Phenotypic plasticity allows many organisms to respond to their environment by changing their phenotype, but the mechanisms to do so are not well understood. Yellow Monkeyflower (formerly Mimulus guttatus; now Erythranthe guttata) is one such organism that can serve as a model to promote our understanding of these mechanisms due to its striking response to insect herbivory. Monkeyflower responds to leaf damage by increasing the number of hair-like glandular trichomes, a putative defensive trait that reduces the magnitude of damage by insects. This plastic response is transgenerationally inherited in a way that is sensitive to genome-wide demethylation when transmitted through the maternal but not the paternal germline. Investigation of this phenomenon has been hampered by a lack of computational tools to analyze pooled methylome and genome sequence data. In this study, two distinct software pipelines were developed and tested on data from Monkeyflower. The first pipeline detects regions that are differentially methylated and identifies adjacent candidate genes, using Nanopore data. This was tested on data from a Monkeyflower recombinant inbred line (RIL) subject to either parental damage or control conditions. The second pipeline uses pooled DNA sequence data to identify genomic regions that exhibit statistically significant divergence in allele frequencies. This was tested on genome sequence data from an experiment involving artificial selection for increased trichome production. Results indicate that epigenetic inheritance of the damage response in a particular RIL is associated with 59 differentially methylated regions. Relevant functions, including anatomical structure development and response to abscisic acid, are significantly overrepresented in the set of genes that lie closest to these DMRs. Artificial selection for high trichome production produced one highly divergent region adjacent to a gene associated with seed coat mucilage development. These findings identify candidate epigenetic and genetic factors associated with glandular trichome development while providing an effective test case for the development of two new software pipelines
