Comparative genomics of Xanthomonas fragariae and Xanthomonas arboricola pv. fragariae reveals intra- and interspecies variations

Abstract

The quarantine bacterium Xanthomonas fragariae causes angular leaf spots on strawberry. Its population structure was recently found to be divided into four (sub)groups resulting from two distinct main groups. Xanthomonas arboricola pv. fragariae causes bacterial leaf blight, but the bacterium has an unclear virulence status on strawberry. In this study, we use comparative genomics to provide an overview of the genomic variations of a set of 58 X. fragariae and five X. arboricola pv. fragariae genomes with a focus on virulence-related proteins. Structural differences within X. fragariae such as differential plasmid presence and large-scale genomic rearrangements were observed. On the other hand, the virulence-related protein repertoire was found to vary greatly at the interspecies level. In three out of five sequenced X. arboricola pv. fragariae strains, the major part of the Hrp type III secretion system was lacking. An inoculation test with strains from all four X. fragariae (sub)groups and X. arboricola pv. fragariae resulted in an interspecies difference in symptom induction since no symptoms were observed on the plants inoculated with X. arboricola pv. fragariae. Our analysis suggests that all X. fragariae (sub)groups are pathogenic on strawberry plants. On the other hand, the first genomic investigations of X. arboricola pv. fragariae revealed a potential lack of certain key virulence-related factors which may be related to the difficulties to reproduce symptoms on strawberry and could question the plant-host interaction of the pathovar.

Host–Pathogen Interactions between Xanthomonas fragariae and Its Host Fragaria × ananassa Investigated with a Dual RNA-Seq Analysis

“…For each differentially expressed bacterial gene, the gene annotation from the reference genome PD 885 T was assigned, and gene ontology (GO) categorization was subsequently added with Blast2Go [54]. Additionally, virulence-related genes in X. fragariae, such as T3SS, T3E, T4SS, and T6SS, retrieved from the annotated genome PD 885 T [26], were specifically screened for expression levels for both collection days and compared with housekeeping genes.…”

“…Complete reference genomes from both groups of strains are available [24,25], thus providing an ideal base for gene expression analyses. Both groups were reported as being pathogenic on strawberry and harbored similar virulence-related protein repertoires including a type III secretion system (T3SS) and its effectors (T3E), a type IV secretion system (T4SS), and a type VI secretion system (T6SS) [26].…”

Xanthomonas rydalmerensis sp. nov., a non-pathogenic member of Group 1 Xanthomonas

“…The presence and absence of Xanthomonas -specific virulence-associated factors was examined using BLASTX in Diamond v2.0.15 [62] with no limit on maximum target sequences. A reference database was constructed using 163 previously characterised genes for T3SS, Type III effectors (T3E), flagellar T3SS, type IV secretion system (T4SS), type VI secretion system (T6SS), LPS and EPS from members of the genus Xanthomonas published by Gétaz et al [63]. Additional proxy genes ( estA , fhaB , hlyB , pctB , raxB , xadA , xcs and xps ) were used to detect the presence of the type I secretion system (T1SS), type II secretion system (T2SS) and type V secretion system (T5SS) [64].…”

Xanthomonas arboricola pv. juglandis and pv. corylina: Brothers or distant relatives? Genetic clues, epidemiology, and insights for disease management

“…# Pathogenicity towards host of isolation according to published inoculation tests (see reference column). *Reference relative to pathogenicity testing otherwise relative to genome publication: 1, Essakhi et al ( 2015 ); 2, López‐Soriano et al ( 2016 ); 3, Garita‐Cambronero et al ( 2016c ); 4, Garita‐Cambronero et al ( 2016a ); 5, Garita‐Cambronero et al ( 2014 ); 6, Merda et al, 2017 ; 7, Ibarra Caballero et al ( 2013 ); 8, Higuera et al ( 2015 ); 9, Pereira et al ( 2015 ); 10, Martins et al ( 2020 ); 11, Cesbron et al ( 2015 ); 12, Vandroemme et al ( 2013 ); 13, Gétaz et al ( 2018 ); 14, Fischer‐Le Saux et al ( 2015 ); 15, Wang et al ( 2018 ); 16, Harrison et al ( 2016 ); 17, Garita‐Cambronero et al ( 2017 ); 18, Garita‐Cambronero et al ( 2016b ); 19, Gétaz et al ( 2020 ); 20, Vauterin et al ( 1996 ); 21, Ignatov et al ( 2015 ); 22, Ferrante and Scortichini ( 2018 ); 23, Janse et al ( 2001 ) contrary to Vandroemme et al ( 2013 ) and Gétaz et al ( 2020 ), Janse et al ( 2001 ) and Ferrante and Scortichini ( 2018 ) found the strain to be pathogenic…”

“…By contrast, most strains from the recombinant network (Group B) have been shown to be nonpathogenic (Essakhi et al, 2015 ; Garita‐Cambronero et al, 2016a , 2016c ) or to exhibit a doubtful virulence, like the ones of pv. fragariae (Ferrante & Scortichini, 2018 ; Gétaz et al, 2020 ; Vandroemme et al, 2013 ). They do not cluster according to the host of isolation (Figure 4 ) (Merda et al, 2016 ).…”