Clarification of Taxonomic Status within the Pseudomonas syringae Species Group Based on a Phylogenomic Analysis

Abstract

The Pseudomonas syringae phylogenetic group comprises 15 recognized bacterial species and more than 60 pathovars. The classification and identification of strains is relevant for practical reasons but also for understanding the epidemiology and ecology of this group of plant pathogenic bacteria. Genome-based taxonomic analyses have been introduced recently to clarify the taxonomy of the whole genus. A set of 139 draft and complete genome sequences of strains belonging to all species of the P. syringae group available in public databases were analyzed, together with the genomes of closely related species used as outgroups. Comparative genomics based on the genome sequences of the species type strains in the group allowed the delineation of phylogenomic species and demonstrated that a high proportion of strains included in the study are misclassified. Furthermore, representatives of at least 7 putative novel species were detected. It was also confirmed that P. ficuserectae, P. meliae, and P. savastanoi are later synonyms of P. amygdali and that “P. coronafaciens” should be revived as a nomenspecies.

GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genusStenotrophomonas

“…They are consistently supported by the species-trees estimated with both programs. This result underlines the utility of GET_PHYLOMARKERS to identify misclassified genomes in public sequence repositories, a problem found in many genera (Gomila et al, 2017;Sangal et al, 2016). GET_PHYLOMARKERS is unique in its ability to combine core-genome phylogenomics with ML and parsimony phylogeny estimation from the pan-genome matrix.…”

Genome‐based evolutionary history of Pseudomonas spp

“…For the P. syringae group, we identified 2743 CDSs conserved among 13 type strains, which corresponds well with the core genome size (3397) estimated from a previous analysis of 19 genomes (Baltrus et al ., ). Both values are far smaller than the core genome size (343) estimated recently from an analysis of 127 genomes, including 14 type strains (Gomila et al ., ). Although comparisons across studies are confounded by differences in scope and methodology, it is clear that there is substantial genomic diversity within each of the 13 groups of Pseudomonas : even the smallest group, P. resinovorans , is composed of two strains sharing only about 60% of their genomes.…”

“…Of the eighteen species represented by the eight sets, all but ‘ P. pseudoalcaligenes ’ have standing in prokaryotic nomenclature currently (Euzéby, ). Nevertheless, the similarities of some of these sets ( P. oryzihabitans and P. psychrotolerans ; P. ficuserectae, P. meliae, P. savastanoi and P. amygdali ) are recognized in the literature (Gardan et al ., ; Saha et al ., ; Gomila et al ., ; Tran et al ., ; Peix et al ., ). Of the four subspecies of P. chlororaphis included in our analysis, only the subspecies pair aureofaciens and aurantiaca exceed 96.5% ANI.…”

Bacteria from four phylogroups of the Pseudomonas syringae complex can cause bacterial canker of apricot

“…() and Gomila et al . (), and the 30 strains from this study. Alignment of sequences was made using dambe v. 5.3.70 and a neighbour‐joining tree was built with mega v. 6.06.…”

“…Analysis of partial cts gene sequences was performed using P. syringae strains for phylogroup (PG), clade (a, b, c, d, e) and pathovar (pv.) identification as described by Berge et al (2014) and Gomila et al (2017), and the 30 strains from this study. Alignment of sequences was made using DAMBE v. 5.3.70 and a neighbour-joining tree was built with MEGA v. 6.06.…”