Novel genetic traits in<i>Xanthomonas</i>unveiled by the complete genome sequencing of three clade-1 xanthomonads

Peduzzi, Chloé; Sagia, Angeliki; Burokienė, Daiva; Nagy, Ildikó K.; Saux, Marion Fischer-Le; Portier, Pérrine; Dereeper, Alexis; Cunnac, Sébastien; Román-Reyna, Verónica; Jacobs, Jonathan M.; Bragard, Claude; Koebnik, Ralf

doi:10.1101/2022.10.10.511549

Cited by 2 publications

(2 citation statements)

References 63 publications

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“…However, our ANI analysis also reveals the existence of multiple potential species-level clades within X. albilineans, X. arboricola, X. dyei, X. euroxanthea, X. hortorum, X. sacchari, and X. translucens. These species level clades, particularly in earlybranching species, have been well-documented in the literature and recent efforts to sequence more representative strains in these clades is a promising step toward determining the extent to which diversity is continuous or clustered in these early-branching lineages (Parkinson et al, 2009;Peduzzi et al, 2023).…”

Section: Convergent Evolution Of Distantly Related Xanthomonas Strain...mentioning

confidence: 97%

Pangenome insights into the diversification and disease specificity of worldwide Xanthomonas outbreaks

Agarwal,

Stubits,

Nassrullah

et al. 2023

Front. Microbiol.

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The bacterial genus Xanthomonas is responsible for disease outbreaks in several hundred plant species, many of them economically important crops. In the era of next-generation sequencing, thousands of strains from this genus have now been sequenced as part of isolated studies that focus on outbreak characterization, host range, diversity, and virulence factor identification. However, these data have not been synthesized and we lack a comprehensive phylogeny for the genus, with some species designations in public databases still relying on phenotypic similarities and representative sequence typing. The extent of genetic cohesiveness among Xanthomonas strains, the distribution of virulence factors across strains, and the impact of evolutionary history on host range across the genus are also poorly understood. In this study, we present a pangenome analysis of 1,910 diverse Xanthomonas genomes, highlighting their evolutionary relationships, the distribution of virulence-associated genes across strains, and rates of horizontal gene transfer. We find a number of broadly conserved classes of virulence factors and considerable diversity in the Type 3 Secretion Systems (T3SSs) and Type 3 Secreted Effector (T3SE) repertoires of different Xanthomonas species. We also use these data to re-assign incorrectly classified strains to phylogenetically informed species designations and find evidence of both monophyletic host specificity and convergent evolution of phylogenetically distant strains to the same host. Finally, we explore the role of recombination in maintaining genetic cohesion within the Xanthomonas genus as a result of both ancestral and recent recombination events. Understanding the evolutionary history of Xanthomonas species and the relationship of key virulence factors with host-specificity provides valuable insight into the mechanisms through which Xanthomonas species shift between hosts and will enable us to develop more robust resistance strategies against these highly virulent pathogens.

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Section: Convergent Evolution Of Distantly Related Xanthomonas Strain...mentioning

confidence: 97%

Pangenome insights into the diversification and disease specificity of worldwide Xanthomonas outbreaks

Agarwal,

Stubits,

Nassrullah

et al. 2023

Front. Microbiol.

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“…Example: (1) Rhizophagy is a mechanism where plant can internalize and digest nutrients from symbiotic microbes (bacteria and fungi; White et al, 2018). (2) The genus Xanthomonas often are plant associated bacteria, collectively causing diseases on hundreds of host plants, including crops and ornamental plants (Mansfield et al, 2012;Peduzzi et al, 2022).…”

Section: Plant-endophyte Multifaceted Relations Back To the Roots-def...mentioning

confidence: 99%

Bacterial endophytome sources, profile and dynamics—a conceptual framework

Lengrand,

Pesenti,

Bragard

et al. 2024

Front. Sustain. Food Syst.

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Currently, it seems inconceivable to dispute the major role of microorganisms in human health or insects with endosymbionts. Although microbial endophytes were discovered long ago, little is known about the roles of plant-associated microorganisms. Some endophytes are horizontally transmitted, whereas others are seed-borne; together, they influence plant health. Beneficial endophytes can promote plant growth and yield by increasing plant resistance to biotic and abiotic stresses. Recently, the tools available to study the phytobiome have much improved, opening doors for a better understanding of the fascinating interactions taking place at the plant level. This review redefines the conceptual framework for “endophyte” and “endophytome,” focusing on the intricate dynamics of bacterial endophytomes. Systematically examining the formation pathways and profiling endophytes allows for a comprehensive exploration of the intricate dynamics governing plant-microbe interactions. Additionally, the assessment of how endophytomes are influenced by both biotic and abiotic factors provides essential insights into the adaptability and resilience of plant-associated microorganisms. Our comprehensive analysis integrates genomic insights with environmental considerations, offering a nuanced perspective on the functional roles of bacterial endophytomes. Therefore, a new, inclusive definition is essential to accurately represent the complexity of interactions within the plant microbiome as well as having the whole picture of associated concepts.

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Novel genetic traits inXanthomonasunveiled by the complete genome sequencing of three clade-1 xanthomonads

Cited by 2 publications

References 63 publications

Pangenome insights into the diversification and disease specificity of worldwide Xanthomonas outbreaks

Pangenome insights into the diversification and disease specificity of worldwide Xanthomonas outbreaks

Bacterial endophytome sources, profile and dynamics—a conceptual framework

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