title: Genome-wide DNA methylation patterns in wild samples of two morphotypes of threespine stickleback (Gasterosteus aculeatus).
abstract: Epigenetic marks such as DNA methylation play important biological roles in gene expression regulation and cellular differentiation during development. To examine whether DNA methylation patterns are potentially associated with naturally occurring phenotypic differences, we examined genome-wide DNA methylation within Gasterosteus aculeatus, using reduced representation bisulfite sequencing. First, we identified highly methylated regions of the stickleback genome, finding such regions to be located predominantly within genes, and associated with genes functioning in metabolism and biosynthetic processes, cell adhesion, signaling pathways, and blood vessel development. Next, we identified putative differentially methylated regions (DMRs) of the genome between complete and low lateral plate morphs of G. aculeatus. We detected 77 DMRs that were mainly located in intergenic regions. Annotations of genes associated with these DMRs revealed potential functions in a number of known divergent adaptive phenotypes between G. aculeatus ecotypes, including cardiovascular development, growth, and neuromuscular development.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Irvine gsmith1@uci.edu.
authors.forename: Gilbert
authors.initials: G
authors.lastname: Smith
authors.affiliation: School of Biology, University of St Andrews, St. Andrews, Fife, United Kingdom.
authors.forename: Carl
authors.initials: C
authors.lastname: Smith
authors.affiliation: Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
authors.forename: John G
authors.initials: JG
authors.lastname: Kenny
authors.affiliation: Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
authors.forename: Roy R
authors.initials: RR
authors.lastname: Chaudhuri
authors.affiliation: School of Biology, University of St Andrews, St. Andrews, Fife, United Kingdom.
authors.forename: Michael G
authors.initials: MG
authors.lastname: Ritchie
mesh_terms: D000818:Animals; D001483:Base Sequence; D002448:Cell Adhesion / Q000235:genetics; D019175:DNA Methylation; D005260:Female; D005796:Genes; D016678:Genome; D048788:Growth and Development / Q000235:genetics; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008969:Molecular Sequence Data; D010641:Phenotype; D015398:Signal Transduction / Q000235:genetics; D023701:Smegmamorpha / Q000235:genetics*
keywords: adaptation; ecotype; epigenetic mechanism; lateral plate morph; phenotypic plasticity