Evolution of the Rdr1 TNL-cluster in roses and other Rosaceous species
Creators: name: Terefe-Ayana, Diro
name: Kaufmann, Helgard
name: Linde, Marcus
name: Debener, Thomas
Publisher: name: London : BioMed Central Ltd.
Year: 2012
Subjects: subject: apple
subject: article
subject: chromosome analysis
subject: controlled study
subject: Fragaria
subject: Fragaria vesca
subject: gene cluster
subject: gene conversion
subject: gene deletion
subject: gene duplication
subject: gene locus
subject: gene rearrangement
subject: gene sequence
subject: genetic recombination
subject: genetic similarity
subject: genetic variability
subject: nonhuman
subject: nucleotide sequence
subject: peach
subject: phylogeny
subject: plant gene
subject: point mutation
subject: promoter region
subject: R gene
subject: Rdr1 gene
subject: Rosa multiflora
subject: Rosa rugosa
subject: Rosaceae
subject: rose
subject: Rosoideae
subject: sequence alignment
subject: species difference
subject: Spiraeoideae
subject: strawberry
subject: TNL gene
subject: transposon
subject: Chromosomes
subject: Cluster Analysis
subject: Contig Mapping
subject: Evolution, Molecular
subject: Genes, Plant
subject: Genetic Loci
subject: Malus
subject: Phylogeny
subject: Plant Proteins
subject: Prunus
subject: Repressor Proteins
subject: Rosa
subject: Fragaria x ananassa
subject: Malus x domestica
subject: Prunus persica
subject: Dewey Decimal Classification::500 | Naturwissenschaften
subject: Dewey Decimal Classification::500 | Naturwissenschaften::570 | Biowissenschaften, Biologie

description: Background: The resistance of plants to pathogens relies on two lines of defense: a basal defense response and a pathogen-specific system, in which resistance (R) genes induce defense reactions after detection of pathogen-associated molecular patterns (PAMPS). In the specific system, a so-called arms race has developed in which the emergence of new races of a pathogen leads to the diversification of plant resistance genes to counteract the pathogens' effect. The mechanism of resistance gene diversification has been elucidated well for short-lived annual species, but data are mostly lacking for long-lived perennial and clonally propagated plants, such as roses. We analyzed the rose black spot resistance gene, Rdr1, in five members of the Rosaceae: Rosa multiflora, Rosa rugosa, Fragaria vesca (strawberry), Malus x domestica (apple) and Prunus persica (peach), and we present the deduced possible mechanism of R-gene diversification.Results: We sequenced a 340.4-kb region from R. rugosa orthologous to the Rdr1 locus in R. multiflora. Apart from some deletions and rearrangements, the two loci display a high degree of synteny. Additionally, less pronounced synteny is found with an orthologous locus in strawberry but is absent in peach and apple, where genes from the Rdr1 locus are distributed on two different chromosomes. An analysis of 20 TIR-NBS-LRR (TNL) genes obtained from R. rugosa and R. multiflora revealed illegitimate recombination, gene conversion, unequal crossing over, indels, point mutations and transposable elements as mechanisms of diversification.A phylogenetic analysis of 53 complete TNL genes from the five Rosaceae species revealed that with the exception of some genes from apple and peach, most of the genes occur in species-specific clusters, indicating that recent TNL gene diversification began prior to the split of Rosa from Fragaria in the Rosoideae and peach from apple in the Spiraeoideae and continued after the split in individual species. Sequence similarity of up to 99% is obtained between two R. multiflora TNL paralogs, indicating a very recent duplication.Conclusions: The mechanisms by which TNL genes from perennial Rosaceae diversify are mainly similar to those from annual plant species. However, most TNL genes appear to be of recent origin, likely due to recent duplications, supporting the hypothesis that TNL genes in woody perennials are generally younger than those from annuals. This recent origin might facilitate the development of new resistance specificities, compensating for longer generation times in woody perennials.