Category: Dinoflagellate genomics

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Applications of next-generation sequencing to unravelling the evolutionary history of algae.
Int J Syst Evol Microbiol. 2014 Feb;64(Pt 2):333-45
Authors: Kim KM, Park JH, Bhattacharya D, Yoon HS
Abstr…

Horizontal gene transfer and redundancy of tryptophan biosynthetic enzymes in dinotoms.
Genome Biol Evol. 2014 Jan 21;
Authors: Imanian B, Keeling PJ
Abstract
A tertiary endosymbiosis between a dinoflagellate…

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Transcriptome de novo assembly sequencing and analysis of the toxic dinoflagellate Alexandrium catenella using the Illumina platform.
Gene. 2014 Jan 15;
Authors: Zhang S, Sui Z, Chang L, Kang K, Ma J, Kong F…

Acyl-homoserine lactone quorum sensing in the roseobacter clade.
Int J Mol Sci. 2014;15(1):654-69
Authors: Zan J, Liu Y, Fuqua C, Hill RT
Abstract
Members of the Roseobacter clade are ecologically important a…

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Extensive Differences in Gene Expression between Symbiotic and Aposymbiotic Cnidarians.
G3 (Bethesda). 2013 Dec 24;
Authors: Lehnert EM, Mouchka ME, Burriesci MS, Gallo ND, Schwarz JA, Pringle JR
Abs…

Colponemids Represent Multiple Ancient Alveolate Lineages.

Curr Biol. 2013 Dec 3;

Authors: Janouškovec J, Tikhonenkov DV, Mikhailov KV, Simdyanov TG, Aleoshin VV, Mylnikov AP, Keeling PJ

Abstract
The alveolates comprise three well-studied protist lineages of significant environmental, medical, and economical importance: apicomplexans (e.g., Plasmodium), dinoflagellates (e.g., Symbiodinium), and ciliates (e.g., Tetrahymena). These major lineages have evolved distinct and unusual characteristics, the origins of which have proved to be difficult evolutionary puzzles. Mitochondrial genomes are a prime example: all three groups depart from canonical form and content, but in different ways. Reconstructing such ancient transitions is difficult without deep-branching lineages that retain ancestral characteristics. Here we describe two such lineages and how they illuminate the ancestral state of alveolate mitochondrial genomes. We established five clonal cultures of colponemids, predatory alveolates without cultured representatives and molecular data. Colponemids represent at least two independent lineages at the phylum level in multilocus phylogenetic analysis; one sister to apicomplexans and dinoflagellates, and the other at a deeper position. A genome survey from one strain showed that ancestral state of the mitochondrial genomes in the three major alveolate lineages consisted of an unusual linear chromosome with telomeres and a substantially larger gene set than known alveolates. Colponemid sequences also identified several environmental lineages as colponemids, altogether suggesting an untapped potential for understanding the origin and evolution of apicomplexans, dinoflagellates, and ciliates.

PMID: 24316202 [PubMed – as supplied by publisher]

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The Chloroplast Genome of a Symbiodinium sp. Clade C3 Isolate.
Protist. 2013 Oct 17;165(1):1-13
Authors: Barbrook AC, Voolstra CR, Howe CJ
Abstract
Dinoflagellate algae of the genus Symbiodini…

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Endosymbiotic gene transfer in tertiary plastid-containing dinoflagellates.
Eukaryot Cell. 2013 Dec 2;
Authors: Burki F, Imanian B, Hehenberger E, Hirakawa Y, Maruyama S, Keeling PJ
Abstract
P…

Horizontal Gene Transfer is a Significant Driver of Gene Innovation in Dinoflagellates.
Genome Biol Evol. 2013 Nov 19;
Authors: Wisecaver JH, Brosnahan ML, Hackett JD
Abstract
The dinoflagellates are an evolu…

The case of horizontal gene transfer from bacteria to the peculiar dinoflagellate plastid genome.

Mob Genet Elements. 2013 Jul 1;3(4):e25845

Authors: Mackiewicz P, Bodył A, Moszczyński K

Abstract
Organelle genomes lose their genes by transfer to host nuclear genomes, but only occasionally are enriched by foreign genes from other sources. In contrast to mitochondria, plastid genomes are especially resistant to such horizontal gene transfer (HGT), and thus every gene acquired in this way is notable. An exceptional case of HGT was recently recognized in the peculiar peridinin plastid genome of dinoflagellates, which is organized in plasmid-like minicircles. Genomic and phylogenetic analyses of Ceratium horridum and Pyrocystis lunula minicircles revealed four genes and one unannotated open reading frame that probably were gained from bacteria belonging to the Bacteroidetes. Such bacteria seem to be a good source of genes because close endosymbiotic associations between them and dinoflagellates have been observed. The HGT-acquired genes are involved in plastid functions characteristic of other photosynthetic eukaryotes, and their arrangement resembles bacterial operons. These studies indicate that the peridinin plastid genome, usually regarded as having resulted from reduction and fragmentation of a typical plastid genome derived from red algae, may have a chimeric origin that includes bacterial contributions. Potential contamination of the Ceratium and Pyrocystis plastid genomes by bacterial sequences and the controversial localization of their minicircles in the nucleus are also discussed.

PMID: 24195014 [PubMed – as supplied by publisher]