Trans-specificity at loci near the self-incompatibility loci in Arabidopsis

Abstract

We compared allele sequences of two loci near the Arabidopsis lyrata self-incompatibility (S) loci with sequences of A. thaliana orthologs and found high numbers of shared polymorphisms, even excluding singletons and sites likely to be highly mutable. This suggests maintenance of entire S-haplotypes for long evolutionary times and extreme recombination suppression in the region.

Figure 1.

Lineages at an S-locus under long-term balancing selection and the effects of speciation. As an example, two haplotypes are shown with different S-alleles, x and y, which diverged before the common ancestor of two species (1 and 2). The different alleles at the pistil and pollen S-loci, SRK and SCR, are denoted by solid and shaded boxes. Mutations in the regions in and around the S-locus (thin horizontal lines in the tree) before the species became isolated remain associated with the haplotype in which they arose (shown as thin vertical lines in the haplotypes) until recombination occurs with a different haplotype. Species-specific differences (dotted lines) will also accumulate.

Figure 2.

Variants in the B80 (U-box) gene within A. thaliana and A. lyrata, excluding fixed differences from A. glabra and singleton variants other than in the A. thaliana Cvi-0 strain. For A. thaliana and A. lyrata, a single sequence of each type seen within the species is shown. For A. thaliana, the haplogroups of the strains (defined by SRK sequences; see the U-box gene in Shimizu et al. 2004) are shown; for A. lyrata, the SRK allele, when known, is shown for each haplotype whose B80 sequence was used in the analysis (the numbers of each A. lyrata S-haplotype sequenced are also shown in the left column). The nine shared variants between the two species are boxed with thin double lines; the nonsynonymous one is at position 245.