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The rpoB gene was evaluated as an alternative molecular marker for the differentiation of Xanthomonas species and in order to understand better the phylogenetic relationships within the genus. PCR-RFLP experiments using HaeIII allowed differentiation of Xanthomonas species, particularly those that affect the same plant host such as Xanthomonas albilineans and X. sacchari, pathogenic to sugar cane, Xanthomonas cucurbitae and X. melonis, which cause disease in melon, and Xanthomonas gardneri, X. vesicatoria and X. euvesicatoria/X. perforans, pathogenic to tomato. Phylogenetic relationships within the genus Xanthomonas were also examined by comparing partial rpoB gene sequences (612 nt) and the Xanthomonas species were separated into two main groups. Group I, well supported by bootstrap values of 99 %, comprised X. euvesicatoria, X. perforans, X. alfalfae, X. citri, X. dyei, X. axonopodis, X. oryzae, X. hortorum, X. bromi, X. vasicola, X. cynarae, X. gardneri, X. campestris, X. fragariae, X. arboricola, X. cassavae, X. cucurbitae, X. pisi, X. vesicatoria, X. codiaei and X. melonis. Group II, again well supported by bootstrap values of 99 %, comprised X. albilineans, X. sacchari, X. theicola, X. translucens and X. hyacinthi. The rpoB gene sequence similarity observed among the species in this study ranged from 87.8 to 99.7 %. The results of PCR-RFLP of the rpoB gene indicated that this technique can be used for diagnosis and identification of most Xanthomonas strains, including closely related species within the genus. However, species that showed identical profiles could be differentiated clearly only by sequence analysis. The results obtained in our phylogenetic analysis suggested that the rpoB gene can be used as an alternative molecular marker for genetic relatedness in the genus Xanthomonas. The results of PCR-RFLP of the rpoB gene indicate that this technique can be used for diagnosis and identification of closely related species within the genus, representing a rapid and inexpensive tool that can be easily standardized between laboratories.

In the present study the atpD gene was evaluated as an alternative molecular marker for differentiation of Streptomyces species causing potato scab and to establish the phylogenetic relationships within this group. PCR-RFLP experiments using HaeIII and CfoI restriction enzymes allowed differentiation of most Streptomyces species, except the genomospecies S. reticuliscabiei and S. turgidiscabies which showed identical profiles between them. Phylogenetic relationships within Streptomyces spp. were also examined by comparing partial atpD gene sequences (858 nt) and the strains were separated in three main groups: Group I, supported by bootstrap values of 79%, comprised of S. scabiei, S. europaeiscabiei, S. stelliscabiei, S. reticuliscabiei, S. turgidiscabies and S. acidiscabies; Group II, supported by bootstrap values of 100%, comprised of S. sampsonii; and Group III supported by bootstrap values of 100%, comprised of S. caviscabies, S. setonii, S. luridiscabiei and S. puniciscabiei. The atpD gene sequence similarity observed among the species in this study ranged from 89.2% to 100%. Twenty-nine Streptomyces isolates obtained from potato growing areas in Brazil were analyzed by PCR-RFLP of atpD gene technique and identified as S. scabiei (15 strains), S. caviscabies/ S. setonii (12) and S. sampsonii (2). Using this tool S. europaeiscabiei strains were also detected from import material from the Netherlands. The presence of genes associated with the S. turgidiscabies pathogenicity island (PAI) was also determined and potato tuber slice assays were performed to confirm the pathogenicity of the strains. The data obtained herein indicated that the PCR-RFLP of atpD gene technique can be used for diagnosis and identification of phytopathogenic Streptomyces strains, representing a rapid and inexpensive tool. Moreover, this gene can be useful for phylogenetic analysis of Streptomyces spp. associated with potato scab.

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