title: Frequent sequence exchanges between homologs of RPP8 in Arabidopsis are not necessarily associated with genomic proximity.
abstract: Disease resistance (R) genes are often clustered in plant genomes and may exhibit heterogeneous rates of evolution. Some (type I R genes) have evolved rapidly through frequent sequence exchanges, while others (type II R genes) have evolved independently and tend to be conserved in different genotypes or related species. The RPP8 resistance gene in Arabidopsis thaliana is located at a complex locus that also harbors the sequence-related resistance genes HRT and RCY1 in different ecotypes. We sequenced 98 homologs of RPP8 from A. thaliana, Arabidopsis arenosa and Arabidopsis lyrata. Three lineages of type II and one lineage of type I RPP8 homologs were identified. Two of the three lineages of type II genes are each represented by a single-copy locus on either chromosomes I or V. Chromosome V contains two small clusters of RPP8 paralogs. One cluster contains both type I and type II genes and the other comprises only type I genes. These multi-copy loci have expanded and contracted through unequal crossovers, which have generated chimeric genes as well as variations in copy number. Sequence exchanges, most likely gene conversions, were detected between RPP8 homologs that are spatially separated by 2.2 Mb and 12 cM. The sequence exchanges between type I homologs within a locus have been more frequent than sequence exchanges between homologs from two different loci, indicating the influence of chromosomal position on the evolution of these R genes. However, physical distance was not the only factor determining the frequency of sequence exchange, because some closely linked paralogs exhibited little sequence exchange. At least two distinct lineages of type II RPP8 homologs were identified in different species, with obvious allelic/orthologous relationships within each lineage. Therefore, the differentiation of type I and type II RPP8 homologs seems to have occurred before speciation of A. thaliana, A. arenosa and A. lyrata.
authors.affiliation: The Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616, USA.
authors.forename: Hanhui
authors.initials: H
authors.lastname: Kuang
authors.forename: Katherine S
authors.initials: KS
authors.lastname: Caldwell
authors.forename: Blake C
authors.initials: BC
authors.lastname: Meyers
authors.forename: Richard W
authors.initials: RW
authors.lastname: Michelmore
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics*; D001483:Base Sequence; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D003434:Crossing Over, Genetic; D019143:Evolution, Molecular; D014644:Genetic Variation; D005838:Genotype; D010802:Phylogeny; D012689:Sequence Homology, Nucleic Acid
chemical_list: D029681:Arabidopsis Proteins; C488787:RPP8 protein, Arabidopsis