与菠菜和藜麦的抗病蛋白同源性较高。

In order to clarify the gene members in NBS-LRR family,a group of disease-resistant R genes encoding proteins containing leucine-rich repeat(LRR)and nucleotide binding site(nucleotidebinding site,NBS),and to characterize their functions in sugar beet,the member genes of sugar beet NBS-LRR family were identified by analyzing the full-length sequence of the sugar beet genome using HMMER,TBtools,Pfam,NCBI and other softwares.Subsequently,subfamily classification,chromosome mapping,structural domain analysis,phylogenetic tree construction,cis-element analysis and homologous sequence screening of the identified members were analyzed with bioinformatics methods.The results showed that 267 NBS-LRR family genes were identified from the sugar beet genome,accounting for 0.614%of the sugar beet genome.According to the domain prediction,267 genes were classified into five subfamilies,with 110 N-type,25 NL-type,128 CNL-type,3 TNL-type and 1 RNLtype genes.Most of the beet NBS-LRR family genes were located on chromosomes 2,3,4 and 7.It was found that 73.25%of genes exist in the form of gene clusters.Using online tools such as Clustal Omega and MEME,a total of seven highly conserved domains were found from the 24 genes with complete coiled-coil(CC),NBS,and LRR domains in the CNL subfamily.The phylogenetic tree was constructed using MEGA X on 128 genes of CNL subfamily.The results suggested that the phylogenetic evolution of the CNL subfamily was greatly influenced by the CC,NBS and LRR domains.The NBS-LRR gene family of sugar beet contained a large number of plant hormone-related cis-elements,a variety of stress response elements,and some plant physiological response elements.NBS-LRR family genes of sugar beet showed high homology with some disease resistance proteins in spinach and quinoa.