Interspecific discovery and expression profiling of Eucalyptus micro RNAs by deep sequencing

Background Micro RNAs (miRNAs) are a class of small (~21 nucleotide) non-coding RNAs that recently gained much attention due to their perceived role as master regulators of gene expression in Eukaryotes, responsible for fine tuning gene expression regulation and, in plants, has been shown to be involved in a diverse range of biological processes such as plant development and architecture, flowering, cell differentiation and response to biotic and abiotic stresses [1]. The repertoire of expressed miRNAs differs among cell types, tissues, development, environmental condition, etc [2]. Notwithstanding, the exact function of thousands miRNAs sequences present in miRBase [http://www.mirbase.org/] is not elucidated. At this point, discovery and profiling of new and conserved miRNAs are critical in the attempt to understand their function and mechanism. Deep sequencing through next generation sequencing is the methodology of choice for this purpose as its ultra high throughput permits a comprehensive interrogation of the small RNA transcriptome, permitting de novo identification and relative quantification of different small RNA species [3]. Due to its economic importance the Eucalyptus grandis genome has been sequenced by JGI and the annotation of miRNAs is pivotal. In order to provide the first large scale experimental characterization of Eucalyptus miRNAs we performed an Illumina deep sequencing run that allowed us to discover and quantify the miRNA levels in two different tissues – xylem and leaves. Additionally, to get insights of the observed phenotypic differences in wood quality among Eucalyptus species, we characterized the xylem small RNA transcriptome of two different E. globulus individuals and integrated the results to catalog conserved and Eucalyptus specific miRNA gene families.