Recently discovered miRNA (microribonucleic acids) are a kind of endogenous small RNA that have important regulatory roles during eukaryote development and stress responses by controlling mRNA
degradation or inhibiting translation. However, little is known about miRNA from commercially important woody oil crops. Using a comparative genomics approach and following a series of stringent filtering criteria, we identified 36 woody oil crop miRNA belonging to 22 families using expressed sequence tags and genome survey sequence databases. The numbers of miRNA found in walnut (Juglans regia), oil palm (Elaeis guineensis), tea (Camellia sinensis), tung oil tree (Vernicia fordii) and barbados nut (Jatropha curcas) were 17, 11, 3, 3 and 2, respectively. In addition, 275 potential target genes were predicted for 27 newly identified miRNA utilising mRNA databases of J. curcas, E. guineensis, C. sinensis, J. regia, V. fordii and Olea europaea plant species. Most of the target mRNA encoded transcription factors that regulated plant growth and development, together with a few target genes that were involved in metabolism or stress responses. Sequence alignments of 10 miRNA families from different species showed that miRNA sequences within the same family were variable. Furthermore, the authenticity of 11 novel miRNA candidates from oil palm was verified by semi-quantitative and quantitative reverse transcription-polymerase chain reaction (RT-PCR). A correlation analysis revealed a close correlation between the two PCR assay methods. The expression levels of miRNA transcripts significantly differed between the leaf and the fruit tissues of E. guineensis.