Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

Abstract

<jats:title>Abstract</jats:title> <jats:p><jats:bold>Background: </jats:bold><jats:italic>Dickeya solani</jats:italic> was pointed as a significant trait to potato production in Europe and drew much of scientific attention due to remarkable virulence, great devastating potential and easier spread in contrast to other<jats:italic> Dickeya</jats:italic> spp. In a view of a high need for extensive studies on economically important soft rot <jats:italic>Pectobacteriaceae</jats:italic>, we performed a nearly conclusive pangenome analysis on <jats:italic>D. solani</jats:italic> strains to search for genetic foundations that would explain the differences in the observed virulence levels within the <jats:italic>D. solani </jats:italic>population.<jats:bold>Results:</jats:bold> High quality assemblies of 8 <jats:italic>de novo</jats:italic> sequenced <jats:italic>D. solani</jats:italic> genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes sequences and the sequences of 14 additional strains revealed exceptionally high level of homogeneity among the studied genetic material of <jats:italic>D. solani </jats:italic>strains. With the use of 22 genomes, the pangenome of <jats:italic>D. solani</jats:italic>,<jats:italic> </jats:italic>comprising<jats:italic> </jats:italic>84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the <jats:italic>D. solani</jats:italic> pangenome fractions to functional COG categories revealed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first <jats:italic>D. solani </jats:italic>large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported.<jats:bold>Conclusions: </jats:bold>The almost closed status of<jats:bold> </jats:bold><jats:italic>D. solani</jats:italic> pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic for taxa, whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal spread and population structure. Finally, no obvious correlations between the geographical origin of <jats:italic>D. solani</jats:italic> strains and their phylogeny was found, which might reflect the specificity of the international seed potato market.</jats:p>