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Letter

Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa

¹ Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada; ² University of Washington, Department of Genome Sciences, Seattle, Washington 98195-5065, USA; ³ Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby V5A 1S6, Canada; ⁴ Department of Biochemistry, University of Alberta, Edmonton T6G 2H7, Canada; ⁵ Washington University School of Medicine, Genome Sequencing Center, St. Louis, Missouri 63108, USA; ⁶ Department of Computing Science, Simon Fraser University, Burnaby V5A 1S6, Canada

The diversity of microRNAs and small-interfering RNAs has been extensively explored within angiosperms by focusing on a few key organisms such as Oryza sativa and Arabidopsis thaliana. A deeper division of the plants is defined by the radiation of the angiosperms and gymnosperms, with the latter comprising the commercially important conifers. The conifers are expected to provide important information regarding the evolution of highly conserved small regulatory RNAs. Deep sequencing provides the means to characterize and quantitatively profile small RNAs in understudied organisms such as these. Pyrosequencing of small RNAs from O. sativa revealed, as expected, 21- and 24-nt RNAs. The former contained known microRNAs, and the latter largely comprised intergenic-derived sequences likely representing heterochromatin siRNAs. In contrast, sequences from Pinus contorta were dominated by 21-nt small RNAs. Using a novel sequence-based clustering algorithm, we identified sequences belonging to 18 highly conserved microRNA families in P. contorta as well as numerous clusters of conserved small RNAs of unknown function. Using multiple methods, including expressed sequence folding and machine learning algorithms, we found a further 53 candidate novel microRNA families, 51 appearing specific to the P. contorta library. In addition, alignment of small RNA sequences to the O. sativa genome revealed six perfectly conserved classes of small RNA that included chloroplast transcripts and specific types of genomic repeats. The conservation of microRNAs and other small RNAs between the conifers and the angiosperms indicates that important RNA silencing processes were highly developed in the earliest spermatophytes. Genomic mapping of all sequences to the O. sativa genome can be viewed at http://microrna.bcgsc.ca/cgi-bin/gbrowse/rice_build_3/.

E-mail punrau{at}sfu.ca; fax (778) 782-5583.

[Supplemental material is available online at www.genome.org.]

Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.6897308.

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