Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana
文献类型: 外文期刊
第一作者: Yu, Jingyin
作者: Yu, Jingyin;Tehrim, Sadia;Zhang, Fengqi;Tong, Chaobo;Huang, Junyan;Cheng, Xiaohui;Dong, Caihua;Zhou, Yanqiu;Hua, Wei;Liu, Shengyi;Zhou, Yanqiu;Qin, Rui
作者机构:
关键词: Brassica species;Disease resistance gene;Nucleotide binding site;Tandem duplication;Whole genome duplication
期刊名称:BMC GENOMICS ( 影响因子:3.969; 五年影响因子:4.478 )
ISSN: 1471-2164
年卷期: 2014 年 15 卷
页码:
收录情况: SCI
摘要: Background: 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. Results: 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. Conclusion: 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.
分类号:
- 相关文献
作者其他论文 更多>>
-
Integrated Genetic Diversity and Multi-Omics Analysis of Colour Formation in Safflower
作者:Qin, Yonghua;Fan, Kangjun;Yimamu, Aidiya;Zhan, Peng;Lv, Lu;Li, Gang;Liu, Jiao;Liu, Hong;Qin, Rui;Hu, Zunhong;Hu, Xueli;Yan, Xingchu
关键词:
Carthamus tinctorius L.; genetic diversity; core germplasm; transcriptome; metabolome -
An efficient allotriploid-mediated system of generating genomic introgression from Brassica oleracea to B. rapa
作者:Gu, Aixia;Li, Xiaomin;Wang, Zengfeng;Wang, Yanhua;Xuan, Shuxin;Ma, Wei;Hong, Yiguo;Zhao, Yalei;Chen, Xueping;Luo, Shuangxia;Liu, Yuanming;Liu, Shengyi;Zhao, Jianjun;Shen, Shuxing;Li, Xiaomin;Wang, Zengfeng;Liu, Shengyi;Zhang, Yuanyuan
关键词:allotriploid; Brassica crops; genome introgression; homoeologous recombination; interspecific hybridization; trait variation
-
Sucrose mediates moderate salinity-promoted primary root growth in rapeseed
作者:Fan, Shi-Hang;Huang, Zi-Hong;Liu, Hong-Fang;Zhang, Xin-Fang;Hua, Wei;Fu, Zheng-Wei;Hua, Wei
关键词:Rapeseed; Salt stress; Sucrose; Primary root
-
Effects of Long-Term Organic Substitution on Soil Nitrous Oxide Emissions in a Tea (Camellia sinensis L.) Plantation in China
作者:Wu, Zhidan;Jiang, Fuying;Hua, Wei;Ni, Kang;Yang, Xiangde;Jiang, Fuying
关键词:tea plantation; organic substitution; nitrous oxide emission; tea yield; influencing factors
-
Phylogenomic and super-pangenome analyses unveil the genetic landscape of tomato evolution and domestication
作者:Yu, Jingyin;Chen, Qionglin;Yuan, Lu;Feng, Shouli;Huang, Miaomiao;Zheng, Peng;Tao, Xiaoyuan;Xu, Shengchun;Chen, Guang;Xu, Shengchun;Edwards, David;Edwards, David;Chen, Zhong-Hua
关键词:gene-based super-pangenome; genetic diversity; agronomic traits; presence/absence variation (PAV); crop improvement; sustainable production
-
Targeted mutagenesis and functional marker development of two Bna.TAC1s conferring novel rapeseed germplasm with compact architecture
作者:Feng, Bin;Wang, Yu;Zhang, Xiaolong;Mu, Tingting;Zhang, Biaoming;Li, Yan;Zhang, Haitao;Yuan, Wenya;Li, Haitao;Hua, Wei
关键词:
-
Bioactive Components and Color Variation Mechanism Among Three Differently Colored Peppers Based on Transcriptomics and Non-Targeted Metabolomics
作者:Mo, Yunrong;Hua, Wei;Cheng, Hong;Zhang, Ruihao;Deng, Minghua;Li, Pingping
关键词:bioactive components; fruit color; transcriptomics; non-targeted metabolomics; anthocyanins; chili pepper