A Proposal for a genome similarity-based taxonomy for plant-pathogenic bacteria that is sufficiently precise to reflect phylogeny, host range, and outbreak affiliation applied to $Pseudomonas\ syringae\ sensu\ lato$ as a proof of concept - CNRS - Centre national de la recherche scientifique Accéder directement au contenu
Article Dans Une Revue Phytopathology Année : 2017

A Proposal for a genome similarity-based taxonomy for plant-pathogenic bacteria that is sufficiently precise to reflect phylogeny, host range, and outbreak affiliation applied to $Pseudomonas\ syringae\ sensu\ lato$ as a proof of concept

Résumé

Taxonomy of plant pathogenic bacteria is challenging because pathogens of different crops often belong to the same named species but current taxonomy does not provide names for bacteria below the subspecies level. The introduction of the host range-based pathovar system in the 1980s provided a temporary solution to this problem but has many limitations. The affordability of genome sequencing now provides the opportunity for developing a new genome-based taxonomic framework. We already proposed to name individual bacterial isolates based on pairwise genome similarity. Here, we expand on this idea and propose to use genome similarity-based codes, which we now call life identification numbers (LINs), to describe and name bacterial taxa. Using 93 genomes of $Pseudomonas\ syringae\ sensu\ lato$, LINs were compared with a $P.\ syringae$ genome tree whereby the assigned LINs were found to be informative of a majority of phylogenetic relationships. LINs also reflected host range and outbreak association for strains of $P.\ syringae$ pathovar $actinidiae$, a pathovar for which many genome sequences are available. We conclude that LINs could provide the basis for a new taxonomic framework to address the shortcomings of the current pathovar system and to complement the current taxonomic system of bacteria in general.

Dates et versions

hal-03336943 , version 1 (07-09-2021)

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Citer

Boris A. Vinatzer, Alexandra J. Weisberg, Caroline Monteil, Haitham A. Elmarakeby, Samuel K. Sheppard, et al.. A Proposal for a genome similarity-based taxonomy for plant-pathogenic bacteria that is sufficiently precise to reflect phylogeny, host range, and outbreak affiliation applied to $Pseudomonas\ syringae\ sensu\ lato$ as a proof of concept. Phytopathology, 2017, 107 (1), pp.18-28. ⟨10.1094/phyto-07-16-0252-r⟩. ⟨hal-03336943⟩
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