Phylogenetics of Historical Host Switches in a Bacterial Plant Pathogen

Abstract

Xylella fastidiosa is a globally important bacterial plant pathogen with many hosts; however, the underpinnings of host specificity are not known. This paper contains important findings about the usage of phylogenetics to understand the history of host specificity in this bacterial species, as well as convergent evolution in the pan-genome.

Using genomes and evolutionary analyses to screen for host-specificity and positive selection in the plant pathogen Xylella fastidiosa

“…In our study, we have found a significant, non-random association between phylogenetic relationships and both the species and taxonomic order of plant hosts (P < 0.0001) based on core phylogenies. These results are consistent with some level of specialization of X. fastidiosa to plant hosts and with the recent analysis of Kahn and Almeida (2022). Moreover, these results were robust to phylogenetic treatment -i.e., the inclusion or exclusion of genomic regions inferred to have histories of recombination.…”

“…As an example, the cluster corresponding to multiplex displayed the most discordance between the core and accessory trees, with all OTUs contributing to phylogenetic incongruence (Figure 3). Interestingly, our multiplex sample also had more plant host species than our fastidiosa and pauca samples, suggesting the possibility (but by no means proving) that host factors may affect or moderate genome content (27). Nonetheless, we found a significant correlation between distance matrices based on the core and accessory phylogenies (Mantel test, R = 0.1144, P = 0.019), which is consistent with the fact that the two trees had the same three major clades.…”

“…In one, Uceda-Campos et al (2022) found that X. fastidiosa isolates grouped on the phylogeny by geography, but not by plant host species, suggesting host specificity is not correlated with phylogenetic relationships and genetic divergence (26). In contrast, Kahn and Almeida (2022) used the phylogeny to infer the ancestral character states of plant hosts and found that the ancestral host plant could be inferred for most ancestral nodes (27). They concluded that genetic history affects host range and also identified ~30 genes whose presence/absence correlated with specific plant hosts.…”

“…For host-specificity analyses, we focused on core genes, but we also assessed the phylogenetic signal, pattern of gene gain and loss, and potential host associations of accessory (i.e., non-core) genes. Our goals for these analyses were to add to the growing literature about genetic correlations between phylogenetic history and host specificity but also to further consider the dynamic evolution of accessory genes in this context (27). In addition, we performed extensive analyses of the ratio of nonsynonymous to synonymous (dN/dS or ω) substitutions to identify genes under positive selection (ω > 1.0).…”

Use of traC Gene to Type the Incidence and Distribution of pXFAS_5235 Plasmid-Bearing Strains of Xylella fastidiosa subsp. fastidiosa ST1 in Spain

“…In these cases, an in-depth genomic analysis is required to determine whether this gene is conserved in the plasmid or whether it is inserted in the chromosome as with the strains 3124, U24d, J1a12, 9a5c, Hib4 from Brazil. Patterns of inter-and intrasubspecific homologous recombination between Xf subspecies pauca showed that these Brazilian strains have a high number of recombination events [32,33] (M.P. Velasco-Amo, L.F. and B.B.…”