Category: Dinoflagellate genomics

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…

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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, …

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]

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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…

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]

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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 …

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Diversification of the Light-Harvesting Complex Gene Family via Intra- and Intergenic Duplications in the Coral Symbiotic Alga Symbiodinium.
PLoS One. 2015;10(3):e0119406
Authors: Maruyama S, Shogu…

Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives.

Proc Natl Acad Sci U S A. 2015 Feb 25;

Authors: Janouškovec J, Tikhonenkov DV, Burki F, Howe AT, Kolísko M, Mylnikov AP, Keeling PJ

Abstract
Apicomplexans are a major lineage of parasites, including causative agents of malaria and toxoplasmosis. How such highly adapted parasites evolved from free-living ancestors is poorly understood, particularly because they contain nonphotosynthetic plastids with which they have a complex metabolic dependency. Here, we examine the origin of apicomplexan parasitism by resolving the evolutionary distribution of several key characteristics in their closest free-living relatives, photosynthetic chromerids and predatory colpodellids. Using environmental sequence data, we describe the diversity of these apicomplexan-related lineages and select five species that represent this diversity for transcriptome sequencing. Phylogenomic analysis recovered a monophyletic lineage of chromerids and colpodellids as the sister group to apicomplexans, and a complex distribution of retention versus loss for photosynthesis, plastid genomes, and plastid organelles. Reconstructing the evolution of all plastid and cytosolic metabolic pathways related to apicomplexan plastid function revealed an ancient dependency on plastid isoprenoid biosynthesis, predating the divergence of apicomplexan and dinoflagellates. Similarly, plastid genome retention is strongly linked to the retention of two genes in the plastid genome, sufB and clpC, altogether suggesting a relatively simple model for plastid retention and loss. Lastly, we examine the broader distribution of a suite of molecular characteristics previously linked to the origins of apicomplexan parasitism and find that virtually all are present in their free-living relatives. The emergence of parasitism may not be driven by acquisition of novel components, but rather by loss and modification of the existing, conserved traits.

PMID: 25717057 [PubMed – as supplied by publisher]

Metagenomic characterisation of viral communities in corals: Mining biological signal from methodological noise.
Environ Microbiol. 2015 Feb 24;
Authors: Wood-Charlson EM, Weynberg KD, Suttle CA, Roux S, van Oppen…

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Metagenomic characterisation of viral communities in corals: Mining biological signal from methodological noise.
Environ Microbiol Rep. 2015 Feb 13;
Authors: Wood-Charlson EM, Weynberg KD, Suttle CA…