Two different classes of avrD alleles occur in pathovars of Pseudomonas syringae.

Considerable variation was observed in the occurrence of avirulence gene D (avrD) in different isolates and pathovars of Pseudomonas syringae. Three functional alleles of avrD were cloned and characterized from P. s. pv. phaseolicola and P. s. pv. lachrymans. These avrD genes occurred on indigenous plasmids in both pathovars, like the allele originally cloned from P. s. pv. tomato. P. s. pv. lachrymans was unique in that it carried two different alleles on plasmids of different sizes. These alleles were cloned on 5.6- or 3.8-kb HindIII fragments that are conserved in several other P. syringae pathovars. Surprisingly, the two avrD alleles from P. s. pv. lachrymans were the most divergent of those compared, with only 85% amino acid identity. Allele 1 from P. s. pv. lachrymans was 95% identical to avrD from P. s. pv. tomato but less similar to the other three avrD genes. These two alleles were accordingly called homology class I. The avrD gene from P. s. pv. phaseolicola and allele 2 from P. s. pv. lachrymans were 97 and 98% identical, respectively, at the amino acid level with the nonfunctional P. s. pv. glycinea allele. These three alleles were therefore grouped into homology class II. Comparison of all the avrD alleles permitted the identification of four amino acid substitutions unique to the P. s. pv. glycinea allele at positions 19, 245, 280, and 304.