title: Integrating DNA Methylation and Gene Expression Data in the Development of the Soybean-Bradyrhizobium N2-Fixing Symbiosis.
abstract: Very little is known about the role of epigenetics in the differentiation of a bacterium from the free-living to the symbiotic state. Here genome-wide analysis of DNA methylation changes between these states is described using the model of symbiosis between soybean and its root nodule-forming, nitrogen-fixing symbiont, Bradyrhizobium diazoefficiens. PacBio resequencing of the B. diazoefficiens genome from both states revealed 43,061 sites recognized by five motifs with the potential to be methylated genome-wide. Of those sites, 3276 changed methylation states in 2921 genes or 35.5% of all genes in the genome. Over 10% of the methylation changes occurred within the symbiosis island that comprises 7.4% of the genome. The CCTTGAG motif was methylated only during symbiosis with 1361 adenosines methylated among the 1700 possible sites. Another 89 genes within the symbiotic island and 768 genes throughout the genome were found to have methylation and significant expression changes during symbiotic development. Of those, nine known symbiosis genes involved in all phases of symbiotic development including early infection events, nodule development, and nitrogenase production. These associations between methylation and expression changes in many B. diazoefficiens genes suggest an important role of the epigenome in bacterial differentiation to the symbiotic state.
authors.affiliation: Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA.
authors.forename: Austin G
authors.initials: AG
authors.lastname: Davis-Richardson
authors.affiliation: Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA.
authors.forename: Jordan T
authors.initials: JT
authors.lastname: Russell
authors.affiliation: Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA.
authors.forename: Raquel
authors.initials: R
authors.lastname: Dias
authors.affiliation: Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: McKinlay
authors.affiliation: Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA.
authors.forename: Ronald
authors.initials: R
authors.lastname: Canepa
authors.affiliation: Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA.
authors.forename: Jennie R
authors.initials: JR
authors.lastname: Fagen
authors.affiliation: Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA.
authors.forename: Kristin T
authors.initials: KT
authors.lastname: Rusoff
authors.affiliation: Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA.
authors.forename: Jennifer C
authors.initials: JC
authors.lastname: Drew
authors.affiliation: Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA.
authors.forename: Bryan
authors.initials: B
authors.lastname: Kolaczkowski
authors.affiliation: Biochemistry Department, University of Missouri Columbia, MO, USA.
authors.forename: David W
authors.initials: DW
authors.lastname: Emerich
authors.affiliation: Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA.
authors.forename: Eric W
authors.initials: EW
authors.lastname: Triplett
keywords: DNA methyltransferase; epigenetics; glycine max; nitrogen fixation; root nodulation