Here, we studied the evolutionary histories of three major classes of small non protein-coding Rnon protein-coding nucleaRNAsAs (sncRNAs, small nuclearaRNAsAsnRNAsRNAsmallnucleolareRNAsAsnoRNAss)—in Candorhabditransfertodes.
Three major classes of small regulatory RNAs are microRNAs (miRNAs), endogenous small interfering RNAs, and Piwi-interacting RNAs (piRNAs) (Liu and Paroo 2010).
MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are two major classes of small RNAs.
The international efforts of the tammar wallaby genome project have provided the opportunity to survey the major classes of small RNAs in this Australian marsupial model.
The two major classes of small nucleolar RNA (snoRNA), H/ACA and C/D, guide the pseudouridylation and 2′- O-methylation of rRNA, respectively (Kiss, 2002).
Using next generation sequencing, we have characterized the major classes of small RNAs, micro (mi) RNAs, piwi interacting (pi) RNAs, and the centromere repeat associated short interacting (crasi) RNAs in the tammar.
While the three major classes of small RNAs (siRNAs, miRNAs and piRNAs) and variants within each class (e.g. endo-siRNAs), have been well studied in various model systems, a fourth major class, crasiRNAs, was first identified in the tammar [ 15].
This study encompasses the first analyses of the major classes of small RNAs for the newly completed tammar genome, validates preliminary annotations using deep sequencing and computational approaches, and provides a foundation for future work on tammar-specific as well as conserved, but previously unknown small RNA progenitors and targets identified herein.
In eukaryotic cells, two major classes of small nucleolar ncRNA (snoRNA) have been identified: C/D box snoRNAs, which are involved in the 20-O-methylation of ribosomal, spliceosomal, and transfer RNAs (the latter in Archaea only), and H/ACA snoRNAs, which guide pseudouridylation in these RNA species [ 29, 30].
