A comprehensive resource for studying microRNA evolution and microRNA-mediated development and whole-body regeneration in the acoel worm Hofstenia miamia

The acoel worm Hofstenia miamia (H. miamia) has recently emerged as a model organism for studying whole-body regeneration and embryonic development, providing an opportunity to probe post-transcriptional mechanisms in both processes in the same organism. Here, we establish a resource for studying H. miamia microRNA-mediated gene regulation, a major aspect of post-transcriptional control in animals. We generated a PacBio long-read sequencing-based genome assembly. We developed a stringent microRNA annotation framework for H. miamia using small RNA-sequencing samples spanning key developmental stages. Our analysis uncovered 545 microRNA loci, including 154 highest-confidence loci based on structural features, expression levels, and prediction quality metrics. Comparison of microRNA seed sequences with those in other bilaterian species revealed that H. miamia encodes many known conserved bilaterian microRNA families and that several microRNA families previously reported only in protostomes or deuterostomes likely have ancient bilaterian origins. We profiled and characterized the expression dynamics and strand preference of microRNAs in H. miamia embryonic and post-embryonic development. An intron that is spliced in the primary transcript of co-transcribed let-7 and mir-125 microRNAs. To generate hypotheses for microRNA function, we annotated the 3 UTRs of H. miamia protein-coding genes and performed microRNA target site predictions. Focusing on genes that are known to function in the wound response, posterior patterning, and neural differentiation in H. miamia, we found that these processes may be under substantial microRNA regulation. Notably, we found that microRNAs in MIR-7 and MIR-9 families, which have target sites in the posterior genes fz-1, wnt-3, and sp5 are indeed expressed in the anterior of the animal, consistent with an anterior-biased repressive effect on their corresponding target genes. Our annotation provides a resource for future studies of post-transcriptional regulation of gene expression during development and regeneration.