Category: Dinoflagellate genomics

Sep 01

Paralytic shellfish toxin biosynthesis in cyanobacteria and dinoflagellates: a molecular overview.

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Paralytic shellfish toxin biosynthesis in cyanobacteria and dinoflagellates: a molecular overview.
J Proteomics. 2015 Aug 24;
Authors: Wang DZ, Zhang SF, Zhang Y, Lin L
Abstract
Para…

Aug 07

Heterologous DNA Uptake in Cultured Symbiodinium spp. Aided by Agrobacterium tumefaciens.

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Heterologous DNA Uptake in Cultured Symbiodinium spp. Aided by Agrobacterium tumefaciens.

PLoS One. 2015;10(7):e0132693

Authors: Ortiz-Matamoros MF, Islas-Flores T, Voigt B, Menzel D, Baluška F, Villanueva MA

Abstract
Plant-targeted pCB302 plasmids containing sequences encoding gfp fusions with a microtubule-binding domain; gfp with the fimbrin actin-binding domain 2; and gfp with AtRACK1C from Arabidopsis thaliana, all harbored in Agrobacterium tumefaciens, were used to assay heterologous expression on three different clades of the photosynthetic dinoflagellate, Symbiodinium. Accessibility to the resistant cell wall and through the plasma membrane of these dinoflagellates was gained after brief but vigorous shaking in the presence of glass beads and polyethylene glycol. A resistance gene to the herbicide Basta allowed appropriate selection of the cells expressing the hybrid proteins, which showed a characteristic green fluorescence, although they appeared to lose their photosynthetic pigments and did not further divide. Cell GFP expression frequency measured as green fluorescence emission yielded 839 per every 106 cells for Symbiodinium kawagutii, followed by 640 and 460 per every 106 cells for Symbiodinium microadriaticum and Symbiodinium sp. Mf11, respectively. Genomic PCR with specific primers amplified the AtRACK1C and gfp sequences after selection in all clades, thus revealing their presence in the cells. RT-PCR from RNA of S. kawagutii co-incubated with A. tumefaciens harboring each of the three vectors with their respective constructs, amplified products corresponding to the heterologous gfp sequence while no products were obtained from three distinct negative controls. The reported procedure shows that mild abrasion followed by co-incubation with A. tumefaciens harboring heterologous plasmids with CaMV35S and nos promoters can lead to expression of the encoded proteins into the Symbiodinium cells in culture. Despite the obvious drawbacks of the procedure, this is an important first step towards a stable transformation of Symbiodinium.

PMID: 26167858 [PubMed – in process]

Aug 07

Single-cell transcriptomics using spliced leader PCR: Evidence for multiple losses of photosynthesis in polykrikoid dinoflagellates.

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Single-cell transcriptomics using spliced leader PCR: Evidence for multiple losses of photosynthesis in polykrikoid dinoflagellates.
BMC Genomics. 2015;16:528
Authors: Gavelis GS, White RA, Suttle…

Aug 07

The large mitochondrial genome of Symbiodinium minutum reveals conserved non-coding sequences between dinoflagellates and apicomplexans.

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The large mitochondrial genome of Symbiodinium minutum reveals conserved non-coding sequences between dinoflagellates and apicomplexans.
Genome Biol Evol. 2015 Jul 20;
Authors: Shoguchi E, Shinzato …

Aug 07

Genome sequence of the Roseovarius mucosus type strain (DSM 17069(T)), a bacteriochlorophyll a-containing representative of the marine Roseobacter group isolated from the dinoflagellate Alexandrium ostenfeldii.

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Genome sequence of the Roseovarius mucosus type strain (DSM 17069(T)), a bacteriochlorophyll a-containing representative of the marine Roseobacter group isolated from the dinoflagellate Alexandrium ostenfeldii.

Stand Genomic Sci. 2015;10:17

Authors: Riedel T, Spring S, Fiebig A, Scheuner C, Petersen J, Göker M, Klenk HP

Abstract
Roseovarius mucosus Biebl et al. 2005 is a bacteriochlorophyll a-producing representative of the marine Roseobacter group within the alphaproteobacterial family Rhodobacteraceae, which was isolated from the dinoflagellate Alexandrium ostenfeldii. The marine Roseobacter group was found to be abundant in the ocean and plays an important role for global and biogeochemical processes. Here we describe the features of the R. mucosus strain DFL-24(T) together with its genome sequence and annotation generated from a culture of DSM 17069(T). The 4,247,724 bp containing genome sequence encodes 4,194 protein-coding genes and 57 RNA genes. In addition to the presence of four plasmids, genome analysis revealed the presence of genes associated with host colonization, DMSP utilization, cytotoxins, and quorum sensing that could play a role in the interrelationship of R. mucosus with the dinoflagellate A. ostenfeldii and other marine organisms. Furthermore, the genome encodes genes associated with mixotrophic growth, where both reduced inorganic compounds for lithotrophic growth and a photoheterotrophic lifestyle using light as additional energy source could be used.

