Abstract
BackgroundPeridinin-containing dinoflagellates have a highly reduced chloroplast genome, which is unlike that found in other chloroplast containing organisms. Genome reduction appears to be the result of extensive transfer of genes to the nuclear genome. Unusually the genes believed to be remaining in the chloroplast genome are found on small DNA 'minicircles'. In this study we present a comparison of sets of minicircle sequences from three dinoflagellate species.ResultsPCR 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.ConclusionComparative 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.
Highlights
Peridinin-containing dinoflagellates have a highly reduced chloroplast genome, which is unlike that found in other chloroplast containing organisms
PCR amplification of A. carterae minicircles A DNA fraction from A. carterae which had been previously shown to be enriched in minicircles was used as a template for PCR [3]
Fragments of the A. carterae genes for psbB, petD and atpB were initially obtained by PCR using degenerate primers based on the corresponding translated gene sequences from A. operculatum and 'universal' primers to the core region (Table 1)
Summary
Peridinin-containing dinoflagellates have a highly reduced chloroplast genome, which is unlike that found in other chloroplast containing organisms. The genes believed to be remaining in the chloroplast genome are found on small DNA 'minicircles'. The genome is unusual in that the remaining chloroplast genes are confined to small circular DNA molecules (minicircles) of between 2–10 kb ( larger molecules have been reported in some species [11]), rather than a single large circularly mapping molecule [12]. A report from one species indicates a possible location of minicircles in the nuclear compartment [4] This contradiction is not yet resolved, and it remains possible that different dinoflagellate species have circular DNA molecules present in different compartments
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