Phylogenetic analysis of Xanthomonas based on partial rpoB gene sequences and species differentiation by PCR-RFLP

Abstract

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.

Genetic diversity and virulence of Xanthomonas campestris pv. campestris isolates from Brassica napus and six Brassica oleracea crops in Serbia

“…bilvae. Use of rpoB or gyrB alone can provide better insight into Xanthomonas taxonomy than the use of (partial) sequences of 16S and 16S-23S rRNA (Parkinson et al, 2007;Ferreira-Tonin et al, 2012). Also, for identification of Xcc, just a single gene such as gyrB (Parkinson et al, 2007) could be used as a reliable method, or a pathogenicity test in a susceptible host.…”

Genetic characterization of strains named as Xanthomonas axonopodis pv. dieffenbachiae leads to a taxonomic revision of the X. axonopodis species complex

“…Recent phylogenetic analyses of the genus Xanthomonas based on comparison of housekeeping gene sequences, including the gyrase B gene (gyrB) (Parkinson et al, 2009) and the RNA polymerase b subunit gene (rpoB) (Ferreira-Tonin et al, 2012), proved successful to reliably discriminate Xanthomonas species. In the study of Parkinson et al (2009), four phylogenetic clades were discriminated among known X. axonopodis pathotype strains.…”

Rapid, specific, simple, in-field detection ofXanthomonas campestrispathovarmusacearumby loop-mediated isothermal amplification

“…These are primarily comprised of lab-based techniques, which are typically culturing or molecular approaches. Culture-based techniques include the use of semi-selective media (Mwangi et al 2007;Tripathi et al 2007) and biochemical profiling, while molecular-based techniques predominately use PCR, rep-PCR and RFLP (Versalovic et al 1994;Lewis Ivey et al 2010;Adikini et al 2011;Adriko et al 2012;Ferreira-Tonin et al 2012;Wasukira et al 2012). These techniques provide a range of specificities, and have associated advantages and disadvantages.…”