Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 16 (1), 27

Transcriptomic Characterisation and Genomic Glimps Into the Toxigenic Dinoflagellate Azadinium Spinosum, With Emphasis on Polykeitde Synthase Genes


Transcriptomic Characterisation and Genomic Glimps Into the Toxigenic Dinoflagellate Azadinium Spinosum, With Emphasis on Polykeitde Synthase Genes

Jan M Meyer et al. BMC Genomics.


Background: Unicellular dinoflagellates are an important group of primary producers within the marine plankton community. Many of these species are capable of forming harmful algae blooms (HABs) and of producing potent phycotoxins, thereby causing deleterious impacts on their environment and posing a threat to human health. The recently discovered toxigenic dinoflagellate Azadinium spinosum is known to produce azaspiracid toxins. These toxins are most likely produced by polyketide synthases (PKS). Recently, PKS I-like transcripts have been identified in a number of dinoflagellate species. Despite the global distribution of A. spinosum, little is known about molecular features. In this study, we investigate the genomic and transcriptomic features of A. spinosum with a focus on polyketide synthesis and PKS evolution.

Results: We identify orphan and homologous genes by comparing the transcriptome data of A. spinosum with a diverse set of 18 other dinoflagellates, five further species out of the Rhizaria Alveolate Stramelopile (RAS)-group, and one representative from the Plantae. The number of orphan genes in the analysed dinoflagellate species averaged 27%. In contrast, within the A. spinosum transcriptome, we discovered 12,661 orphan transcripts (18%). The dinoflagellates toxins known as azaspiracids (AZAs) are structurally polyethers; we therefore analyse the transcriptome of A. spinosum with respect to polyketide synthases (PKSs), the primary biosynthetic enzymes in polyketide synthesis. We find all the genes thought to be potentially essential for polyketide toxin synthesis to be expressed in A. spinosum, whose PKS transcripts fall into the dinoflagellate sub-clade in PKS evolution.

Conclusions: Overall, we demonstrate that the number of orphan genes in the A. spinosum genome is relatively small compared to other dinoflagellate species. In addition, all PKS domains needed to produce the azaspiracid carbon backbone are present in A. spinosum. Our study underscores the extraordinary evolution of such gene clusters and, in particular, supports the proposed structural and functional paradigm for PKS Type I genes in dinoflagellates.


Figure 1
Figure 1
The 20 most abundant protein domains in the Azadinium spinosum transcriptome. Black bars denote the number of proteins with a certain domain. Black and grey bars together indicate the total number of proteins for the first n domains. The subset and order of domains was iteratively chosen to maximize the total number of proteins (black plus grey bars) for the first n domains. The 20 most abundant domains make up 28% of the total proteome (28,357) that could be matched to the PFAM database (e-value 0.001).
Figure 2
Figure 2
Transcriptomic data reveals proteins conserved between different dinoflagellates and outgroup species. Comparison between 19 dinoflagellate species including A. spinosum, three diatoms, the haptophyte Emiliania huxleyi, and the cryptomonad Guillardia theta. The size of the pie charts is proportional to the number of sequences analysed. The colour code indicates the hierarchical classification into homology groups defined by descending evolutionary distance, e.g., if a sequence had BLAST hits in the outgroup species Chlamydomonas reinhardtii, it was classified as “homologues in outgroup” irrespective of potential homologues inside the phylum. The schematic phylogeny to the left of the figure represents the relationship between the species analysed. Details about origin and number of sequences analysed can be found in Additional file 3: Table S1.
Figure 3
Figure 3
Amino acids of the ketoacyl synthase (KS) active site motif conserved throughout different evolutionary sub-groups. The analysis focuses on the protistan Type I PKS in chlorophytes, haptophytes, Apicomplexa and dinoflagellates. The height of the sequence logo given below the alignment represents the degree of conservation. The asterisks indicate the conserved amino acids required for catalytic activity, which are present in all A. spinosum sequences (AS3D901-06) except the probably incomplete AS3D905 sequence.
Figure 4
Figure 4
Phylogeny and multiple alignment of the truncated conserved N-terminal region of the dinoflagellate KS. (A) Maximum likelihood dendrogram of the N-terminus computed with 1,000 bootstrap replicates. Bootstrap support is indicated on the dendrogram branches; (B) Multiple alignment of the conserved N-terminal region. The height of the sequence logo shows the degree of conservation. Each line of the alignment corresponds to the dinoflagellate strain shown in the dendrogram. Outgroup sequences are not shown because they are lacking the N-terminal motif.
Figure 5
Figure 5
Phylogenetic tree of Type I and Type II KS domains from prokaryotic and eukaryotic PKS and fatty acid synthase (FAS). Type I and Type II KS domains from 60 taxa analysed by maximum likelihood approach. Type II PKS and acyl carrier protein synthases (ACPS) were assigned as outgroups. Approximate likelihood fraction (aLRT) and bootstrap values (BT) ≥ 50% are displayed on appropriate branches as aLRT/BT. (A) The dinoflagellate KS sequences form a well-supported group within the protistan Type I FAS/PKS clade, consistent with previous topology estimates; (B) The dinoflagellate KS group splits into two distinct clades; one contains sequences from different species, the other clade consists exclusively of K. brevis sequences.

Similar articles

See all similar articles

Cited by 16 articles

See all "Cited by" articles


    1. Hallegraeff GM. A review of harmful algal blooms and their apparent global increase. Phycologia. 1993;32:79–99. doi: 10.2216/i0031-8884-32-2-79.1. - DOI
    1. Harper JT, Waanders E, Keeling PJ. On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes. Int J Syst Evol Micr. 2005;55:487–96. doi: 10.1099/ijs.0.63216-0. - DOI - PubMed
    1. Moreno-Diaz-de-la-Espina S, Alverca E, Cuadrado A, Franca S. Organization of the genome and gene expression in a nuclear environment lacking histons and nucleosomes: the amazing dinoflagellates. Eur J Cell Biol. 2005;84:137–49. doi: 10.1016/j.ejcb.2005.01.002. - DOI - PubMed
    1. Lowe CD, Mello LV, Samatar N, Martin LE, Montagnes DJS. The transcriptome of the novel dinoflagellate Oxyrrhis marina (Alveolata: Dinophyceae): response to salinity examined by 454 sequencing. BMC genomics. 2011;12:519. doi: 10.1186/1471-2164-12-519. - DOI - PMC - PubMed
    1. Jaeckisch N, Yang I, Wohlrab S, Gloeckner G, Kroymann J, Vogel H, et al. Comparative genomic and transcriptomic characterization of the toxigenic marine dinoflagellate Alexandrium ostenfeldii. PLoS ONE. 2011;6:e28012. doi: 10.1371/journal.pone.0028012. - DOI - PMC - PubMed

Publication types