Origin, diversity and evolution of NBS-type disease-resistance gene homologues in coffee trees (Coffea L.)

The majority of plant disease-resistance genes (R-genes) isolated so far en code a predicted nucleotide-binding site (NBS) domain. NBS domains related to R-genes show a highly conserved backbone of amino acid motifs, which mak es it possible to isolate resistance gene analogues (RGAs) by PCR with dege nerate primers. Multiple combinations of primers with low degeneracy, desig ned from two conserved motifs in the NBS regions of R-genes of various plan ts, were used on genomic DNA from coffee trees, an important perennial trop ical crop. Nine distinct classes of RGAs of the NBS-like type, representing a highly diverse sample., were isolated from Coffea arabica and C. canepho ra species. The analysis of one coffee RGA family suggested point mutations as the primary source of diversity. With one exception, coffee RGA familie s appeared to be closely related in sequence to at least one cloned R-gene. In addition, deduced amino acid sequences of coffee RGAs were identified t hat showed strong sequence similarity to almost all known non-TIR (Toll/Int erleukin 1 Receptor)-type R-genes. The high degree of similarity between pa rticular coffee RGAs and R-genes isolated from other angiosperm species, su ch as Arabidopsis, tomato and rice, indicates an ancestral relationship and the existence of common ancestors. The data obtained from coffee species s uggests that the evolution of NBS-encoding sequences involves the gradual a ccumulation of mutations and slow rates of divergence within distinct R-gen e families, rather than being a rapid process. Functional inferences drawn from the suggested pattern of evolution of NBS-type R-genes is also discuss ed.