Genome-wide DNA methylation patterns in wild samples of two morphotypes of threespine stickleback (Gasterosteus aculeatus)

Gilbert Smith, Carl Smith, John Kenny, Roy Chaudhuri, Michael Gordon Ritchie

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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 G. aculeatus, using reduced representation bisulfite sequencing (RRBS). 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.

Original languageEnglish
Pages (from-to)888-895
JournalMolecular Biology and Evolution
Issue number4
Early online date21 Dec 2014
Publication statusPublished - Apr 2015


  • Adaptation
  • Lateral plate morph
  • Ecotype
  • Epigenetic mechanism
  • Phenotypic plasticity


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