Draft genome sequence for virulent and avirulent strains of Xanthomonas arboricola isolated from Prunus spp. in Spain

Abstract

Xanthomonas arboricola is a species in genus Xanthomonas which is mainly comprised of plant pathogens. Among the members of this taxon, X. arboricola pv. pruni, the causal agent of bacterial spot disease of stone fruits and almond, is distributed worldwide although it is considered a quarantine pathogen in the European Union. Herein, we report the draft genome sequence, the classification, the annotation and the sequence analyses of a virulent strain, IVIA 2626.1, and an avirulent strain, CITA 44, of X. arboricola associated with Prunus spp. The draft genome sequence of IVIA 2626.1 consists of 5,027,671 bp, 4,720 protein coding genes and 50 RNA encoding genes. The draft genome sequence of strain CITA 44 consists of 4,760,482 bp, 4,250 protein coding genes and 56 RNA coding genes. Initial comparative analyses reveals differences in the presence of structural and regulatory components of the type IV pilus, the type III secretion system, the type III effectors as well as variations in the number of the type IV secretion systems. The genome sequence data for these strains will facilitate the development of molecular diagnostics protocols that differentiate virulent and avirulent strains. In addition, comparative genome analysis will provide insights into the plant-pathogen interaction during the bacterial spot disease process.

Comparative Genomic and Phenotypic Characterization of Pathogenic and Non-Pathogenic Strains of Xanthomonas arboricola Reveals Insights into the Infection Process of Bacterial Spot Disease of Stone Fruits

“…All the strains harbored CDS that encoded for HpaR2, HpaS, HrpG and HrpX, which are involved in the regulation of the T3SS, and for many of the T3Es and some cell-wall degrading enzymes [43]. However, the strains 3004, CFBP 7634 and CITA 44, as described before [7,17,19], did not present the components of the T3SS that have been found in other Xanthomonas . Besides the master regulons mentioned above, all the remaining X .…”

Pan-Genomic Analysis Permits Differentiation of Virulent and Non-virulent Strains of Xanthomonas arboricola That Cohabit Prunus spp. and Elucidate Bacterial Virulence Factors

“…Genome sequencing conditions and features for CITA 44 have been discussed in a previous paper (Garita-Cambronero et al, 2016b). In addition, in this study the genome features of the Xap -look-a-like strains CITA 14 and CITA 124 are described.…”

Xanthomonas arboricola pv. pruni, causal agent of bacterial spot of stone fruits and almond: its genomic and phenotypic characteristics in the X. arboricola species context

“…in the pathovars celebensis , fragariae and populi , and other non‐pathovar‐assigned strains, have been considered to be non‐pathogenic, low‐virulent or opportunistic pathogens (Essakhi et al ., ). Moreover, some of these non‐pathogenic xanthomonads strains have been found to cohabit with pathogenic strains on the same host plant (Cesbron et al ., ; Garita‐Cambronero et al ., ). The existence of pathogenic and non‐pathogenic strains phylogenetically close, but drastically different in their phenotype, makes X. arboricola a useful model to perform comparative microbe–plant interaction studies in order to reveal the pathogenicity and host range mechanisms.…”

“…Moreover, new studies based on whole‐genome analysis, using either concatenated sequences of the core group of genes of X. arboricola (Cesbron et al ., ; Garita‐Cambronero et al ., ) or pangenomic analysis of at least 7074 protein coding sequences, established pathovar pruni as a monophyletic group; however, in contrast with the observations of MLSA, slight differences were observed in strains from different geographical origins. Despite this, the average nucleotide identity amongst all members of this pathovar was over 99% (Garita‐Cambronero et al ., ) (Fig.…”

“…pruni (Vauterin et al ., ) ( Gammaproteobacteria , Xanthomonadales , Xanthomonadaceae ) is a Gram‐negative, rod‐shaped, monoflagellated, motile, non‐sporulating aerobic bacterium. According to the reactions in the Biolog GN2 system, strains from this pathovar are able to metabolize α‐ d ‐glucose, α‐ketoglutaric acid, bromosuccinic acid, d ‐cellobiose, d ‐fructose, d ‐mannose, d ‐psicose, d ‐trehalose, dextrin, glycyl‐ l ‐glutamic acid, l ‐glutamic acid, l ‐proline, l ‐serine, pyruvic acid methyl ester, succinic acid, succinic acid monomethyl ester, sucrose and Tween 20 (Garita‐Cambronero et al ., ).…”