Comparative Genomics of Xanthomonas citri pv. citri A* Pathotype Reveals Three Distinct Clades with Varying Plasmid Distribution

Abstract

Citrus bacterial canker (CBC) is an important disease of citrus cultivars worldwide that causes blister-like lesions on host plants and leads to more severe symptoms such as plant defoliation and premature fruit drop. The causative agent, Xanthomonas citri pv. citri, exists as three pathotypes—A, A*, and Aw—which differ in their host range and elicited host response. To date, comparative analyses have been hampered by the lack of closed genomes for the A* pathotype. In this study, we sequenced and assembled six CBC isolates of pathotype A* using second- and third-generation sequencing technologies to produce complete, closed assemblies. Analysis of these genomes and reference A, A*, and Aw sequences revealed genetic groups within the A* pathotype. Investigation of accessory genomes revealed virulence factors, including type IV secretion systems and heavy metal resistance genes, differentiating the genetic groups. Genomic comparisons of closed genome assemblies also provided plasmid distribution information for the three genetic groups of A*. The genomes presented here complement existing closed genomes of A and Aw pathotypes that are publicly available and open opportunities to investigate the evolution of X. citri pv. citri and the virulence factors that contribute to this serious pathogen.

Molecular epidemiology of the citrus bacterial pathogen Xanthomonas citri pv. citri from the Arabian Peninsula reveals a complex structure of specialist and generalist strains

“…citri was first reported in pathotype A strains from Argentina in the mid-1990s (Canteros et al, 2017) and more recently in remote territories (Huang et al, 2021;Richard et al, 2016Richard et al, , 2017. Moreover, a recent genomic study revealed its presence in pathotype A* strains from Southeast Asia (Webster et al, 2020). Because of the risk of future emergence of copperresistant strains and the environmental issues caused by massive copper applications, research of alternative control strategies should be pursued.…”

“…Pathotype A w has the unique feature of inducing a hypersensitive reaction (HR) when inoculated at high titer into some non-host citrus lines, such as grapefruit (C x paradisi) and sweet orange (C. x sinensis) (Rybak et al, 2009;Sun et al, 2004). This phenotype was found to be associated with the specific presence in A w strains of the type III effector avrGf1 (Rybak et al, 2009;Webster et al, 2020). This suggests that the genetic basis of the restricted host range in A* and A w is likely to be different.…”

“…x sinensis ) (Rybak et al, 2009; Sun et al, 2004). This phenotype was found to be associated with the specific presence in A w strains of the type III effector avrGf1 (Rybak et al, 2009; Webster et al, 2020). This suggests that the genetic basis of the restricted host range in A* and A w is likely to be different.…”

Molecular characterization of Pectobacterium atrosepticum infecting potato and its management through chemicals

“…After identification of the pathogen, several actions can be taken to control the disease, for instance, the use of resistant potato varieties ( Chiesa et al, 2013 ; Lu et al, 2022 ), the design of effective control measures based on the genetic diversity, population characteristics, and virulence of Pa ( Izadiyan, Taghavi & Farahbakhsh, 2018 ; Timilsina et al, 2020 ; Webster, Bogema & Chapman, 2020 ), and the determination of the gene content differences within the genetic groups ( Richard et al, 2017 ). Through the implementation of these measures blackleg can be prevented from spreading.…”

Citrus Canker Pathogen, Its Mechanism of Infection, Eradication, and Impacts

“…It is suggested that the acquisition of productive genes and lack of detrimental genes is most probably the reason behind the ability of pathotype A to attack a broader host range than A* and pathotypes [ 58 ]. Many types of research have been conducted to study their comparative genomic analysis and evolutionary history in detail [ 42 , 48 , 51 , 59 , 60 , 61 ].…”