Genetic and Pathological Diversity Among Xanthomonas Strains Responsible for Bacterial Spot on Tomato and Pepper in the Southwest Indian Ocean Region

Abstract

Bacterial spot of tomato and pepper, a major problem in tropical climates, can be caused by several Xanthomonas genospecies. We examined the genetic and pathological diversity of a collection of 72 strains from the southwest Indian Ocean region as part of a regional research and development program to update inventories of agricultural pests and pathogens. Xanthomonas euvesicatoria, X. perforans, X. gardneri, and X. vesicatoria were identified in our strain collection. The identification of strains at the species level was consistently achieved by amplified fragment length polymorphism (AFLP) and multilocus sequence analysis (MLSA). Overall, X. euvesicatoria was the species recovered prevalently. MLSA data based on four housekeeping genes identified two to three sequence types per genospecies. It suggested that sequence variations primarily consisted of synonymous mutations, although a recombination event spanning several hundred nucleotides was detected for some strains of X. euvesicatoria on the atpD gene coding for the F1-F0-ATPase β subunit. The pathogenicity of strains was consistent with data found in the literature. Some pathological variations were primarily observed among strains identified as X. euvesicatoria. This study provides the first ever comprehensive description of the status of Xanthomonas species that cause bacterial spot of tomato and pepper in the southwest Indian Ocean region.

Identification of Xanthomonas species associated with bacterial leaf spot of tomato, capsicum and chilli crops in eastern Australia

“…The assays were developed with isolates from various geographic regions and subsequently validated with Brazilian isolates, though did not include any Australian isolates (Araujo et al 2012). MLSA of four genes resolved Australian BLS-causing isolates in species clades consistent with the literature (Hamza et al 2010) and distinguished them from non-pathogenic strains. The presence of Xanthomonas spp.…”

“…atpD, dnaK, efp, and gyrB genes (supplementary Table 3) available on GenBank (Benson et al 2005) using clustalW (Larkin et al 2007). Sequences from Hamza et al (2010Hamza et al ( , 2012 and the top BLASTn hit for each gene of isolates in unresolved clades were included in the MLSA analysis. The outgroup taxa were Stenotrophomonas maltophilia, X. albilineans and X. campestris pv.…”

“…All Australian isolates in this clade were sourced from capsicum and chilli at Bundaberg and Gatton, Qld and Glastonbury and Hawkesbury Heights, NSW. Five X. euvesicatoria reference isolates from Hamza et al (2010) grouped outside the largest X. euvesicatoria clade, closest to but separate from the N. physalodes (BRIP 39016) isolate. The clade containing the type strain of X. perforans (NCPPB 4321) from tomato (USA) also included 13 Australian isolates and a GenBank reference of X. perforans (LH 3).…”

PM 7/110 (1) Xanthomonas spp. (Xanthomonas euvesicatoria, Xanthomonas gardneri, Xanthomonas perforans, Xanthomonas vesicatoria) causing bacterial spot of tomato and sweet pepper

“…However, comparisons of commercially sequenced PCR products amplified from selected housekeeping gene loci now offer equivalent resolution with significantly reduced cost and effort. For example, single gene sequencing methods of Parkinson et al (2009) and multilocus sequencing methods of Young et al (2008) and Hamza et al (2010) have been shown to adequately distinguish strains of X. gardneri, X. vesicatoria, X. euvesicatoria and X. perforans. Procedures are described in the EPPO Standard PM 7/XXX on DNA barcoding as an identification tool for plant pests (in preparation).…”

“…vesicatoria is no longer a valid name (Bull et al, 2010). However, recent phylogenetic analyses based on DNA sequence similarity between single and multiple gene loci (Young et al, 2008;Parkinson et al, 2009;Hamza et al, 2010) support three distinct species, showing X. euvesicatoria and X. perforans to be highly related to (if not synonymous with) each other and also with the recently described X. alfalfa. Furthermore, X. gardneri was found to be synonymous with the established X. hortorum and the more recently described X. cynarae.…”