Characterization of the Small RNA Transcriptome of the Diatom, Thalassiosira pseudonana

This study presents the first characterization of endogenous small RNAs in a diatom, Thalassiosira pseudonana.  Small RNAs play important roles in regulating gene expression at multiple levels over a wide variety of biological functions. Diatoms are unicellular photosynthetic phytoplankton, responsible for 20% of global carbon fixation.  Diatoms are also model organisms for the development of algal biofuels and silica-based nanotechnology. Small RNA cDNA libraries were constructed for exponentially growing T. pseudonana, and then subjected to highly parallel pyrosequencing (454) and sequencing-by-ligation (Applied Biosystems SOLiD). From the computational analysis of approximately 300,000 sequences in the 454 library and over 17 million sequences in the SOLiD libraries, there exists evidence of a core set of small RNA genes including novel microRNAs, repeat-associated short interfering RNAs, and endogenous short interfering RNAs. Possible gene targets for the putative microRNAs were also predicted, whose binding properties in the coding section of the genes, rather than in the 3’UTR, suggest plant-like gene regulation.  The diatom genome contains additional elements similar to plant small RNA systems, such as the RNAi machinery, and a high percentage of short interfering RNAs originating from protein-coding genes. The techniques implemented in this study can be applied to the large datasets produced from next generation sequencing of small RNA cDNA libraries from other organisms.  Additionally, because of the evolutionary history of diatoms, this study has significance for comparative surveys of small RNAs with numerous unicellular and multicellular organisms.