BACKGROUND: The Synurophyceae is one of most important photosynthetic stramenopile algal lineages in freshwater ecosystems. They are characterized by siliceous scales covering the cell or colony surface and possess plastids of red-algal secondary or tertiary endosymbiotic origin. Despite their ecological and evolutionary significance, the relationships amongst extant Synurophyceae are unclear, as is their relationship to most other stramenopiles. RESULTS: Here we report a comparative analysis of plastid genomes sequenced from five representative synurophycean algae. Most of these plastid genomes are highly conserved with respect to genome structure and coding capacity, with the exception of gene re-arrangements and partial duplications at the boundary of the inverted repeat and single-copy regions. Several lineage-specific gene loss/gain events and intron insertions were detected (e.g., cemA, dnaB, syfB, and trnL). CONCLUSIONS: Unexpectedly, the cemA gene of Synurophyceae shows a strong relationship with sequences from members of the green-algal lineage, suggesting the occurrence of a lateral gene transfer event. Using a molecular clock approach based on silica fossil record data, we infer the timing of genome re-arrangement and gene gain/loss events in the plastid genomes of Synurophyceae.

Department of Biochemistry and Molecular Biology Dalhousie University Halifax Nova Scotia B3H 4R2 Canada

Department of Biological Sciences Sungkyunkwan University Suwon 16419 South Korea

Department of Biology Chungnam National University Daejeon 34134 South Korea

Department of Botany Faculty of Science Charles University Benátská 2 CZ 12800 Prague 2 Czech Republic

Department of General Education Hongik University Seoul 04066 South Korea

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