Receptor-like genes in the major resistance locus of lettuce are subject to divergent selection.

Meyers, B.C., Shen, K.A., Rohani, P., Gaut, B.S., Michelmore, R.W.

Plant Cell 10:1833-1846 (1998).

(http://www.plantcell.org/)

Abstract

Disease resistance genes in plants are often found in complex multigene families. The largest known cluster of disease resistance specificities in lettuce contains the RGC2 family of genes. We compared the sequences of nine full-length genomic copies of RGC2 representing the diversity in the cluster to determine the structure of genes within this family and to examine the evolution of its members. The transcribed regions range from at least 7.0 to 13.1 kb. The cDNAs contain deduced open reading frames of approximately 5.5 kb. The predicted RGC2 proteins contain a nucleotide binding site (NBS) and irregular leucine-rich repeats (LRRs) that are characteristic of resistance genes cloned from other species. Unique features of the RGC2 gene products include a bipartite LRR region with more than 40 repeats. At least eight members of this family are transcribed. The level of sequence diversity between family members varied in different regions of the gene. The ratio of nonsynonymous (Ka) to synonymous (Ks) nucleotide substitutions was lowest in the region encoding the NBS, which is the presumed effector domain of the protein. The LRR-encoding region showed an alternating pattern of conservation and hypervariability. This alternating pattern of variation was also found in all comparisons within families of resistance genes cloned from other species. The Ka/Ks ratios indicate that diversifying selection has resulted in increased variation at these codons. The patterns of variation support the predicted structure of LRR regions with solvent-exposed hypervariable residues that are potentially involved in binding pathogen-derived ligands.

 

 

Synonymous (Ks) and nonsynonymous (Ka) substitutions were calculated for pairwise comparisons within resistance gene families. These values were plotted in the form (Ks, Ka). The diagonal corresponds to Ks = Ka, representing neutral evolution; points above this line provide evidence for diversifying selection, without implying statistical significance. Points below the diagonal suggest selection for conservation.

  1. Synonymous and nonsynonymous substitution frequencies in the RGC2 family and other plant disease resistance genes.5’ and spacer regions of RGC2 genes

  2. Regions encoding putative effector domains

  3. RGC2 5’-encoded LRR

  4. RGC2 3’-encoded LRR

  5. The LRR-encoding region of other R-gene families