Category: Dinoflagellate genomics

Jul 07

Heat Shock Protein 70 and 90 Genes in the Harmful Dinoflagellate Cochlodinium polykrikoides: Genomic Structures and Transcriptional Responses to Environmental Stresses.

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Heat Shock Protein 70 and 90 Genes in the Harmful Dinoflagellate Cochlodinium polykrikoides: Genomic Structures and Transcriptional Responses to Environmental Stresses.
Int J Genomics. 2015;2015:484626

Jul 07

Eye-like ocelloids are built from different endosymbiotically acquired components.

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Eye-like ocelloids are built from different endosymbiotically acquired components.
Nature. 2015 Jul 1;
Authors: Gavelis GS, Hayakawa S, White Iii RA, Gojobori T, Suttle CA, Keeling PJ, Leander BS

Jul 07

Culture-Independent Study of the Late-Stage of a Bloom of the Toxic Dinoflagellate Ostreopsis cf. ovata: Preliminary Findings Suggest Genetic Differences at the Sub-Species Level and Allow ITS2 Structure Characterization.

Culture-Independent Study of the Late-Stage of a Bloom of the Toxic Dinoflagellate Ostreopsis cf. ovata: Preliminary Findings Suggest Genetic Differences at the Sub-Species Level and Allow ITS2 Structure Characterization.
T…

May 21

Paralytic shellfish toxin content is related to genomic sxtA4 copy number in Alexandrium minutum strains.

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Paralytic shellfish toxin content is related to genomic sxtA4 copy number in Alexandrium minutum strains.

Front Microbiol. 2015;6:404

Authors: Stüken A, Riobó P, Franco J, Jakobsen KS, Guillou L, Figueroa RI

Abstract
Dinoflagellates are microscopic aquatic eukaryotes with huge genomes and an unusual cell regulation. For example, most genes are present in numerous copies and all copies seem to be obligatorily transcribed. The consequence of the gene copy number (CPN) for final protein synthesis is, however, not clear. One such gene is sxtA, the starting gene of paralytic shellfish toxin (PST) synthesis. PSTs are small neurotoxic compounds that can accumulate in the food chain and cause serious poisoning incidences when ingested. They are produced by dinoflagellates of the genera Alexandrium, Gymnodium, and Pyrodinium. Here we investigated if the genomic CPN of sxtA4 is related to PST content in Alexandrium minutum cells. SxtA4 is the 4th domain of the sxtA gene and its presence is essential for PST synthesis in dinoflagellates. We used PST and genome size measurements as well as quantitative PCR to analyze sxtA4 CPN and toxin content in 15 A. minutum strains. Our results show a strong positive correlation between the sxtA4 CPN and the total amount of PST produced in actively growing A. minutum cells. This correlation was independent of the toxin profile produced, as long as the strain contained the genomic domains sxtA1 and sxtA4.

PMID: 25983733 [PubMed]

May 14

Dinoflagellate Gene Structure and Intron Splice Sites in a Genomic Tandem Array.

Dinoflagellate Gene Structure and Intron Splice Sites in a Genomic Tandem Array.
J Eukaryot Microbiol. 2015 May 12;
Authors: Mendez GS, Delwiche CF, Apt KE, Lippmeier JC
Abstract
Dinoflagellates are…

Apr 23

Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate.

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Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate.
Proc Natl Acad Sci U S A. 2015 Apr 20;
Authors: Gornik SG, Febrimarsa, Cassin AM, MacRae JI, Ramaprasad A, …

Apr 20

Intra-genomic variation in symbiotic dinoflagellates: recent divergence or recombination between lineages?

Intra-genomic variation in symbiotic dinoflagellates: recent divergence or recombination between lineages?

