Comparative analysis of dinoflagellate chloroplast genomes reveals rRNA and tRNA genes

PCR was used to amplify several minicircles from Amphidinium carterae so that a homologous set of gene-containing minicircles was available for Amphidinium carterae and Amphidinium operculatum, two apparently closely related peridinin-containing dinoflagellates. We compared the sequences of these minicircles to determine the content and characteristics of their chloroplast genomes. We also made comparisons with minicircles which had been obtained from Heterocapsa triquetra, another peridinin-containing dinoflagellate. These in silico comparisons have revealed several genetic features which were not apparent in single species analyses. The features include further protein coding genes, unusual rRNA genes, which we show are transcribed, and the first examples of tRNA genes from peridinin-containing dinoflagellate chloroplast genomes.Comparative analysis of minicircle sequences has allowed us to identify previously unrecognised features of dinoflagellate chloroplast genomes, including additional protein and RNA genes. The chloroplast rRNA gene sequences are radically different from those in other organisms, and in many ways resemble the rRNA genes found in some highly reduced mitochondrial genomes. The retention of certain tRNA genes in the dinoflagellate chloroplast genome has important implications for models of chloroplast-mitochondrion interaction.The organisation of the chloroplast genome in many peridinin-containing dinoflagellates has been shown to be very unusual [1-5]. A massive reduction in the gene content of the organelle genome is observed in these organisms relative to all other photosynthetic chloroplasts [6]. EST data from a number of dinoflagellate species suggest that many genes that are typically located within the chloroplast genome have been transferred to the nuclear genome [7-10]. Furthermore, the genome is unusual in that the remaining chloroplast genes are confined to small circular DNA molecules (minicircles) of between 2–10 kb (although large