Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana.
Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana.
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芸苔属植物和拟南芥之间 NBS 编码基因的全基因组比较分析。
DOI：
10.1186/1471-2164-15-3
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发表时间：
2014-01-03
期刊：
影响因子：
4.4
通讯作者：
Liu S
中科院分区：
文献类型：
--
作者：
Yu J;Tehrim S;Zhang F;Tong C;Huang J;Cheng X;Dong C;Zhou Y;Qin R;Hua W;Liu S
具有核苷酸结合位点（NBS）的植物抗病基因在提供抗病性方面起着重要作用。甘蓝和芜菁全基因组序列的获得为研究人员鉴定和表征芸苔属物种中编码NBS-R基因以及基于比较基因组学方法与拟南芥中类似物进行比较提供了重要机会。然而，关于NBS编码基因在芸苔属植物中从A. thaliana.在这里，我们提出了在B的NBS编码基因的全基因组分析。oleracea，B. B. rapa和A. thaliana.通过HMM搜索和人工筛选，我们在B中分别鉴定出157、206和167个编码NBs的基因。oleracea，B. B. rapa和A. thaliana基因组。系统发育分析将3个物种的NBS编码基因分为6个亚类。串联重复和全基因组三倍体（WGT）分析表明，在芸苔属祖先中，三倍体区域上的NBS编码同源基因对在WGT后迅速缺失或丢失，而在芸苔属物种中，B分化后，NBS编码基因通过串联重复发生种特异性基因扩增。rapa和B.甘蓝属植物NBS编码的直链淀粉基因对的表达谱表明，在B中保留的直链淀粉基因拷贝的差异表达模式。oleracea和B.拉帕。此外，对3个物种CNL型NBS-DNA编码基因对的进化分析表明，B.芜菁种比B. oleracea种经历了更强的负选择。但对于TNL型，两种鱼的直向同源基因对没有显著差异。本研究是首次在B中鉴定和鉴定NBS-C编码基因。rapa和B.基于全基因组序列的甘蓝。通过B的串联重复和全基因组三倍体分析。oleracea，B. B. rapa和A. thaliana基因组，我们的研究提供了深入了解NBS-encoding基因的进化历史后，分歧的A。thaliana和Brassica谱系。这些结果以及NBS编码基因的表达模式分析为NBS基因的功能鉴定和相关作物的遗传改良提供了有用的资源。本文的在线版本（doi：10.1186/1471 - 2164 - 15 - 3）包含补充材料，可供授权用户使用。
Plant disease resistance (R) genes with the nucleotide binding site (NBS) play an important role in offering resistance to pathogens. The availability of complete genome sequences of Brassica oleracea and Brassica rapa provides an important opportunity for researchers to identify and characterize NBS-encoding R genes in Brassica species and to compare with analogues in Arabidopsis thaliana based on a comparative genomics approach. However, little is known about the evolutionary fate of NBS-encoding genes in the Brassica lineage after split from A. thaliana. Here we present genome-wide analysis of NBS-encoding genes in B. oleracea, B. rapa and A. thaliana. Through the employment of HMM search and manual curation, we identified 157, 206 and 167 NBS-encoding genes in B. oleracea, B. rapa and A. thaliana genomes, respectively. Phylogenetic analysis among 3 species classified NBS-encoding genes into 6 subgroups. Tandem duplication and whole genome triplication (WGT) analyses revealed that after WGT of the Brassica ancestor, NBS-encoding homologous gene pairs on triplicated regions in Brassica ancestor were deleted or lost quickly, but NBS-encoding genes in Brassica species experienced species-specific gene amplification by tandem duplication after divergence of B. rapa and B. oleracea. Expression profiling of NBS-encoding orthologous gene pairs indicated the differential expression pattern of retained orthologous gene copies in B. oleracea and B. rapa. Furthermore, evolutionary analysis of CNL type NBS-encoding orthologous gene pairs among 3 species suggested that orthologous genes in B. rapa species have undergone stronger negative selection than those in B .oleracea species. But for TNL type, there are no significant differences in the orthologous gene pairs between the two species. This study is first identification and characterization of NBS-encoding genes in B. rapa and B. oleracea based on whole genome sequences. Through tandem duplication and whole genome triplication analysis in B. oleracea, B. rapa and A. thaliana genomes, our study provides insight into the evolutionary history of NBS-encoding genes after divergence of A. thaliana and the Brassica lineage. These results together with expression pattern analysis of NBS-encoding orthologous genes provide useful resource for functional characterization of these genes and genetic improvement of relevant crops. The online version of this article (doi:10.1186/1471-2164-15-3) contains supplementary material, which is available to authorized users.
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影响因子：
7
作者：
Blanc, G;Hokamp, K;Wolfe, KH
通讯作者：
Wolfe, KH
影响因子：
5.8
作者：
Delorenzi, M;Speed, T
通讯作者：
Speed, T
DOI：
10.1071/fp09304
发表时间：
2010-05-20
期刊：
Functional plant biology : FPB
影响因子：
--
作者：
Anderson JP;Gleason CA;Foley RC;Thrall PH;Burdon JB;Singh KB
通讯作者：
Singh KB
影响因子：
14.9
作者：
Huala, E;Dickerman, AW;Rhee, SY
通讯作者：
Rhee, SY
影响因子：
4.4
作者：
Jupe F;Pritchard L;Etherington GJ;Mackenzie K;Cock PJ;Wright F;Sharma SK;Bolser D;Bryan GJ;Jones JD;Hein I
通讯作者：
Hein I