Discovery and Transcriptional Dynamics of Small Noncoding RNAs in Source, Transport and Woody Sink Tissues in Eucalyptus grandis

Rapid progress is being made in understanding the transcriptional networks and interactions governing xylogenesis and the regulation of lignocellulosic biopolymer synthesis in plants. Despite this, much is still unknown regarding the small noncoding RNAs (sRNAs) that regulate gene expression through complementary sequence targeting, RNA degradation and epigenetic modifications. miRNAs are a well known category of sRNA species, and several highly conserved miRNAs are known to play essential roles in vascular tissue differentiation. The small interfering RNAs (siRNAs) are another more complex and diverse, yet highly pervasive sRNA type in plant genomes, and may indeed contribute significantly to species-specific biology. Here, we report on the discovery and quantification of a comprehensive catalog of Eucalyptus grandis sRNAs – including miRNAs and siRNAs – in leaves, secondary phloem and immature xylem, representing major points in carbon sequestration, transport and utilization for lignocellulosic biomass, respectively. Expression analysis of these sRNAs has revealed tissue- specific clusters occuring in vascular and leaf tissue (including high-confidence examples of known miRNA:target interactions). Target prediction and gene set enrichment analysis revealed new regulatory interactions in the xylogenesis transcriptome. In parallel, long noncoding RNA (lncRNA) discovery and expression analysis is being performed to gain insight into potential competition and sequestration of these sRNA species. These putative competitive endogenous (ce)RNAs, their diversity and regulatory functions in xylogenesis remain largely unexplored. This work will allow revision of the multidimensional transcriptional modules underlying xylogenesis in Eucalyptus, and may provide insights necessary for the genetic improvement of wood production in this lignocellulosic biomass crop.