GSE110494
Identification and comprehensive analysis of microRNAs and phased small interfering RNAs in Rosa rugosa Thunb [degradome]
MicroRNAs (miRNAs) are small non-coding RNAs that regulate target mRNAs by inducing degradation or preventing translation of their target mRNAs. Rose, Rosa rugosa Thunb., is an important ornamental and edible plant, yet there are only a few studies on the miRNAs of rose. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in rose by analyzing 10 small RNA profiles from roots, petals, pollens, stamens, and leaves. To identify the targets of miRNAs and phasiRNAs, we generated a degradome profile for rose leaf which is analyzed using the SeqTar algorithm. This study identified 25 conserved pre-miRNAs, of which 24 have not been reported previously. We also found 22 novel pre-miRNAs. Three hundred and thirty nine 21 nucleotide (nt) PHAS loci, and forty nine 24 nt PHAS loci were also identified. We identified more than 4000 putative targets of the conserved miRNAs using a criteria of less than 4 mismatches between miRNA and targets. Among these targets, at least 171 have shown significant accumulation of degradome reads. Our results demonstrate that the miR482 family triggers the generations of phasiRNAs by targeting nucleotide-binding, leucine-rich repeat (NB-LRR) disease resistance genes in rose. These results significantly enhanced our knowledge of the miRNAs and phasiRNAs, as well as their potential functions in rose. Overall design: Identification and comprehensive analysis of conserved microRNAs, phased small interfering RNAs and their targets in rose using Illumina HiSeq 2000 sequencer.