Comparative analysis of Ralstonia solanacearum methylomes
Erill, Ivan (Centre de Recerca en Agrigenòmica)
Puigvert, Marina (Centre de Recerca en Agrigenòmica)
Legrand, Ludovic (Institut National de la Recherche Agronomique (França))
Guarischi-Sousa, Rodrigo (Universidade de São Paulo. Departamento de Bioquímica)
Vandecasteele, Céline (Institut National de la Recherche Agronomique (França))
Setuba, João C. (Universidade de São Paulo. Departamento de Bioquímica)
Genin, Stephane (Institut National de la Recherche Agronomique (França))
Guidot, Alice (Institut National de la Recherche Agronomique (França))
Valls, Marc (Centre de Recerca en Agrigenòmica)

Date:	2017
Abstract:	Ralstonia solanacearum 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 R. solanacearum 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 R. solanacearum is unknown. Sequencing of R. solanacearum strains GMI1000 and UY031 using Single Molecule Real-Time technology allowed us to perform a comparative analysis of R. solanacearum methylomes. Our analysis identified a novel methylation motif associated with a DNA methylase that is conserved in all complete Ralstonia spp. genomes and across the Burkholderiaceae, as well as a methylation motif associated to a phage-borne methylase unique to R. solanacearum 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 R. solanacearum 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 R. solanacearum evolution and its adaptation to different plants.
Grants:	Ministerio de Economía y Competitividad AGL2016-78002-R Ministerio de Economía y Competitividad SEV-2015-0533 Ministerio de Economía y Competitividad AGL2013-46898-R
Note:	Altres ajuts: COST Action SUSTAIN (FA1208) from the European Union.
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Ralstonia ; Methylome ; Comparative genomics ; Epigenomics ; Transcriptional regulation ; Transposon ; Nucleotide modification ; Genome
Published in:	Frontiers in plant science, Vol. 28 (April 2017) , art. 504, ISSN 1664-462X

DOI: 10.3389/fpls.2017.00504
PMID: 28450872

16 p, 2.3 MB

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Research literature > UAB research groups literature > Research Centres and Groups (research output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
Articles > Research articles
Articles > Published articles