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Open Access Research article

The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum

Alessandra Rogato123, Hugues Richard12*, Alexis Sarazin4, Björn Voss5, Soizic Cheminant Navarro12, Raphaël Champeimont12, Lionel Navarro6, Alessandra Carbone127, Wolfgang R Hess5 and Angela Falciatore12*

Author Affiliations

1 Sorbonne Universités, UPMC Univ Paris 06, UMR 7238, Laboratory of Computational and Quantitative Biology, F-75006 Paris, France

2 CNRS UMR7238, LCQB, F-75006 Paris, France

3 Institute of Biosciences and Bioresources, CNR, Naples, Italy

4 Swiss Federal Institute of Technology Zürich (ETH-Z), Department of Biology, Zürich, Switzerland

5 Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany

6 Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique UMR8197, Institut National de la Santé et de la Recherche Médicale, U1024 Paris, France

7 Institut Universitaire de France, Paris, France

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BMC Genomics 2014, 15:698  doi:10.1186/1471-2164-15-698

Published: 20 August 2014

Abstract

Background

Marine diatoms constitute a major component of eukaryotic phytoplankton and stand at the crossroads of several evolutionary lineages. These microalgae possess peculiar genomic features and novel combinations of genes acquired from bacterial, animal and plant ancestors. Furthermore, they display both DNA methylation and gene silencing activities. Yet, the biogenesis and regulatory function of small RNAs (sRNAs) remain ill defined in diatoms.

Results

Here we report the first comprehensive characterization of the sRNA landscape and its correlation with genomic and epigenomic information in Phaeodactylum tricornutum. The majority of sRNAs is 25 to 30 nt-long and maps to repetitive and silenced Transposable Elements marked by DNA methylation. A subset of this population also targets DNA methylated protein-coding genes, suggesting that gene body methylation might be sRNA-driven in diatoms. Remarkably, 25-30 nt sRNAs display a well-defined and unprecedented 180 nt-long periodic distribution at several highly methylated regions that awaits characterization. While canonical miRNAs are not detectable, other 21-25 nt sRNAs of unknown origin are highly expressed. Besides, non-coding RNAs with well-described function, namely tRNAs and U2 snRNA, constitute a major source of 21-25 nt sRNAs and likely play important roles under stressful environmental conditions.

Conclusions

P. tricornutum has evolved diversified sRNA pathways, likely implicated in the regulation of largely still uncharacterized genetic and epigenetic processes. These results uncover an unexpected complexity of diatom sRNA population and previously unappreciated features, providing new insights into the diversification of sRNA-based processes in eukaryotes.

Keywords:
Diatoms; Phaeodactylum tricornutum; Small RNAs; tRNAs; U2 snRNA; Transposable Elements; DNA methylation; Periodic small RNAs distribution