Unique evolutionary mechanism in R-genes under the presence/absence polymorphism in Arabidopsis thaliana - PubMed (original) (raw)

Unique evolutionary mechanism in R-genes under the presence/absence polymorphism in Arabidopsis thaliana

Jingdan Shen et al. Genetics. 2006 Feb.

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.

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Figures

Figure 1.

Figure 1.

Schematic comparison of _R-_gene presence and absence alleles. Insertions with the _R_-gene are represented for At4g10780 (A), At5g05400 (B), At5g49140 (C), At5g18350 (D), Rpm1 (E), and Rps5 (F). (E and F are drawn on the basis of reports by H

enk

et al. 1999 and G

rant

et al. 1998.) In all absence alleles examined, the _R-_genes were replaced by 98–∼639-bp junk DNA of unknown origin.

Figure 2.

Figure 2.

Grouping of A. thaliana accessions with respect to the presence/absence of the nine R-P/A. This tree was constructed by the neighbor-joining method using PAUP*4.0 (S

wofford

2000).

Figure 3.

Figure 3.

Relationship between presence allele frequency (_F_[presence]) and nucleotide diversity of the LRR region in the nine R-P/A. Correlation coefficient was 0.093.

Figure 4.

Figure 4.

Phylogenetic relationship of _R_-genes in the Col genome in A. thaliana. The tree was dissected from the one constructed by M

eyers

et al. (2003), using amino acid sequences of the NBS domain of _R_-genes by the neighbor-joining method. Nine R-P/A loci investigated in this study are indicated by boldface type. The Streptomyces sequence rooted the tree as the outgroup (M

eyers

et al. 2003).

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