甜菜NBS-LRR家族基因的鉴定与分析

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。

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

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.