PRJNA186507
Panagrellus redivivus Small RNA-Seq data (the microworm)
Panagrellus redivivus is a free-living nematode that has been used as a model system for understanding evolution of developmental and behavioral processes, and is often compared to its well studied relative Caenorhabditis elegans. Here we report the de novo sequencing of the miRNAome of P. redivivus. RNA seq analysis of mixed stage whole animal cultures revealed 248 micro RNA hairpins of which 63 have close homologs in other species including lin-4 (4.9 % of miRNA reads), miR-1 (2.1%) and let-7 (0.5%). The 248 mature miRNAs belong to 171 different miRNA seed families, of which 89 (52%) are conserved. 42 miRNA precursors are organized to form 14 miRNA clusters, which include two or three miRNA hairpins each, and 23 miRNA sequences have more than one possible origin in the genome. These data suggest high conservation of miRNA structures across diverse species and provide insight into the transcriptional regulation of a non-parasitic gonochoristic nematode. Overall design: Small RNAs were isolated from mixed cultures of P. redivivus using miRVana kit (Ambion) according to the manufacturer’s instructions. A small RNA library was then produced from the isolated RNAs using NEBNext small RNA sample prep Set 1 (New England Biolabs). The library was then size selected on a 6% PAGE gel with the cut band corresponding to ~90-120 bp. Library quality and size was confirmed prior to sequencing on a Bioanalyzer (Agilent).