Epigenomic maps of the rainbow trout reveal epiQTL signatures of genetic selection and regulatory elements involved in controlling gene expression and genome evolution
Over the last century, rainbow trout (RBT) has been widely used as a biological model in many biological disciplines and has become one of the best-studied fish.  For example, RBT is an excellent model to study gene evolution as it is a partially tetraploid organism that underwent a whole-genome duplication (salmonid-specific 4th WGD) followed by a partial re-diploidization and significant genome rearrangements.  In the meantime, RBT domestication spread quickly and globally to six continents for aquaculture and recreation. Efforts to sequence a pangenome reference have begun, and genome sequence is available for at least three rainbow trout clonal lines.  However, epigenome reference annotations are needed to understand the functional genomic basis of RBT's phenotypic, environmental, and evolutional variations. This study provides a comprehensive catalog and epigenome annotation tracks of the rainbow trout.  Gene regulatory elements, including chromatin histone modifications, chromatin accessibility, and DNA methylation, were identified by integrating data from ChIP-seq, ATAC-seq, and Methyl Mini-seq across RBT tissues together with RNA-seq gene expression data sets. Overall design: Two biological replicates for six tissues (Brain, Intestine, Kidney, Liver, Spleen, and White muscle) were used for ChIP-Seq (H3K4me3, H3K4me1, H3K27ac, H3K27me3, input control) Two biological replicates for six tissues (Brain, Intestine, Kidney, Liver, Spleen, and White muscle) were used for Bisulfite Methylation and Three tissue with two bioloical replicates (Brain, Liver, and Spleen) used for ATAC seq.