Diatoms are important planktons that are believed to be responsible for one-fifth of the primary productivity on Earth [1, 2]. There are two major classes of diatoms, the pennates and the centrics. With their vital role in silica cycling [3, 4], the unusual evolutionary position of secondary endosymbiotic origin [5–9], the presence of C4 photosynthesis in some species , and potential as sources of biodiesel fuel , diatoms have attracted increasing attention. As early as 2002, Scala et al.  analyzed EST (expression sequence tag) data of the pennate diatom Phaeodactylum tricornutum and found that some of its genes were more similar to those of animals than of photosynthetic counterparts, implying an unusual evolutionary history. The genome of P. tricornutum and the centric diatom Thalassiosira pseudonana have been sequenced, shedding light on significant features of diatom genomes, including the mosaic genome that contains 'animal-like', 'plant-like' and 'bacteria-like' genes, performing fatty acid metabolism in both peroxisomes and mitochondria, and the presence of enzymes necessary for a complete urea cycle [7, 13, 14]. These characteristics prompted us to hypothesize that the gene expression regulators (e.g. miRNAs) of diatoms may show some different specificity to other photosynthetic organisms.
miRNAs are important post-transcriptional regulators. They regulate gene expression in eukaryotes by targeting mRNAs for translational repression or cleavage [15–17]. It is believed that miRNAs exist extensively in eukaryotes such as animals and plants with high conservation in each kingdom [18, 19]. The expression of miRNAs has a spatio-temporal pattern [15, 17, 20–22] and they influence the transcription and translation of many genes . Generally, their functions involve various processes, including developmental patterning, organ separation, cell differentiation and proliferation, tumor generation, cell death and cell apoptosis, stress resistance, auxin response, fat metabolism and miRNA biogenesis . In higher plants and animals, miRNAs have been extensively studied but rarely so in algae.
P. tricornutum is an atypical diatom with a weakly silicified outer shell, and the unusual property of being pleiomorphic with three convertible morphotypes  (i.e. oval, fusiform and triradiate), and silicification essentially restricted to one valve of the oval cells [24–28]. With its characteristics of short life-cycle, small genome size and ease of transformation, P. tricornutum has become an attractive photosynthetic model [12, 14, 29, 30]. Additionally, being rich in polyunsaturated fatty acid (PUFA), especially in eicosapentaenoic acid (EPA), P. tricornutum has been used as a food organism and is considered a potential source of EPA. There have been many studies investigating the factors affecting its cell composition [31–34]. There were reports that microalgae accumulated lipids under nitrogen-limited as well as silicon-limited conditions [35, 36], with similar studies conducted on P. tricornutum [33, 34]. Accumulation of lipids in cells and a significant change in fatty acid composition were observed in P. tricornutum under low nitrogen conditions. Using suppression subtractive hybridization technology, Tang et al. separated a number of upregulated genes from P. tricornutum under nitrogen starvation, seven of which had high similarity with functional genes related to nitrogen utilization . Studies of lipid metabolism of P. tricornutum under silicon-limited conditions are scarce. Notwithstanding, Sapriel et al. identified 223 genes regulated by silicic acid availability, including 13 upregulated and 210 downregulated genes, from P. tricornutum under silicon-limited conditions . Interestingly, they also observed some upregulated genes coding for transporters of metabolites related to nitrogen assimilation and transfer from P. tricornutum in the complete medium compared to silicon-limited conditions. A previous study on T. pseudonana showed that a glutamate acetyltransferase was involved in silicon metabolism . How are these genes regulated? Do miRNAs play a role in P. tricornutum nitrogen and silicon metabolism? There have been few studies that address these questions.
In the present study, we constructed small RNA (sRNA) libraries from P. tricornutum under normal, nitrogen-limited and silicon-limited conditions and then used high-throughput Solexa technology to deeply sequence the sRNAs. The sequencing data were analyzed and miRNAs were identified from all samples studied.