Genome-wide identification, phylogeny, and gene duplication of the epigenetic regulators in Fagaceae

Abstract

Epigenetic regulators are proteins involved in controlling gene expression. Informationabout the epigenetic regulators within the Fagaceae, a relevant family of trees andshrubs of the northern hemisphere ecosystems, is scarce. With the intent to character-ize these proteins in Fagaceae, we searched for orthologs of DNA methyltransferases(DNMTs) and demethylases (DDMEs) and Histone modifiers involved in acetylation(HATs), deacetylation (HDACs), methylation (HMTs), and demethylation (HDMTs) inFagus,Quercus,andCastaneagenera. Blast searches were performed in the availablegenomes, and freely available RNA-seq data were used to de novo assemble transcrip-tomes. We identified homologs of seven DNMTs, three DDMEs, six HATs, 11 HDACs,32 HMTs, and 21 HDMTs proteins. Protein analysis showed that most of them havethe putative characteristic domains found in these protein families, which suggeststheir conserved function. Additionally, to elucidate the evolutionary history of thesegenes within Fagaceae, paralogs were identified, and phylogenetic analyses were per-formed with DNA and histone modifiers. We detected duplication events in all speciesanalyzed with higher frequency inQuercusandCastaneaand discuss the evidence oftransposable elements adjacent to paralogs and their involvement in gene duplication.The knowledge gathered from this work is a steppingstone to upcoming studies con-cerning epigenetic regulation in this economically important family of Fagaceae