Population genomics reveals additive and replacing horizontal gene transfers in the emerging pathogen Dickeya solani

Abstract

BackgroundDickeya solani is an emerging pathogen that causes soft rot and blackleg diseases in several crops including Solanum tuberosum, but little is known about its genomic diversity and evolution.ResultsWe combined Illumina and PacBio technologies to complete the genome sequence of D. solani strain 3337 that was used as a reference to compare with 19 other genomes (including that of the type strain IPO2222T) which were generated by Illumina technology. This population genomic analysis highlighted an unexpected variability among D. solani isolates since it led to the characterization of two distinct sub-groups within the D. solani species. This approach also revealed different types of variations such as scattered SNP/InDel variations as well as replacing and additive horizontal gene transfers (HGT). Infra-species (between the two D. solani sub-groups) and inter-species (between D. solani and D. dianthicola) replacing HGTs were observed. Finally, this work pointed that genetic and functional variation in the motility trait could contribute to aggressiveness variability in D. solani.ConclusionsThis work revealed that D. solani genomic variability may be caused by SNPs/InDels as well as replacing and additive HGT events, including plasmid acquisition; hence the D. solani genomes are more dynamic than that were previously proposed. This work alerts on precautions in molecular diagnosis of this emerging pathogen.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1997-z) contains supplementary material, which is available to authorized users.

The effect of temperature on the phenotypic features and the maceration ability of Dickeya solani strains isolated in Finland, Israel and Poland

“…All previously characterized D. solani strains indicated identical rep-PCR and PFGE profiles (Degefu et al 2013;Tsror (Lahkim) et al 2013;van der Wolf et al 2014;Potrykus et al 2016). However, the comparison of genome sequences of several D. solani strains indicated the existence of some differences within the studied strains caused probably by the horizontal gene transfer (Khayi et al 2015).…”

“…Studies show that these pathogens are able to induce diseases at the lower inoculum levels, produce more PCWDE and in addition possess an arsenal of T5SS/T6SS secreted proteins exhibiting more diverse functions than just destroying the plant cell-wall (Toth et al 2011;Garlant et al 2013;Pedron et al 2014;Khayi et al 2015;Potrykus et al 2016). …”

Complete genome anatomy of the emerging potato pathogen Dickeya solani type strain IPO 2222T

“… D. solani species is genetically highly homogenous with 99.9% in genomic similarity (ANI value) [19, 20]. Between two given D. solani genomes, the number of variations (SNPs/InDels) is below one hundred.…”

“…Between two given D. solani genomes, the number of variations (SNPs/InDels) is below one hundred. For example, when D. solani strain 3337 and D. solani strain IPO 2222 T were compared, 49 variations were observed: 15 were located out of CDS and 34 within CDS [19]. Only a few of D. solani genomes (strains RNS 07.7.3B, PPO 9019 and PPO 9134) exhibited a higher number of variations (>1000) because they acquired D. dianthicola genes by horizontal gene transfer [19].…”

“…Recent comparative analyses underlined the major genetic and metabolic divergences between Dickeya solani species and the nearest clades that are D. dandatii (ANI 94%) and D. dianthicola (ANI 92%) [11, 19]. D. solani is characterized by a low content of phages elements and CRISPR system: in strain IPO 2222 T genome, only one CRISPR cluster (208 bp) was identified.…”