Multilocus Sequence Analysis of Nectar Pseudomonads Reveals High Genetic Diversity and Contrasting Recombination Patterns

Abstract

The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas ‘sensu stricto’ isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA) of four core housekeeping genes (rrs, gyrB, rpoB and rpoD). A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs) 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1); P. fluorescens, P. lutea and P. syringae (NG 2); and P. rhizosphaerae (NG 3). Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria.

Genetic Stability and Evolution of thesigBAllele, Used for Listeria Sensu Stricto Subtyping and Phylogenetic Inference

“…Bootscan, Maxchi, LARD recombination events detected by only half of the nine methods in RDP4 were considered significant (25,26), and the results obtained by three programs, PHI test, Recco, and RDP4, were not consistent, we concluded that only limited HR occurred in sigB of Listeria sensu stricto.…”

Contributions of ancestral inter-species recombination to the genetic diversity of extant Streptomyces lineages

“…We included only those recombination events that are supported by at least three out of the nine methods in RDP to avoid dependence on a single methodology (RDP, BOOTSCAN, GENE-CONV, MAXCHI, CHIMAERA, SISCAN, PhylPro, LARD and 3Seq). Previous recombination studies using RDP have used the 3/9 criterion, with the expectation that true recombination events will likely be detected using different approaches (Bilhère et al, 2009;Cadillo-Quiroz et al, 2012;Alvarez-Pérez et al, 2013). The strength of RDP is its implementation of a variety of detection approaches to both identify and characterize recombination events, such as phylogenetic conflicts clustering of nucleotide substitutions and fitting of substitutions to an expected statistical distribution.…”

Multilocus Sequence Analysis for Assessment of Phylogenetic Diversity and Biogeography in Thalassospira Bacteria from Diverse Marine Environments

“…In general, the several housekeeping genes are widely applied in MLSA schemes, such as acsA , gyrB , mutL , rpoD , etc [22]–[25], because they encode core metabolic enzymes and own by all members of the organisms. Furthermore, the concatenated housekeeping genes could overcome conflicting signals from horizontal gene transfer and recombination.…”