PMID: 26203330 [PubMed]

Jul 07

Ancient origin of the biosynthesis of lignin precursors.

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Ancient origin of the biosynthesis of lignin precursors.
Biol Direct. 2015;10:23
Authors: Labeeuw L, Martone PT, Boucher Y, Case RJ
Abstract
BACKGROUND: Lignin plays an important r…

Jul 07

Integration of plastids with their hosts: Lessons learned from dinoflagellates.

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Integration of plastids with their hosts: Lessons learned from dinoflagellates.
Proc Natl Acad Sci U S A. 2015 May 20;
Authors: Dorrell RG, Howe CJ
Abstract
After their endosymbiotic…

Jul 07

Sterol Composition and Biosynthetic Genes of Vitrella brassicaformis, A Recently Discovered Chromerid: Comparison to Chromera velia and Phylogenetic Relationship to Apicomplexan Parasites.

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Sterol Composition and Biosynthetic Genes of Vitrella brassicaformis, A Recently Discovered Chromerid: Comparison to Chromera velia and Phylogenetic Relationship to Apicomplexan Parasites.

J Eukaryot Microbiol. 2015 May 20;

Authors: Khadka M, Salem M, Leblond JD

Abstract
Vitrella brassicaformis is the second discovered species in the Chromerida, and first in the family Vitrellaceae. Chromera velia, the first discovered species, forms an independent photosynthetic lineage with V. brassicaformis, and both are closely related to peridinin-containing dinoflagellates and non-photosynthetic apicomplexans; both also show phylogenetic closeness with red algal plastids.. We have utilized gas chromatography/mass spectrometry (GC/MS) to identify two free sterols, 24-ethylcholest-5-en-3β-ol, and a minor unknown sterol which appeared to be a C28:4 compound. We have also used RNA Seq analysis to identify seven genes found in the non-mevalonate/methylerythritol pathway (MEP) for sterol biosynthesis. Subsequent genome analysis of V. brassicaformis showed the presence of two mevalonate (MVA) pathway genes, though the genes were not observed in the transcriptome analysis. Transcripts from four genes (dxr, ispf, ispd, and idi) were selected and translated into proteins to study the phylogenetic relationship of sterol biosynthesis in V. brassicaformis and C. velia to other groups of algae and apicomplexans. Based on our genomic and transcriptomic analyses, we hypothesize that the MEP pathway was the primary pathway that apicomplexans used for sterol biosynthesis before they lost their sterol biosynthesis ability, although contribution of the MVA pathway cannot be discounted. This article is protected by copyright. All rights reserved.

PMID: 25996517 [PubMed – as supplied by publisher]

Jul 07

The Plastid Genome of the Cryptomonad Teleaulax amphioxeia.

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The Plastid Genome of the Cryptomonad Teleaulax amphioxeia.
PLoS One. 2015;10(6):e0129284
Authors: Kim JI, Yoon HS, Yi G, Kim HS, Yih W, Shin W
Abstract
Teleaulax amphioxeia is a p…

Jul 07

Polyketide synthesis genes associated with toxin production in two species of Gambierdiscus (Dinophyceae).

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Polyketide synthesis genes associated with toxin production in two species of Gambierdiscus (Dinophyceae).

BMC Genomics. 2015;16:410

Authors: Kohli GS, John U, Figueroa RI, Rhodes LL, Harwood DT, Groth M, Bolch CJ, Murray SA

Abstract
BACKGROUND: Marine microbial protists, in particular, dinoflagellates, produce polyketide toxins with ecosystem-wide and human health impacts. Species of Gambierdiscus produce the polyether ladder compounds ciguatoxins and maitotoxins, which can lead to ciguatera fish poisoning, a serious human illness associated with reef fish consumption. Genes associated with the biosynthesis of polyether ladder compounds are yet to be elucidated, however, stable isotope feeding studies of such compounds consistently support their polyketide origin indicating that polyketide synthases are involved in their biosynthesis.
RESULTS: Here, we report the toxicity, genome size, gene content and transcriptome of Gambierdiscus australes and G. belizeanus. G. australes produced maitotoxin-1 and maitotoxin-3, while G. belizeanus produced maitotoxin-3, for which cell extracts were toxic to mice by IP injection (LD50 = 3.8 mg kg(-1)). The gene catalogues comprised 83,353 and 84,870 unique contigs, with genome sizes of 32.5 ± 3.7 Gbp and 35 ± 0.88 Gbp, respectively, and are amongst the most comprehensive yet reported from a dinoflagellate. We found three hundred and six genes involved in polyketide biosynthesis, including one hundred and ninty-two ketoacyl synthase transcripts, which formed five unique phylogenetic clusters.
CONCLUSIONS: Two clusters were unique to these maitotoxin-producing dinoflagellate species, suggesting that they may be associated with maitotoxin biosynthesis. This work represents a significant step forward in our understanding of the genetic basis of polyketide production in dinoflagellates, in particular, species responsible for ciguatera fish poisoning.

PMID: 26016672 [PubMed – in process]