The medium-size noncoding RNA transcriptome of , the smallest living eukaryote, reveals a large family of small nucleolar RNAs displaying multiple genomic expression strategies.

The small nucleolar RNAs (snoRNAs), essential for ribosome biogenesis, constitute a major family of medium-size noncoding RNAs (mncRNAs) in all eukaryotes. We present here, for the first time in a marine unicellular alga, the characterization of the snoRNAs family in , the smallest photosynthetic eukaryote. Using a transcriptomic approach, we identified 131 snoRNAs (Ot-snoRNA) distributed in three classes: the C/D snoRNAs, the H/ACA snoRNAs and the MRP RNA. Their genomic organization revealed a unique combination of both the intronic organization of animals and the polycistronic organization of plants. Remarkably, clustered genes produced Ot-snoRNAs with unusual structures never previously described in plants. Their abundances, based on quantification of reads and northern blots, showed extreme differences in Ot-snoRNA accumulation, mainly determined by their differential stability. Most of these Ot-snoRNAs were predicted to target rRNAs or snRNAs. Seventeen others were orphan Ot-snoRNAs that would not target rRNA. These were specific to or Mamiellophyceae and could have functions unrelated to ribosome biogenesis. Overall, these data reveal an 'evolutionary response' adapted to the extreme compactness of the genome that accommodates the essential Ot-snoRNAs, developing multiple strategies to optimize their coordinated expression with a minimal cost on regulatory circuits.