BMC Evol Biol. 2015;15(1):46

Authors: Wilkinson SP, Fisher PL, van Oppen MJ, Davy SK

Abstract
BACKGROUND: The symbiosis between corals and the dinoflagellate alga Symbiodinium is essential for the development and survival of coral reefs. Yet this fragile association is highly vulnerable to environmental disturbance. A coral’s ability to tolerate temperature stress depends on the fitness of its resident symbionts, whose thermal optima vary extensively between lineages. However, the in hospite population genetic structure of Symbiodinium is poorly understood and mostly based on analysis of bulk DNA extracted from thousands to millions of cells. Using quantitative single-cell PCR, we enumerated DNA polymorphisms in the symbionts of the reef-building coral Pocillopora damicornis, and applied a model selection approach to explore the potential for recombination between coexisting Symbiodinium populations.
RESULTS: Two distinct Symbiodinium ITS2 sequences (denoted C100 and C109) were retrieved from all P. damicornis colonies analysed. However, the symbiont assemblage consisted of three distinct Symbiodinium populations: cells featuring pure arrays of ITS2 type C109, near-homogeneous cells of type C100 (with trace ITS2 copies of type C109), and those with co-dominant C100 and C109 ITS2 repeats. The symbiont consortia of some colonies consisted almost entirely of these putative C100 × C109 recombinants.
CONCLUSIONS: Our results are consistent with the occurrence of sexual recombination between Symbiodinium types C100 and C109. While the multiple-copy nature of the ITS2 dictates that the observed pattern of intra-genomic co-dominance may be a result of incomplete concerted evolution of intra-genomic polymorphisms, this is a less likely explanation given the occurrence of homogeneous cells of the C109 type. Conclusive evidence for inter-lineage recombination and introgression in this genus will require either direct observational evidence or a single-cell genotyping approach targeting multiple, single-copy loci.

PMID: 25887753 [PubMed – as supplied by publisher]

Apr 05

Plastid genome-based phylogeny pinpointed the origin of the green-colored plastid in the dinoflagellate Lepidodinium chlorophorum.

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Plastid genome-based phylogeny pinpointed the origin of the green-colored plastid in the dinoflagellate Lepidodinium chlorophorum.
Genome Biol Evol. 2015 Apr 2;
Authors: Kamikawa R, Tanifuji G, Kawa…

Mar 19

Intra-genomic variation in symbiotic dinoflagellates: recent divergence or recombination between lineages?

Related Articles

Intra-genomic variation in symbiotic dinoflagellates: recent divergence or recombination between lineages?

BMC Evol Biol. 2015 Dec;15(1):325

Authors: Wilkinson SP, Fisher PL, van Oppen MJ, Davy SK

Abstract
BACKGROUND: The symbiosis between corals and the dinoflagellate alga Symbiodinium is essential for the development and survival of coral reefs. Yet this fragile association is highly vulnerable to environmental disturbance. A coral’s ability to tolerate temperature stress depends on the fitness of its resident symbionts, whose thermal optima vary extensively between lineages. However, the in hospite population genetic structure of Symbiodinium is poorly understood and mostly based on analysis of bulk DNA extracted from thousands to millions of cells. Using quantitative single-cell PCR, we enumerated DNA polymorphisms in the symbionts of the reef-building coral Pocillopora damicornis, and applied a model selection approach to explore the potential for recombination between coexisting Symbiodinium populations.
RESULTS: Two distinct Symbiodinium ITS2 sequences (denoted C100 and C109) were retrieved from all P. damicornis colonies analysed. However, the symbiont assemblage consisted of three distinct Symbiodinium populations: cells featuring pure arrays of ITS2 type C109, near-homogeneous cells of type C100 (with trace ITS2 copies of type C109), and those with co-dominant C100 and C109 ITS2 repeats. The symbiont consortia of some colonies consisted almost entirely of these putative C100 × C109 recombinants.
CONCLUSIONS: Our results are consistent with the occurrence of sexual recombination between Symbiodinium types C100 and C109. While the multiple-copy nature of the ITS2 dictates that the observed pattern of intra-genomic co-dominance may be a result of incomplete concerted evolution of intra-genomic polymorphisms, this is a less likely explanation given the occurrence of homogeneous cells of the C109 type. Conclusive evidence for inter-lineage recombination and introgression in this genus will require either direct observational evidence or a single-cell genotyping approach targeting multiple, single-copy loci.

PMID: 25776334 [PubMed – in process]

Mar 11

Phylogenomic analysis of Emiliania huxleyi provides evidence for haptophyte-stramenopile association and a chimeric haptophyte nuclear genome.

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Phylogenomic analysis of Emiliania huxleyi provides evidence for haptophyte-stramenopile association and a chimeric haptophyte nuclear genome.
Mar Genomics. 2015 Mar 4;
Authors: Miller JJ, Delwiche …