Comparative Genomic and Transcriptomic Characterization of the Toxigenic Marine Dinoflagellate Alexandrium ostenfeldii

Many dinoflagellate species are notorious for the toxins they produce and ecological and human health consequences associated with harmful algal blooms (HABs). Dinoflagellates are particularly refractory to genomic analysis due to the enormous genome size, lack of knowledge about their DNA composition and structure, and peculiarities of gene regulation, such as spliced leader (SL) trans-splicing and mRNA transposition mechanisms. Alexandrium ostenfeldii is known to produce macrocyclic imine toxins, described as spirolides. We characterized the genome of A. ostenfeldii using a combination of transcriptomic data and random genomic clones for comparison with other dinoflagellates, particularly Alexandrium species. Examination of SL sequences revealed similar features as in other dinoflagellates, including Alexandrium species. SL sequences in decay indicate frequent retro-transposition of mRNA species. This probably contributes to overall genome complexity by generating additional gene copies. Sequencing of several thousand fosmid and bacterial artificial chromosome (BAC) ends yielded a wealth of simple repeats and tandemly repeated longer sequence stretches which we estimated to comprise more than half of the whole genome. Surprisingly, the repeats comprise a very limited set of 79–97 bp sequences; in part the genome is thus a relatively uniform sequence space interrupted by coding sequences. Our genomic sequence survey (GSS) represents the largest genomic data set of a dinoflagellate to date. Alexandrium ostenfeldii is a typical dinoflagellate with respect to its transcriptome and mRNA transposition but demonstrates Alexandrium-like stop codon usage. The large portion of repetitive sequences and the organization within the genome is in agreement with several other studies on dinoflagellates using different approaches. It remains to be determined whether this unusual composition is directly correlated to the exceptionally genome organization of dinoflagellates with a low amount of histones and histone-like proteins

A review of the dinoflagellates and their evolution from fossils to modern

Molecular clock and biogeochemical evidence indicate that the dinoflagellate lineage diverged at around 650 Ma. Unequivocal dinoflagellate cysts/zygotes appeared during the Triassic. These biotas were badly affected by the end-Triassic extinction and recovery from this was relatively slow. During the early Middle Jurassic, the family Gonyaulacaceae underwent an explosive diversification event and taxonomic richness steadily increased throughout the rest of the Jurassic. The entire Cretaceous also recorded increases in diversity. This trend reversed during the Oligocene, probably caused by global cooling. Marine cyst-forming peridiniaceans declined substantially through the Oligocene and Neogene, but protoperidiniaceans continued to diversify. Modern taxa, as evidenced by the molecular tree, comprise three major clades: the first two are composed largely of parasitic forms, marine alveolates of unknown identity and the Syndiniales; free-living dinoflagellates form the third clade, which diverges rapidly and bears short branch lengths with no real support for branching order. This suggests that morphological divergence preceded molecular divergence because, as the fossil record indicates, major groups appeared at different ages. Unique features of the dinoflagellates helped the group take on a predominant role in the marine phytoplankton. Living in marine or fresh water, dinoflagellates have demonstrated innovative capacities that have enabled them to live among the phytoplankton or benthos as autotrophic, heterotrophic, mixotrophic free-living organisms or symbiotic and/or as parasitic forms

Osmium ammine: review of current applications to visualize DNA in electron microscopy.

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