Genome-Wide Discovery of Non-Coding RNAs in Willow (Salix purpurea)

Non-coding RNA (ncRNA) genes encode RNA molecules with various functions rather than translating into proteins. The newly-sequenced genome of willow (Salix purpurea), an important bioenergy crop, provides a foundation for genome-wide discovery of ncRNA in this species. Through computational analysis of the genome sequence, we identified a total of 194 ncRNA families containing 2,068 genes in willow. Furthermore, we evaluated the predicted ncRNAs using RNA-Seq analysis. Approximately 34% of the predicted ncRNAs were confirmed by sequencing of libraries enriched with small RNAs (20 - 200nt). Specifically, small RNA-enriched libraries were constructed from seven different tissue types including shoot tip, phloem, xylem, young leaf, young stem, mature leaf and root. We mapped the RNA-Seq reads to the willow genome and identified a total of 2,756 transcripts with expression level of RPKM>=35. More than 95% of the 2,756 transcripts were less than 200nt in length. Majority of the small RNAs revealed by RNA-Seq were novel, not captured by the current genome annotation. Our quantitative analysis of small RNA expression profiles identified four ncRNA expression clusters that showed preferential expressions in young leaves, xylem, phloem and mature leaves, respectively. The biological roles of these tissue specific ncRNAs were explored using bioinformatics approach. The results from this research increase our understanding of ncRNAs in willow.