Dinoflagellate plastid genes are believed to be encoded on small generally unigenic plasmid-like minicircles. The minicircle gene complement has reached saturation with an incomplete set of plastid genes (18) compared with typical functional plastids (60-200). While some of the missing plastid genes have recently been found in the nucleus, it is still unknown if additional genes, not located on minicircles, might also contribute to the plastid genome. Sequencing of tailed RNA showed that transcripts derived from the known minicircle genes psbA and atpB contained a homogenous 3' polyuridine tract of 25-40 residues. This unusual modification suggested that random sequencing of a poly(dA) primed cDNA library could be used to characterize the plastid transcriptome. We have recovered only 12 different polyuridylylated transcripts from our library, all of which are encoded on minicircles in several dinoflagellate species. The correspondence of all polyuridylylated transcripts with previously described minicircle genes thus supports the dinoflagellate plastid as harbouring the smallest genome of any functional chloroplast. Interestingly, northern blots indicate that the majority of transcripts are modified, suggesting that polyuridylylation is unlikely to act as a degradation signal as do the heterogeneous poly(A)-rich extensions of transcripts in cyanobacteria and other plastids.