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Background  Most microbial eukaryotes are uncultivated and thus poorly suited to standard genomic techniques. This is the case for  Polykrikos lebouriae , a dinoflagellate with ultrastructurally aberrant plastids. It has been suggested that these plastids stem from a novel symbiosis with either a diatom or haptophyte, but this hypothesis has been difficult to test as  P. lebouriae  dwells in marine sand rife with potential genetic contaminants.    Results  We applied spliced-leader targeted PCR (SLPCR) to obtain dinoflagellate-specific transcriptomes on single-cell isolates of  P. lebouriae  from marine sediments.  Polykrikos lebouriae  expressed nuclear-encoded photosynthetic genes that were characteristic of the peridinin-plastids of dinoflagellates, rather than those from a diatom of haptophyte. We confirmed these findings at the genomic level using multiple displacement amplification (MDA) to obtain a partial plastome of  P. lebouriae .    Conclusion  From these data, we infer that  P. lebouriae  has retained the peridinin plastids ancestral for dinoflagellates as a whole, while its closest relatives have lost photosynthesis multiple times independently. We discuss these losses with reference to mixotrophy in polykrikoid dinoflagellates. Our findings demonstrate new levels of variation associated with the peridinin plastids of dinoflagellates and the usefulness of SLPCR approaches on single cell isolates. Unlike other transcriptomic methods, SLPCR has taxonomic specificity, and can in principle be adapted to different splice-leader bearing groups.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1636-8) contains supplementary material, which is available to authorized users.

Single-cell transcriptomics using spliced leader PCR: Evidence for multiple losses of photosynthesis in polykrikoid dinoflagellates