title: 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.
abstract: 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.
authors.affiliation: First, second, and third authors: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Virginia; second author: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon; fourth and sixth authors: Department of Computer Science, Virginia Tech, Blacksburg, Virginia; and fifth author: Department of Biology & Biotechnology, University of Bath, Claverton Down, Bath, United Kingdom.
authors.forename: Boris A
authors.initials: BA
authors.lastname: Vinatzer
authors.affiliation: First, second, and third authors: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Virginia; second author: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon; fourth and sixth authors: Department of Computer Science, Virginia Tech, Blacksburg, Virginia; and fifth author: Department of Biology & Biotechnology, University of Bath, Claverton Down, Bath, United Kingdom.
authors.forename: Alexandra J
authors.initials: AJ
authors.lastname: Weisberg
authors.affiliation: First, second, and third authors: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Virginia; second author: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon; fourth and sixth authors: Department of Computer Science, Virginia Tech, Blacksburg, Virginia; and fifth author: Department of Biology & Biotechnology, University of Bath, Claverton Down, Bath, United Kingdom.
authors.forename: Caroline L
authors.initials: CL
authors.lastname: Monteil
authors.affiliation: First, second, and third authors: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Virginia; second author: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon; fourth and sixth authors: Department of Computer Science, Virginia Tech, Blacksburg, Virginia; and fifth author: Department of Biology & Biotechnology, University of Bath, Claverton Down, Bath, United Kingdom.
authors.forename: Haitham A
authors.initials: HA
authors.lastname: Elmarakeby
authors.affiliation: First, second, and third authors: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Virginia; second author: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon; fourth and sixth authors: Department of Computer Science, Virginia Tech, Blacksburg, Virginia; and fifth author: Department of Biology & Biotechnology, University of Bath, Claverton Down, Bath, United Kingdom.
authors.forename: Samuel K
authors.initials: SK
authors.lastname: Sheppard
authors.affiliation: First, second, and third authors: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Virginia; second author: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon; fourth and sixth authors: Department of Computer Science, Virginia Tech, Blacksburg, Virginia; and fifth author: Department of Biology & Biotechnology, University of Bath, Claverton Down, Bath, United Kingdom.
authors.forename: Lenwood S
authors.initials: LS
authors.lastname: Heath
mesh_terms: D016680:Genome, Bacterial / Q000235:genetics*; D058507:Host Specificity; D010802:Phylogeny; D010935:Plant Diseases / Q000382:microbiology*; D010944:Plants / Q000382:microbiology*; D044224:Pseudomonas syringae / Q000145:classification* / Q000235:genetics / Q000502:physiology; D017422:Sequence Analysis, DNA
keywords: average genome identity; core genome phylogeny