Comparative Analysis of Ralstonia solanacearum Methylomes

Abstract

<i>Ralstonia solanacearum</i> is an important soil-borne plant pathogen with broad geographical distribution and the ability to cause wilt disease in many agriculturally important crops. Genome sequencing of multiple <i>R. solanacearum</i> strains has identified both unique and shared genetic traits influencing their evolution and ability to colonize plant hosts. Previous research has shown that DNA methylation can drive speciation and modulate virulence in bacteria, but the impact of epigenetic modifications on the diversification and pathogenesis of <i>R. solanacearum</i> is unknown. Sequencing of <i>R. solanacearum</i> strains GMI1000 and UY031 using Single Molecule Real-Time technology allowed us to perform a comparative analysis of <i>R. solanacearum</i> methylomes. Our analysis identified a novel methylation motif associated with a DNA methylase that is conserved in all complete <i>Ralstonia</i> spp. genomes and across the <i>Burkholderiaceae</i>, as well as a methylation motif associated to a phage-borne methylase unique to <i>R. solanacearum</i> UY031. Comparative analysis of the conserved methylation motif revealed that it is most prevalent in gene promoter regions, where it displays a high degree of conservation detectable through phylogenetic footprinting. Analysis of hyper- and hypo-methylated loci identified several genes involved in global and virulence regulatory functions whose expression may be modulated by DNA methylation. Analysis of genome-wide modification patterns identified a significant correlation between DNA modification and transposase genes in <i>R. solanacearum</i> UY031, driven by the presence of a high copy number of ISrso3 insertion sequences in this genome and pointing to a novel mechanism for regulation of transposition. These results set a firm foundation for experimental investigations into the role of DNA methylation in <i>R. solanacearum</i> evolution and its adaptation to different plants.