Abstract
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.
Highlights
Dinoflagellates are important marine primary producers and contribute significantly to the functioning of marine food webs
Yang et al [34] found putative different splice variants in about 3% of the contigs of an EST library of A. minutum. Another reason for the high number of unique sequences comes from the general trend of dinoflagellate genes to form large families
Several other dinoflagellate EST projects showed similar library complexity, including those that were the source of EST data used for the comparison of Alexandrium species (e.g. [34,35,36,37])
Summary
Dinoflagellates are important marine primary producers and contribute significantly to the functioning of marine food webs. Many dinoflagellates are a rich source of marine toxins and can form dense aggregations of cells known as harmful algal blooms (HABs). These dinoflagellates and their toxins pose a threat for fish, wildlife, and to humans via consumption of contaminated seafood or direct exposure to HABs, in coastal regions throughout the world. In recent decades the frequency and expansion of toxic Alexandrium blooms and related toxic events has increased, as have HABs in general, possibly due to increased scientific awareness of toxic species and their effects, as well as to shifts in environmental regimes associated with climate change, cultural eutrophication, transport of resting cysts either in ship’s ballast water or by movement of shellfish stocks from one area to another [3,4]
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