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The  Rdr1  gene confers resistance to black spot in roses and belongs to a large TNL gene family, which is organized in two major clusters at the distal end of chromosome 1. We used the recently available chromosome scale assemblies for the  R .  chinensis  ‘Old Blush’ genome, re-sequencing data for nine rose species and genome data for  Fragaria ,  Rubus ,  Malus  and  Prunus  to identify  Rdr1  homologs from different taxa within Rosaceae. Members of the  Rdr1  gene family are organized into two major clusters in  R .  chinensis  and at a syntenic location in the  Fragaria  genome. Phylogenetic analysis indicates that the two clusters existed prior to the split of Rosa and Fragaria and that one cluster has a more recent origin than the other. Genes belonging to cluster 2, such as the functional  Rdr1  gene  muRdr1A , were subject to a faster evolution than genes from cluster 1. As no  Rdr1  homologs were found in syntenic positions for  Prunus persica ,  Malus  x  domestica  and  Rubus occidentalis , a translocation of the  Rdr1  clusters to the current positions probably happened after the Rubeae split from other groups within the Rosoideae approximately 70–80 million years ago during the Cretaceous period.

plos one

Analysis of the Rdr1 gene family in different Rosaceae genomes reveals an origin of an R-gene cluster after the split of Rubeae within the Rosoideae subfamily