Tag: genomes

Jan 21

Unique nucleocytoplasmic dsDNA and +ssRNA viruses are associated with the dinoflagellate endosymbionts of corals.

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Unique nucleocytoplasmic dsDNA and +ssRNA viruses are associated with the dinoflagellate endosymbionts of corals.

ISME J. 2013 Jan;7(1):13-27

Authors: Correa AM, Welsh RM, Vega Thurber RL

Abstract
The residence of dinoflagellate algae (genus: Symbiodinium) within scleractinian corals is critical to the construction and persistence of tropical reefs. In recent decades, however, acute and chronic environmental stressors have frequently destabilized this symbiosis, ultimately leading to coral mortality and reef decline. Viral infection has been suggested as a trigger of coral-Symbiodinium dissociation; knowledge of the diversity and hosts of coral-associated viruses is critical to evaluating this hypothesis. Here, we present the first genomic evidence of viruses associated with Symbiodinium, based on the presence of transcribed +ss (single-stranded) RNA and ds (double-stranded) DNA virus-like genes in complementary DNA viromes of the coral Montastraea cavernosa and expressed sequence tag (EST) libraries generated from Symbiodinium cultures. The M. cavernosa viromes contained divergent viral sequences similar to the major capsid protein of the dinoflagellate-infecting +ssRNA Heterocapsa circularisquama virus, suggesting a highly novel dinornavirus could infect Symbiodinium. Further, similarities to dsDNA viruses dominated (∼69%) eukaryotic viral similarities in the M. cavernosa viromes. Transcripts highly similar to eukaryotic algae-infecting phycodnaviruses were identified in the viromes, and homologs to these sequences were found in two independently generated Symbiodinium EST libraries. Phylogenetic reconstructions substantiate that these transcripts are undescribed and distinct members of the nucleocytoplasmic large DNA virus (NCLDVs) group. Based on a preponderance of evidence, we infer that the novel NCLDVs and RNA virus described here are associated with the algal endosymbionts of corals. If such viruses disrupt Symbiodinium, they are likely to impact the flexibility and/or stability of coral-algal symbioses, and thus long-term reef health and resilience.

PMID: 22791238 [PubMed – in process]

Jan 21

The repertoire of chemical defense genes in the coral Acropora digitifera genome.

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The repertoire of chemical defense genes in the coral Acropora digitifera genome.
Zoolog Sci. 2012 Aug;29(8):510-7
Authors: Shinzato C, Hamada M, Shoguchi E, Kawashima T, Satoh N
Abstract
Scle…

Jan 21

Tertiary endosymbiosis in two dinotoms has generated little change in the mitochondrial genomes of their dinoflagellate hosts and diatom endosymbionts.

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Tertiary endosymbiosis in two dinotoms has generated little change in the mitochondrial genomes of their dinoflagellate hosts and diatom endosymbionts.
PLoS One. 2012;7(8):e43763
Authors: Imanian B, Pombert…

Jan 21

Study of cnidarian-algal symbiosis in the "omics" age.

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Study of cnidarian-algal symbiosis in the “omics” age.
Biol Bull. 2012 Aug;223(1):44-65
Authors: Meyer E, Weis VM
Abstract
The symbiotic associations between cnidarians and dinoflagellate alg…

Jan 21

The Complex NOD-Like Receptor Repertoire of the Coral Acropora digitifera Includes Novel Domain Combinations.

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The Complex NOD-Like Receptor Repertoire of the Coral Acropora digitifera Includes Novel Domain Combinations.

