乌拉尔图小麦NBS-LRR家族生物信息学分析  

Bioinformatics Analysis of NBS-LRR Gene Family in Triticum urartu

作　　者：刘小芳[1] 袁欣 聂迎彬[1] 张晶[2] Liu Xiaofang;Yuan Xin;Nie Yingbin;Zhang Jing(Xinjiang Academy of Agricultural Sciences, Shihezi,832000;Horticulture Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou,450002)

机构地区：[1]新疆农垦科学院,石河子832000 [2]河南省农业科学院园艺研究所,郑州450002

出　　处：《分子植物育种》2018年第23期7587-7597,共11页Molecular Plant Breeding

基　　金：国家自然基金项目(31460346)资助

摘　　要：乌拉尔图小麦(Triticum urartu)为二倍体小麦,是普通小麦(Triticum aestivum,由A,B,D三个亚基因组成的异源六倍体)A基因组供体。普通小麦基因组庞大,异源六倍体性质导致其基因组研究存在困难。伴随普通小麦供体A基因组和D基因组的测序完成,为小麦A基因组供体NBS-LRR基因家族的研究提供了重要生物信息学数据。目前获得的抗病(R)基因大部分具有NBS(nucleotide-bindingsite)和LRR(leucine-rich-repeat)结构域,属于NBS-LRR基因家族。本研究采用HMMER对乌拉尔图小麦蛋白序列信息进行了NBS-LRR家族基因筛选,通过Paircoi2网站进行coil-coil结构域分析,采用Uniprot和NCBIBlast进行了验证和排除,经Bioedit、MEGA5.1、ClustalW、Jalview等软件进行了NBS-LRR基因序列分析,确定了乌拉尔图小麦的NBS-LRR基因数量、类型、结构特点和系统发育学关系。最终从乌拉尔图小麦中获得485个NBS-LRR基因,占基因组1.503%,其中331个N型,163个CNL型(其中34个CN型),60个NL型,无Tir型。随后经MEME网站筛选获得CNL亚家族中的15个相对保守的motif,N末端结构均保守性较高。此外,PLN00113出现在LRR的位置,在系统进化树的各分支中随机性分布。乌拉尔图小麦NBS-LRR基因的分类、蛋白序列的motif分析和系统进化树的研究为小麦NBS-LRR家族基因的功能研究提供重要依据。Triticum urartu as a diploid wheat, is a donor of A genome to bread wheat (Triticum aestivum, a heterologous hexaploid composed of three subgenes A, B, D). The genome of common wheat is so large that it is difficult to do genome research due to the nature of heterologous hexaploid. With the completion of A and D donor genomes sequencing of common wheat, it provided important bioinformatic data for the research of NBS-LRR gene family in A genome donor of common wheat. Most of the disease resistance (R) genes had the NBS (nucleotide-binding site) and LRR (leucine-rich-repeat) domains, belonging to the NBS-LRR gene family. In this study, HMMER was used to screen the NBS-LRR family genes from protein sequence information of Triticum urartu. The coil-coil domain was analyzed by Paircoi2. Uniprot and NCBI Blast were used to verify and exclude the wheat NBS-LRR family genes. Bioedit, MEGA 5.1, Clustal W, Jalview and other software were used to analyze NBS-LRR gene sequence and determine NBS-LRR gene number, type, structural characteristics and phylogenetic relationship of Triticum urartu. Finally, 485 NBS-LRR genes were obtained from Triticum urartu, about 1.503% ofthe genome, of which 331 were N-type, 163 were CNL-type (including 34 CN), 60 were NL-type and no Tir-type. Subsequently, 15 relatively conserved motifs in the CNL subfamily were screened by the MEME website, and the N-terminal structure was highly conserved. In addition, PLN00113 appeared at the LRR location and was randomly distributed in all branches of the phylogenetic tree. The classification of NBS-LRR genes, the motif analysis of protein sequences and phylogenetic tree of wheat in Triticum urartu might provide an important basis for the functional studies of NBS-LRR family genes in wheat.

关 键 词：乌拉尔图小麦 NBS-LRR R基因 基因家族 生物信息学分析 

分 类 号：S512.1[农业科学—作物学] Q811.4[生物学—生物工程]