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Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana.

Yu J, Tehrim S, Zhang F, Tong C, Huang J, Cheng X, Dong C, Zhou Y, Qin R, Hua W, Liu S - BMC Genomics (2014)

Bottom Line: But for TNL type, there are no significant differences in the orthologous gene pairs between the two species.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.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Biology and Genetic Improvement of Oil crops, the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China. liusy@oilcrops.cn.

ABSTRACT

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.

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NBS-encoding genes and corresponding clusters distribution of NBS-encoding genes inB. rapaandB. oleraceagenomes. A. A01 ~ A10 represent pseudo-chromosomes of B. rapa genome. B. C01 ~ C09 represent pseudo-chromosomes of B. oleracea genome. Green bars represent pseudo-chromosomes. Black line on green bars stands for the location of NBS-encoding genes on pseudo-chromosomes. Colorful boxes stand for clusters of NBS-encoding genes in corresponding genomes.
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Fig1: NBS-encoding genes and corresponding clusters distribution of NBS-encoding genes inB. rapaandB. oleraceagenomes. A. A01 ~ A10 represent pseudo-chromosomes of B. rapa genome. B. C01 ~ C09 represent pseudo-chromosomes of B. oleracea genome. Green bars represent pseudo-chromosomes. Black line on green bars stands for the location of NBS-encoding genes on pseudo-chromosomes. Colorful boxes stand for clusters of NBS-encoding genes in corresponding genomes.

Mentions: NBS-encoding genes for the three species were mapped onto pseudo-molecules/ chromosomes [121 (77.1%) genes in B. oleracea, 197 (95.6%) genes in B. rapa and 167 (100%) genes in A. thaliana] and the rest [36 (22.9%) genes in B. oleracea and 9 (4.4%) genes in B. rapa] were located on the unanchored scaffolds (Figure 1). The distribution of these genes is uneven: some chromosomes (e. g. C07 in B. oleracea representing the 20.7% of the NBS-encoding genes) have more genes and the rest chromosomes have fewer genes (e. g. C05 in B. oleracea), and many of these genes reside in a cluster manner. R genes existing in clusters may facilitate the evolutionary process through producing novel resistance genes via genome duplication, tandem duplication and gene recombination [43]. According to the cluster defined by Richly et al. [44] and Meyers et al. [10] as two or more genes falling within eight ORFs, we found that the percentage of NBS genes on chromosomes in clusters in B. oleracea (60.3%) and A. thaliana (61.7%) is higher than that of B. rapa (59.4%). In B. oleracea, 73 NBS genes, representing 60.3% of total genes on chromosomes, were located in 24 clusters and the remaining 48 genes were singletons. Five clusters containing 19 NBS genes were identified on the chromosome C07 (Figure 1A). The B. rapa genome carries 117 (59.4%) NBS genes with TIR domain and CC motif in 43 clusters and remaining 80 genes were found as singletons on chromosomes. Among the 43 clusters, 11 with 31 genes were located on chromosome A09 (Figure 1B). In A. thaliana, 103 (61.7%) NBS genes with TIR domain and CC motif were mapped in 37 clusters whereas the remaining 64 genes were found as singletons. The numbers of genes in clusters ranged from two to six in both Brassica species and two to nine in A. thaliana.Figure 1


Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana.

Yu J, Tehrim S, Zhang F, Tong C, Huang J, Cheng X, Dong C, Zhou Y, Qin R, Hua W, Liu S - BMC Genomics (2014)

NBS-encoding genes and corresponding clusters distribution of NBS-encoding genes inB. rapaandB. oleraceagenomes. A. A01 ~ A10 represent pseudo-chromosomes of B. rapa genome. B. C01 ~ C09 represent pseudo-chromosomes of B. oleracea genome. Green bars represent pseudo-chromosomes. Black line on green bars stands for the location of NBS-encoding genes on pseudo-chromosomes. Colorful boxes stand for clusters of NBS-encoding genes in corresponding genomes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4008172&req=5

Fig1: NBS-encoding genes and corresponding clusters distribution of NBS-encoding genes inB. rapaandB. oleraceagenomes. A. A01 ~ A10 represent pseudo-chromosomes of B. rapa genome. B. C01 ~ C09 represent pseudo-chromosomes of B. oleracea genome. Green bars represent pseudo-chromosomes. Black line on green bars stands for the location of NBS-encoding genes on pseudo-chromosomes. Colorful boxes stand for clusters of NBS-encoding genes in corresponding genomes.
Mentions: NBS-encoding genes for the three species were mapped onto pseudo-molecules/ chromosomes [121 (77.1%) genes in B. oleracea, 197 (95.6%) genes in B. rapa and 167 (100%) genes in A. thaliana] and the rest [36 (22.9%) genes in B. oleracea and 9 (4.4%) genes in B. rapa] were located on the unanchored scaffolds (Figure 1). The distribution of these genes is uneven: some chromosomes (e. g. C07 in B. oleracea representing the 20.7% of the NBS-encoding genes) have more genes and the rest chromosomes have fewer genes (e. g. C05 in B. oleracea), and many of these genes reside in a cluster manner. R genes existing in clusters may facilitate the evolutionary process through producing novel resistance genes via genome duplication, tandem duplication and gene recombination [43]. According to the cluster defined by Richly et al. [44] and Meyers et al. [10] as two or more genes falling within eight ORFs, we found that the percentage of NBS genes on chromosomes in clusters in B. oleracea (60.3%) and A. thaliana (61.7%) is higher than that of B. rapa (59.4%). In B. oleracea, 73 NBS genes, representing 60.3% of total genes on chromosomes, were located in 24 clusters and the remaining 48 genes were singletons. Five clusters containing 19 NBS genes were identified on the chromosome C07 (Figure 1A). The B. rapa genome carries 117 (59.4%) NBS genes with TIR domain and CC motif in 43 clusters and remaining 80 genes were found as singletons on chromosomes. Among the 43 clusters, 11 with 31 genes were located on chromosome A09 (Figure 1B). In A. thaliana, 103 (61.7%) NBS genes with TIR domain and CC motif were mapped in 37 clusters whereas the remaining 64 genes were found as singletons. The numbers of genes in clusters ranged from two to six in both Brassica species and two to nine in A. thaliana.Figure 1

Bottom Line: But for TNL type, there are no significant differences in the orthologous gene pairs between the two species.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.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Biology and Genetic Improvement of Oil crops, the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China. liusy@oilcrops.cn.

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus