Genome-Wide Identification and Comprehensive Analysis of Conserved MicroRNAs and Phased small Interfering RNAs in Watermelon [degradome]. Citrullus lanatus

MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwide. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in watermelon by analyzing 14 small RNA profiles from roots, leaves, androecium, flowers, and fruits, and one published small RNA profile of mixed tissues. To identify the targets of miRNAs and phasiRNAs, we generated a degradome profile for watermelon leaf which is analyzed with the SeqTar algorithm. We identified 97 conserved pre-miRNAs, of which 58 have not been reported previously and 348 conserved mature miRNAs without precursors. We also found 9 novel pre-miRNAs encoding 18 mature miRNAs. One hundred and one 21 nucleotide (nt) PHAS loci, and two hundred and forty one 24 nt PHAS loci were also identified. We identified 120 conserved targets of the conserved miRNAs and TAS3-derived tasiRNAs by analyzing a degradome profile of watermelon leaf. The presented results provide a comprehensive view of small regulatory RNAs and their targets in watermelon. Overall design: Identification and comprehensive analysis of conserved microRNAs and phased small interfering RNAs in watermelon or whole plant using Illumina HiSeq 2000 sequencer.