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

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.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-3) contains supplementary material, which is available to authorized users.     

Ancient and current gene flow between two distantly related Mediterranean oak species, Quercus suber and Q. ilex

Background and Aims

Quercus suber and Q. ilex are distantly related and their distributions partially overlap. They hybridize occasionally, but the complete replacement of Q. suber chloroplast DNA (cpDNA) by that of Q. ilex was identified in two specific geographical areas. The objective of this study was to determine whether the contrasting situation reflected current or recent geographical interspecies gene flow variation or was the result of ancient introgression.

Methods

cpDNA PCR-RFLPs (restriction fragment length polymorphisms) and variation at ten nuclear microsatellite loci were analysed in populations of each species, in 16 morphologically intermediate individuals and the progeny of several of them. Interspecies nuclear introgression was based on individual admixture rates using a Bayesian approach with no a priori species assignment, and on a maximum-likelihood (ML) method, using allele frequencies in the allopatric populations of each species as controls. Gene flow was compared specifically between populations located within and outside the specific areas.

Key Results

High interspecies nuclear genetic differentiation was observed, with twice the number of alleles in Q. ilex than in Q. suber. According to Bayesian assignment, approx. 1 % of individuals had a high probability of being F₁ hybrids, and bidirectional nuclear introgression affected approx. 4 % of individuals in each species. Hybrid and introgressed individuals were identified predominantly in mixed stands and may have a recent origin. Higher proportions including allospecific genes recovered from past hybridization were obtained using the ML method. Similar rates of hybridization and of nuclear introgression, partially independent of cpDNA interspecies transfer suggestive of gene filtering, were obtained in the populations located within and outside the areas of complete cpDNA replacement.

Conclusions

The results did not provide evidence for geographical variation in interspecies gene flow. In contrast, historical introgression is supported by palynological records and constitutes the more reliable origin of cpDNA replacement in specific regions.Key words: cpDNA PCR-RFLPs, nuclear microsatellite (nSSR) variation, hybridization, interspecies genetic introgression, Quercus suber, Quercus ilex     

Genome sequencing of two Neorhizobium galegae strains reveals a noeT gene responsible for the unusual acetylation of the nodulation factors

Background

The species Neorhizobium galegae comprises two symbiovars that induce nodules on Galega plants. Strains of both symbiovars, orientalis and officinalis, induce nodules on the same plant species, but fix nitrogen only in their own host species. The mechanism behind this strict host specificity is not yet known. In this study, genome sequences of representatives of the two symbiovars were produced, providing new material for studying properties of N. galegae, with a special interest in genomic differences that may play a role in host specificity.

Results

The genome sequences confirmed that the two representative strains are much alike at a whole-genome level. Analysis of orthologous genes showed that N. galegae has a higher number of orthologs shared with Rhizobium than with Agrobacterium. The symbiosis plasmid of strain HAMBI 1141 was shown to transfer by conjugation under optimal conditions. In addition, both sequenced strains have an acetyltransferase gene which was shown to modify the Nod factor on the residue adjacent to the non-reducing-terminal residue. The working hypothesis that this gene is of major importance in directing host specificity of N. galegae could not, however, be confirmed.

Conclusions

Strains of N. galegae have many genes differentiating them from strains of Agrobacterium, Rhizobium and Sinorhizobium. However, the mechanism behind their ecological difference is not evident. Although the final determinant for the strict host specificity of N. galegae remains to be identified, the gene responsible for the species-specific acetylation of the Nod factors was identified in this study. We propose the name noeT for this gene to reflect its role in symbiosis.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-500) contains supplementary material, which is available to authorized users.