Tag: genomes

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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…

Divergent mitochondrial respiratory chains in phototrophic relatives of apicomplexan parasites.

Mol Biol Evol. 2015 Feb 6;

Authors: Flegontov P, Michálek J, Janouškovec J, Lai H, Jirků M, Hajdušková E, Tomčala A, Otto TD, Keeling PJ, Pain A, Oborník M, Lukeš J

Abstract
Four respiratory complexes and ATP-synthase represent central functional units in mitochondria. In some mitochondria and derived anaerobic organelles, a few or all of these respiratory complexes have been lost during evolution. We show that the respiratory chain of Chromera velia, a phototrophic relative of parasitic apicomplexans, lacks complexes I and III, making it a uniquely reduced aerobic mitochondrion. In Chromera, putative lactate:cytochrome c oxidoreductases are predicted to transfer electrons from lactate to cytochrome c, rendering complex III unnecessary. The mitochondrial genome of Chromera has the smallest known protein-coding capacity of all mitochondria, encoding just cox1 and cox3 on heterogeneous linear molecules. In contrast, another photosynthetic relative of apicomplexans, Vitrella brassicaformis, retains the same set of genes as apicomplexans and dinoflagellates (cox1, cox3 and cob).

PMID: 25660376 [PubMed – as supplied by publisher]

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Trehalose is a chemical attractant in the establishment of coral symbiosis.
PLoS One. 2015;10(1):e0117087
Authors: Hagedorn M, Carter V, Zuchowicz N, Phillips M, Penfield C, Shamenek B, Vallen EA, …

2Transcriptomic characterisation and genomic glimps into the toxigenic dinoflagellate Azadinium spinosum , with emphasis on polykeitde synthase genes.

BMC Genomics. 2015 Jan 23;16(1):27

Authors: Meyer JM, Rödelsperger C, Eichholz K, Tillmann U, Cembella A, McGaughran A, John U

Abstract
BackgroundUnicellular dinoflagellates are an important group of primary producers within the marine plankton community. Many of these species are capable of forming harmful algae blooms (HABs) and of producing potent phycotoxins, thereby causing deleterious impacts on their environment and posing a threat to human health. The recently discovered toxigenic dinoflagellate Azadinium spinosum is known to produce azaspiracid toxins. These toxins are most likely produced by polyketide synthases (PKS). Recently, PKS I-like transcripts have been identified in a number of dinoflagellate species. Despite the global distribution of A. spinosum, little is known about molecular features. In this study, we investigate the genomic and transcriptomic features of A. spinosum with a focus on polyketide synthesis and PKS evolution.ResultsWe identify orphan and homologous genes by comparing the transcriptome data of A. spinosum with a diverse set of 18 other dinoflagellates, five further species out of the Rhizaria Alveolate Stramelopile (RAS)-group, and one representative from the Plantae. The number of orphan genes in the analysed dinoflagellate species averaged 27%. In contrast, within the A. spinosum transcriptome, we discovered 12,661 orphan transcripts (18%). The dinoflagellates toxins known as azaspiracids (AZAs) are structurally polyethers; we therefore analyse the transcriptome of A. spinosum with respect to polyketide synthases (PKSs), the primary biosynthetic enzymes in polyketide synthesis. We find all the genes thought to be potentially essential for polyketide toxin synthesis to be expressed in A. spinosum, whose PKS transcripts fall into the dinoflagellate sub-clade in PKS evolution.ConclusionsOverall, we demonstrate that the number of orphan genes in the A. spinosum genome is relatively small compared to other dinoflagellate species. In addition, all PKS domains needed to produce the azaspiracid carbon backbone are present in A. spinosum. Our study underscores the extraordinary evolution of such gene clusters and, in particular, supports the proposed structural and functional paradigm for PKS Type I genes in dinoflagellates.

PMID: 25612855 [PubMed – as supplied by publisher]

Neptunomonas phycophila sp. nov. isolated from a culture of Symbiodinium sp. a dinoflagellate symbiont of the sea anemone Aiptasia tagetes.

Int J Syst Evol Microbiol. 2015 Jan 6;

Authors: Frommlet JC, Guimarães B, Sousa L, Serôdio J, Alves A

Abstract
A gram staining negative, facultative anaerobic, oxidase-positive and catalase-positive, rod-shaped bacterium strain SYM1T was isolated from a ITS2-type B1 culture of Symbiodinium spp., an algal symbiont of the sea anemone Aiptasia tagetes collected in Puerto Rico. Growth was observed at 4-40 °C (optimum 30 °C), at pH 5.0-11.0 (optimum pH 8.0) and with 0.5-8% (optimum 2%) NaCl (w/v). Phylogenetic analyses of 16S rRNA gene sequences showed that strain SYM1T was a member of the genus Neptunomonas with the type strain of Neptunomonas naphthovorans as the closest phylogenetic relative with a pairwise sequence similarity of 98.15%. However, DNA-DNA relatedness between SYM1T and N. naphthovorans CIP 106451T was 24%. Moreover, SYM1T could be distinguished from its closest relative by several phenotypic characteristics such as NaCl, pH and temperature tolerance, nitrate reduction and utilization of carbon substrates. The major cellular fatty acids were C16:0, C18:1ω7c and summed feature 3 (comprising C16:1ω7c and/or iso-C15:0 2-OH). Genomic DNA G+C content of strain SYM1T was 45 mol%. Q-8 was the only respiratory quinone detected. Based on a polyphasic taxonomic characterization, strain SYM1T represents a novel species in the genus Neptunomonas for which the name Neptunomonas phycophila sp. nov. is proposed. The type strain is SYM1T (= LMG 28329T = CECT 8716T).

PMID: 25563909 [PubMed – as supplied by publisher]

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Metatranscriptome profiling of a harmful algal bloom.
Harmful Algae. 2014 Jul;37:75-83
Authors: Cooper ED, Bentlage B, Gibbons TR, Bachvaroff TR, Delwiche CF
Abstract
Metagenomic met…

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Molecular characterisation and expression analysis of a novel calreticulin (CRT) gene in the dinoflagellate Prorocentrum minimum.
Mol Biol Rep. 2014 Nov 15;
Authors: Ponmani T, Guo R, Suh YS, Ki JS…