Developmental small RNA transcriptomics reveals divergent evolution of the conserved microRNA miR-100 and the let-7-complex in nematodes

Abstract

Background Over the last three decades, small RNAs have emerged as one of the key post-transcriptional regulators, and are categorised into microRNAs (miRNAs), small interfering RNAs (siRNAs), and PIWI-interacting RNAs (piRNAs). Since their discovery as regulators of developmental timing in the nematode Caenorhabditis elegans, some miRNAs have been found to be highly conserved throughout animal evolution. miR-100 is one such highly conserved miRNA, possibly predating the origin of bilaterians. Furthermore, mir-100 is a member of the conserved let-7-complex, a locus containing three conserved miRNA-coding genes (mir-100, let-7, and mir-125/lin-4) that does not exist in the same arrangement in C. elegans. Results We performed small RNA sequencing across four developmental time-points in the satellite nematode Pristionchus pacificus, identifying 64 novel and ontogenically specifically expressed miRNAs. We also identified miR-100 as the most abundant miRNA in post-embryonic juvenile stages. Additionally, P. pacificus exhibited a novel constellation of the let-7-complex, wherein mir-100 is closely linked to let-7, but without mir-125/lin-4 in the same locus. Mutants of mir-100 and let-7, individually as well as simultaneously, resulted in viable but developmentally defective worms, showing misregulation in collagen and astacin gene families. Interestingly, lin-4 mutants a delayed but otherwise normal development. Conclusion This study provides the first developmental small RNA transcriptome of P. pacificus, providing a community resource for future evo-devo studies. Furthermore, we identify miR-100 as the most abundant ontogenically-specific miRNA, which, along with let-7, regulates normal development in P. pacificus. Lastly, we observe two alternative arrangements of the highly conserved miRNA locus let-7-complex.