Mol Biol Evol. 2013 Jan;30(1):167-76

Authors: Hamada M, Shoguchi E, Shinzato C, Kawashima T, Miller DJ, Satoh N

Abstract
Innate immunity in corals is of special interest not only in the context of self-defense but also in relation to the establishment and collapse of their obligate symbiosis with dinoflagellates of the genus Symbiodinium. In innate immunity system of vertebrates, approximately 20 tripartite nucleotide oligomerization domain (NOD)-like receptor proteins that are defined by the presence of a NAIP, CIIA, HET-E and TP1 (NACHT) domain, a C-terminal leucine-rich repeat (LRR) domain, and one of three types of N-terminal effector domain, are known to function as the primary intracellular pattern recognition molecules. Surveying the coral genome revealed not only a larger number of NACHT- and related domain nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 (NB-ARC)-encoding loci (∼500) than in other metazoans but also surprising diversity of domain combinations among the coral NACHT/NB-ARC-containing proteins; N-terminal effector domains included the apoptosis-related domains caspase recruitment domain (CARD), death effector domain (DED), and Death, and C-terminal repeat domains included LRRs, tetratricopeptide repeats, ankyrin repeats, and WD40 repeats. Many of the predicted coral proteins that contain a NACHT/NB-ARC domain also contain a glycosyl transferase group 1 domain, a novel domain combination first found in metazoans. Phylogenetic analyses suggest that the NACHT/NB-ARC domain inventories of various metazoan lineages, including corals, are largely products of lineage-specific expansions. Many of the NACHT/NB-ARC loci are organized in pairs or triplets in the Acropora genome, suggesting that the large coral NACHT/NB-ARC repertoire has been generated at least in part by tandem duplication. In addition, shuffling of N-terminal effector domains may have occurred after expansions of specific NACHT/NB-ARC-repeat domain types. These results illustrate the extraordinary complexity of the innate immune repertoire of corals, which may in part reflect adaptive evolution to a symbiotic lifestyle in a uniquely complex and challenging environment.

PMID: 22936719 [PubMed – in process]

Jan 21

Dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic.

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Dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic.
Proc Natl Acad Sci U S A. 2012 Sep 25;109(39):15793-8
Authors: Beauchemin M, Roy S, Daoust P, Dagenais-Bellefeuille S,…

Jan 21

ANALYSIS OF ALEXANDRIUM TAMARENSE (DINOPHYCEAE) GENES REVEALS THE COMPLEX EVOLUTIONARY HISTORY OF A MICROBIAL EUKARYOTE().

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ANALYSIS OF ALEXANDRIUM TAMARENSE (DINOPHYCEAE) GENES REVEALS THE COMPLEX EVOLUTIONARY HISTORY OF A MICROBIAL EUKARYOTE().
J Phycol. 2012 Oct 1;48(5):1130-1142
Authors: Chan CX, Soares MB, Bonaldo MF, Wisecav…

Jan 21

Establishment of a Bacterial Expression System and Immunoassay Platform for the Major Capsid Protein of HcRNAV, a Dinoflagellate-Infecting RNA Virus.

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Establishment of a Bacterial Expression System and Immunoassay Platform for the Major Capsid Protein of HcRNAV, a Dinoflagellate-Infecting RNA Virus.
Microbes Environ. 2012 Dec 7;27(4):483-9
Authors: Wada K,…

Jan 21

Counterion-mediated decompaction of liquid crystalline chromosomes.

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Counterion-mediated decompaction of liquid crystalline chromosomes.

DNA Cell Biol. 2012 Dec;31(12):1657-64

Authors: Sun S, Wong JT, Liu M, Dong F

Abstract
Liquid crystalline phases of DNA and nucleosome core particles can be formed in vitro, indicating the crucial roles of these phases in the maintenance and compaction of genomes in vivo. In the present study, sequential levels of liquid crystalline decompaction were identified in highly purified nuclei of Karenia papilionacea in response to the gradual chelation of divalent counterions by ethylenediaminetetraacetic acid (EDTA); the decompaction was observed using polarizing light microscopy, confocal laser scanning microscopy, and transmission electron microscopy and further confirmed utilizing microcalorimetry. Nested fibrous coils in 150 nm arc-like bands of chromatin were observed in the early stages of chromosomal decompaction. The microcalorimetry spectra of isolated nuclei revealed that the dynamic processes of nuclear decompaction occurred in a nonlinear manner; in addition, an EDTA-sensitive thermal transition between 60°C-70°C, corresponding to a liquid-crystalline-phase transition of chromosomes, was found. The results suggested that nested coils of fibrous chromatin filaments are responsible for the establishment and stabilization of the liquid crystalline and birefringence features of the chromosomes of dinoflagellates. The results also indicated that positively charged divalent counterions play significant roles in modulating liquid crystalline phases to compact the chromosomes of dinoflagellates.

PMID: 23072628 [PubMed – in process]

Jan 21

A Tertiary Plastid Gains RNA Editing in Its New Host.

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A Tertiary Plastid Gains RNA Editing in Its New Host.
Mol Biol Evol. 2012 Dec 17;
Authors: Jackson CJ, Gornik SG, Waller RF
Abstract
Dinoflagellates are known for their development of highly a…