Location of miRNAs in the genome
To identify the location of the closest genomic feature to each miRNA, the miRDeep2 output was compared to the annotated features in theP. napi genome using the closest command in BEDTools (Quinlan & Hall, 2010). While the chromosome-level genome used for this project was produced by the Darwin Tree of Life (Lohse et al., 2021), an independent functional annotation was used (Steward, Pruisscher, Roberts, & Wheat, in review ), as the first-generation annotation for this genome had numerous overlapping coding regions and UTRs of predicted genes. The miRNAs inside the coding sequence (CDS) region of a gene were identified as either being in an intron or exon, while miRNAs outside of a CDS region were identified as either closest to a start or stop codon. The identifies miRNA origins were used for subsequent analyses, such as assessing the functional annotations and gene ontology (GO) terms identified for the coding genes nearest miRNA loci.