title: Unique evolutionary mechanism in R-genes under the presence/absence polymorphism in Arabidopsis thaliana.
abstract: While the presence/absence polymorphism is commonly observed in disease resistance (R-) genes in Arabidopsis, only a few R-genes under the presence/absence polymorphism (R-P/A) have been investigated. To understand the mechanism of the molecular evolution of R-P/A, we investigated genetic variation of nine R-P/A in A. thaliana from worldwide populations. The number of possessed R-genes varied widely among accessions (two to nine, on average 4.3 +/- 1.6/accession). No pair of accessions shared the same haplotype, and no clear geographic differentiation was observed with respect to the pattern of presence/absence of the R-genes investigated. Presence allele frequencies also varied among loci (25-70%), and no linkage disequilibrium was detected among them. Although the LRR region in regular R-genes is known to be highly polymorphic and has a high Ka/Ks ratio in A. thaliana, nucleotide sequences of this region in the R-P/A showed a relatively low level of genetic variation (pi = 0.0002-0.016) and low Ka/Ks (0.03-0.70, <1). In contrast, the nucleotide diversities around the deletion junction of R-P/A were constantly high between presence and absence accessions for the R-genes (D(xy) = 0.031-0.103). Our results suggest that R-P/A loci evolved differently from other R-gene loci and that balancing selection plays an important role in molecular evolution of R-P/A.
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, China.
authors.forename: Jingdan
authors.initials: J
authors.lastname: Shen
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Araki
authors.forename: Lingling
authors.initials: L
authors.lastname: Chen
authors.forename: Jian-Qun
authors.initials: JQ
authors.lastname: Chen
authors.forename: Dacheng
authors.initials: D
authors.lastname: Tian
mesh_terms: D000483:Alleles; D017360:Arabidopsis / Q000235:genetics*; D019143:Evolution, Molecular; D005787:Gene Frequency; D007113:Immunity, Innate / Q000235:genetics*; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic