Complete Genome Assemblies of All Xanthomonas translucens Pathotype Strains Reveal Three Genetically Distinct Clades

Abstract

The Xanthomonas translucens species comprises phytopathogenic bacteria that can cause serious damage to cereals and to forage grasses. So far, the genomic resources for X. translucens were limited, which hindered further understanding of the host–pathogen interactions at the molecular level and the development of disease-resistant cultivars. To this end, we complemented the available complete genome sequence of the X. translucens pv. translucens pathotype strain DSM 18974 by sequencing the genomes of all the other 10 X. translucens pathotype strains using PacBio long-read technology and assembled complete genome sequences. Phylogeny based on average nucleotide identity (ANI) revealed three distinct clades within the species, which we propose to classify as clades Xt-I, Xt-II, and Xt-III. In addition to 2,181 core X. translucens genes, a total of 190, 588, and 168 genes were found to be exclusive to each clade, respectively. Moreover, 29 non-transcription activator-like effector (TALE) and 21 TALE type III effector classes were found, and clade- or strain-specific effectors were identified. Further investigation of these genes could help to identify genes that are critically involved in pathogenicity and/or host adaptation, setting the grounds for the development of new resistant cultivars.

Xanthomonas bonasiae sp. nov. and Xanthomonas youngii sp. nov., isolated from crown gall tissues

“…Strains AmX2 T , FX1 and FX4 T were distinct from other clade I xanthomonads such as the non-pathogenic species X. sontii that was isolated from healthy basmati rice (Oryza sativa) seeds [33]. Strains FX1 and FX4 T were clustered in a monophyletic clade closely related to, but still distinct from, the cereal pathogen X. translucens [34]. Strain AmX2 T was also distinct from the closest neighbour species, i.e.…”

Comparative genomics of Minnesotan barley-infecting Xanthomonas translucens shows overall genomic similarity but virulence factor diversity

“…Xtt is classified in the genomic subgroup Xt-I (Sapkota et al 2020; Goettelmann et al 2022), which also includes wheat and barley-infecting Xtu. Xtt was historically divided into three groups (A, B and C) according to multilocus sequencing analysis (MLSA) of four housekeeping genes (Curland et al 2018).…”

Development of genome-driven, lifestyle-informed primers for identification of the cereal-infecting pathogens Xanthomonas translucens pathovars undulosa and translucens

“…Xanthomonas translucens pv. pistaciae was isolated from the dicot pistachio, but recent genetic analysis demonstrated that this pathovar spans multiple genetic groups (Goettelmann et al 2022;Giblot-Ducray et al 2009).…”

“…Recent efforts in genome sequencing and phylogenomic analysis have allowed the reclassification of X. translucens based on evolutionary relationships into three genomic groups I-III (Heiden et al 2022;Goettelmann et al 2022;Sapkota et al 2020). Cereal-infecting pathovars (e.g.…”

“…Cereal-infecting pathovars (e.g. secalis [Xts], translucens [Xtt], and undulosa [Xtu]) belong to genomic group Xt-I (Goettelmann et al 2022). The Xt-I group was also defined using the Life Identification Number (LIN) classification system that provides an average nucleotide identity (ANI)-based coding system to precisely identify genomic subgroups (Heiden et al 2022;Tian et al 2020).…”