title: Comparative genomic and transcriptomic characterization of the toxigenic marine dinoflagellate Alexandrium ostenfeldii.
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.
authors.affiliation: Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany. Nina.Jaeckisch@awi.de
authors.forename: Nina
authors.initials: N
authors.lastname: Jaeckisch
authors.forename: Ines
authors.initials: I
authors.lastname: Yang
authors.forename: Sylke
authors.initials: S
authors.lastname: Wohlrab
authors.forename: Gernot
authors.initials: G
authors.lastname: Glöckner
authors.forename: Juergen
authors.initials: J
authors.lastname: Kroymann
authors.forename: Heiko
authors.initials: H
authors.lastname: Vogel
authors.forename: Allan
authors.initials: A
authors.lastname: Cembella
authors.forename: Uwe
authors.initials: U
authors.lastname: John
mesh_terms: D000595:Amino Acid Sequence; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D018388:Codon, Terminator; D020451:Contig Mapping / Q000379:methods; D004247:DNA / Q000235:genetics; D004251:DNA Transposable Elements; D018076:DNA, Complementary / Q000378:metabolism; D004141:Dinoflagellida / Q000235:genetics* / Q000502:physiology*; D020224:Expressed Sequence Tags; D015723:Gene Library; D016678:Genome; D023281:Genomics; D006657:Histones / Q000737:chemistry; D008969:Molecular Sequence Data; D012333:RNA, Messenger / Q000378:metabolism; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D014158:Transcription, Genetic
chemical_list: D018388:Codon, Terminator; D004251:DNA Transposable Elements; D018076:DNA, Complementary; D006657:Histones; D012333:RNA, Messenger; D004247:DNA