title: Methylome Analysis of TwoXanthomonasspp. Using Single-Molecule Real-Time Sequencing.
abstract: Single-molecule real-time (SMRT) sequencing allows identification of methylated DNA bases and methylation patterns/motifs at the genome level. Using SMRT sequencing, diverse bacterial methylomes including those ofHelicobacter pylori,Lactobacillusspp., andEscherichia colihave been determined, and previously unreported DNA methylation motifs have been identified. However, the methylomes ofXanthomonasspecies, which belong to the most important plant pathogenic bacterial genus, have not been documented. Here, we report the methylomes ofXanthomonas axonopodispv.glycines(Xag) strain 8ra andX. campestrispv.vesicatoria(Xcv) strain 85-10. We identified N6-methyladenine (6mA) and N4-methylcytosine (4mC) modification in both genomes. In addition, we assigned putative DNA methylation motifs including previously unreported methylation motifs via REBASE and MotifMaker, and compared methylation patterns in both species. Although Xag and Xcv belong to the same genus, their methylation patterns were dramatically different. The number of 4mC DNA bases in Xag (66,682) was significantly higher (29 fold) than in Xcv (2,321). In contrast, the number of 6mA DNA bases (4,147) in Xag was comparable to the number in Xcv (5,491). Strikingly, there were no common or shared motifs in the 10 most frequently methylated motifs of both strains, indicating they possess unique species- or strain-specific methylation motifs. Among the 20 most frequent motifs from both strains, for 9 motifs at least 1% of the methylated bases were located in putative promoter regions. Methylome analysis by SMRT sequencing technology is the first step toward understanding the biology and functions of DNA methylation in this genus.
authors.affiliation: Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Korea.
authors.forename: Hoon Je
authors.initials: HJ
authors.lastname: Seong
authors.affiliation: Department of Integrative Plant Science, Chung-Ang University, Anseong 17546, Korea.
authors.forename: Hye-Jee
authors.initials: HJ
authors.lastname: Park
authors.affiliation: Department of Life Science (BK21 Program), Chung-Ang University, Seoul 06974, Korea.
authors.forename: Eunji
authors.initials: E
authors.lastname: Hong
authors.affiliation: Department of Life Science (BK21 Program), Chung-Ang University, Seoul 06974, Korea.
authors.forename: Sung Chul
authors.initials: SC
authors.lastname: Lee
authors.affiliation: Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Korea.
authors.forename: Woo Jun
authors.initials: WJ
authors.lastname: Sul
authors.affiliation: Department of Integrative Plant Science, Chung-Ang University, Anseong 17546, Korea.
authors.forename: Sang-Wook
authors.initials: SW
authors.lastname: Han
keywords: Xanthomonas; methylome; single-molecule real-time sequencing