Abstract
BackgroundPlant 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.ResultsHere 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.ConclusionThis 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-3) contains supplementary material, which is available to authorized users.
Highlights
Plant disease resistance (R) genes with the nucleotide binding site (NBS) play an important role in offering resistance to pathogens
Identification and classification of NBS genes in A. thaliana and Brassica species previously NBS-encoding R genes in A. thaliana and B. rapa were described by Meyers et al [10] and Mun et al [42] respectively, but their analysis were based on old version of TAIR in A. thaliana and incomplete genome sequences in B. rapa
We have identified 157, 206 and 167 NBS-encoding genes in A. thaliana, B. rapa and B. oleracea genomes respectively and total number of NBS-encoding genes in these three species is very close in spite of genome size and WGD/whole genome triplication (WGT) events
Summary
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. In order to cope with disease attacks, the plants have developed multiple layers of defense mechanisms. Plant disease resistance (R) genes which interact/recognize with corresponding pathogen avirulence (avr) genes are considered as plant genetic factors of a major layer. The interactions of this gene-for-gene (or genes-for-genes) manner activate the signal transduction cascades that turn on complex defense responses against pathogen attack and this is called incompatible interaction [1]. Identification of R genes is crucial for resistant variety development and relevant mechanism investigation
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