Abstract
BackgroundIn plant genomes, NB-LRR based resistance (R) genes tend to occur in clusters of variable size in a relatively small number of genomic regions. R-gene sequences mostly differentiate by accumulating point mutations and gene conversion events. Potato and tomato chromosome 4 harbours a syntenic R-gene locus (known as the R2 locus in potato) that has mainly been examined in central American/Mexican wild potato species on the basis of its contribution to resistance to late blight, caused by the oomycete pathogen Phytophthora infestans. Evidence to date indicates the occurrence of a fast evolutionary mode characterized by gene conversion events at the locus in these genotypes.ResultsA physical map of the R2 locus was developed for three Solanum tuberosum genotypes and used to identify the tomato syntenic sequence. Functional annotation of the locus revealed the presence of numerous resistance gene homologs (RGHs) belonging to the R2 gene family (R2GHs) organized into a total of 4 discrete physical clusters, three of which were conserved across S. tuberosum and tomato. Phylogenetic analysis showed clear orthology/paralogy relationships between S. tuberosum R2GHs but not in R2GHs cloned from Solanum wild species. This study confirmed that, in contrast to the wild species R2GHs, which have evolved through extensive sequence exchanges between paralogs, gene conversion was not a major force for differentiation in S. tuberosum R2GHs, and orthology/paralogy relationships have been maintained via a slow accumulation of point mutations in these genotypes.ConclusionsS. tuberosum and Solanum lycopersicum R2GHs evolved mostly through duplication and deletion events, followed by gradual accumulation of mutations. Conversely, widespread gene conversion is the major evolutionary force that has shaped the locus in Mexican wild potato species. We conclude that different selective forces shaped the evolution of the R2 locus in these lineages and that co-evolution with a pathogen steered selection on different evolutionary paths.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0645-8) contains supplementary material, which is available to authorized users.
Highlights
In plant genomes, nucleotide binding (NB)-leucine-rich repeat (LRR) based resistance (R) genes tend to occur in clusters of variable size in a relatively small number of genomic regions
Organization and structure of the R2 gene family in potato and tomato genotypes A total of 9 bacterial artificial chromosome (BAC) clones spanning ~780 Kilobase pair (Kbp) of the R2 locus were sequenced in one haplotype (RH-H0) of the diploid potato clone RH
Lower sequence coverage was achieved for the HB diploid clone, where ~430 Kbp were sequenced in the HB-H0 haplotype and ~122 Kbp in the HB-H1 haplotype, which is known to carry alleles for quantitative resistance to blight derived from an introgression from S. demissum [27]
Summary
NB-LRR based resistance (R) genes tend to occur in clusters of variable size in a relatively small number of genomic regions. Song et al [9] showed that RGHs at the RB locus in potato evolve independently and mostly through point mutations rather than sequence exchanges This sort of evolution contributes to the maintenance of orthologous relationships between homologs in different genotypes, while the frequent sequence exchanges and gene conversion events act to obscure this association [10]. Based on these observations, Kuang et al [10] hypothesized that plant disease R-genes are organized in two classes that explain the evolutionary patterns with contrasting rates of evolution. The two gene types can be present at the same cluster or individually, and they can have different frequencies in natural populations and within species [10, 11]
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