title: Unusual signatures of highly adaptable R-loci in closely-related Arabidopsis species.
abstract: Plant resistance genes (R-genes) evolve rapidly in response to changing environments. What are the most remarkable signatures of fast adaptive genes, besides the commonly revealed rapid divergence and high non-synonymous substitution rate? Here we investigated these changes in five R-loci following recent differentiation between Arabidopsis thaliana and Arabidopsis lyrata. Extreme differences in evolutionary rates were observed: e.g., an overall 5.46-9.83-fold different nucleotide diversity at two R-loci between species, ten-fold higher non-synonymous substitution rates within one species versus the other, significantly different Ka/Ks ratios between species for the same R-gene, and high interspecific divergence at one R-locus. Particularly, we observed an elevated level of trans-specific polymorphism at one R-locus and a differentially maintained presence/absence polymorphism at another. The high frequency of ancestral polymorphisms amongst R-genes suggests that the persistence of some functional variation is an important evolutionary mechanism shaping genetic variation in R-genes, while the variation of presence/absence polymorphisms provides a potential mechanism for malleable activation of adaptive resistance response pathways. The distinct patterns among R-genes suggest that the same R-gene ortholog can be quickly shaped by different evolutionary processes, e.g., purifying selection in one species but positive selection in a closely-related species.
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing, China.
authors.forename: Jiao
authors.initials: J
authors.lastname: Wang
authors.forename: Li
authors.initials: L
authors.lastname: Zhang
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.forename: Amy
authors.initials: A
authors.lastname: Lawton-Rauh
authors.forename: Dacheng
authors.initials: D
authors.lastname: Tian
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D019943:Amino Acid Substitution / Q000235:genetics; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics; D001483:Base Sequence; D017343:Genes, Plant / Q000235:genetics; D056426:Genetic Loci / Q000235:genetics*; D000090263:Leucine-Rich Repeat Proteins; D016013:Likelihood Functions; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000235:genetics; D010802:Phylogeny; D011110:Polymorphism, Genetic; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000235:genetics; D012641:Selection, Genetic; D013045:Species Specificity
chemical_list: D029681:Arabidopsis Proteins; D000090263:Leucine-Rich Repeat Proteins; D009711:Nucleotides; D011506:Proteins