Category: Dinoflagellate genomics

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Cryptic sex in Symbiodinium (Alveolata, Dinoflagellata) is supported by an inventory of meiotic genes.
J Eukaryot Microbiol. 2014 May-Jun;61(3):322-7
Authors: Chi J, Parrow MW, Dunthorn M
Ab…

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Multi-gene analysis of Symbiodinium dinoflagellates: a perspective on rarity, symbiosis, and evolution.
PeerJ. 2014;2:e394
Authors: Pochon X, Putnam HM, Gates RD
Abstract
Symbiodiniu…

Massive gene transfer and extensive RNA editing of a symbiotic dinoflagellate plastid genome.
Genome Biol Evol. 2014 May 31;
Authors: Mungpakdee S, Shinzato C, Takeuchi T, Kawashima T, Koyanagi R, Hisata K, Tanaka …

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Ribosomal DNA Organization Patterns within the Dinoflagellate Genus Alexandrium as Revealed by FISH: Life Cycle and Evolutionary Implications.

Protist. 2014 Apr 18;165(3):343-363

Authors: Figueroa RI, Cuadrado A, Stüken A, Rodríguez F, Fraga S

Abstract
Dinoflagellates are a group of protists whose genome differs from that of other eukaryotes in terms of size (contains up to 250pg per haploid cell), base composition, chromosomal organization, and gene expression. But rDNA gene mapping of the active nucleolus in this unusual eukaryotic genome has not been carried out thus far. Here we used FISH in dinoflagellate species belonging to the genus Alexandrium (genome sizes ranging from 21 to 170 pg of DNA per haploid genome) to localize the sequences encoding the 18S, 5.8S, and 28S rRNA genes. The results can be summarized as follows: 1) Each dinoflagellate cell contains only one active nucleolus, with no hybridization signals outside it. However, the rDNA organization varies among species, from repetitive clusters forming discrete nuclear organizer regions (NORs) in some to specialized “ribosomal chromosomes” in other species. The latter chromosomes, never reported before in other eukaryotes, are mainly formed by rDNA genes and appeared in the species with the highest DNA content. 2) Dinoflagellate chromosomes are first characterized by several eukaryotic features, such as structural differentiation (centromere-like constrictions), size differences (dot chromosomes), and SAT (satellite) chromosomes. 3) NOR patterns prove to be useful in discriminating between cryptic species and life cycle stages in protists.

PMID: 24846057 [PubMed – as supplied by publisher]

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Effects of In Vitro Exposure to Diarrheic Toxin Producer Prorocentrum lima on Gene Expressions Related to Cell Cycle Regulation and Immune Response in Crassostrea gigas.

PLoS One. 2014;9(5):e97181

Authors: de Jesús Romero-Geraldo R, García-Lagunas N, Hernández-Saavedra NY

Abstract
BACKGROUND: Crassostrea gigas accumulates diarrheic shellfish toxins (DSP) associated to Prorocentrum lima of which Okadaic acid (OA) causes specific inhibitions of serine and threonine phosphatases 1 and 2A. Its toxic effects have been extensively reported in bivalve mollusks at cellular and physiological levels, but genomic approaches have been scarcely studied.
METHODOLOGY/PRINCIPAL FINDINGS: Acute and sub-chronic exposure effects of P. lima were investigated on farmed juvenile C. gigas (3-5 mm). The Pacific oysters were fed with three dinoflagellate concentrations: 0.3, 3, and 30×103 cells mL-1 along with a nontoxic control diet of Isochrysis galbana. The effects of P. lima on C. gigas were followed by analyzing expression levels of a total of four genes, three involved in cell cycle regulation and one in immune response by polymerase chain reaction and real time quantitative PCR, where changes in time and cell concentration were found. The highest expression levels were found in oysters fed 3×103 cells mL-1 at 168 h for the cycle regulator p21 protein (9 fold), chromatin assembly factor 1 p55 subunit (8 fold), elongation factor 2 (2 fold), and lipopolysaccharide/β-1, 3 glucan binding protein (13 fold above base line). Additionally, the transcript level of all the genes decreased in oysters fed wich the mixed diet 30×103 cells mL-1 of dinoflagellate after 72 h and was lowest in the chromatin assembly factor 1 p55 subunit (0.9 fold below baseline).
CONCLUSIONS: On C. gigas the whole cell ingestion of P lima caused a clear mRNA modulation expression of the genes involved in cell cycle regulation and immune system. Over-expression could be related to DNA damage, disturbances in cell cycle continuity, probably a genotoxic effect, as well as an activation of its innate immune system as first line of defense.

PMID: 24825133 [PubMed – in process]

Evaluation of photo-reactive siderophore producing bacteria before, during and after a bloom of the dinoflagellate Lingulodinium polyedrum.

Metallomics. 2014 Apr 24;

Authors: Yarimizu K, Polido G, Gärdes A, Carter ML, Hilbern M, Carrano CJ

Abstract
Evidence is increasing for a mutualistic relationship between phytoplankton and heterotrophic marine bacteria. It has been proposed that bacteria producing photoactive iron binding compounds known as siderophores could play an important role in such mutualistic associations by producing bioavailable iron utilizable by phytoplankton and in exchange receive autotrophically derived DOM. In order to understand the potential role photoactive siderophores might be playing in bacterial-algal mutualism or marine biogeochemistry in general, it is important to be able to detect and quantify their presence in various environments. One approach to accomplish that end is to make use of high sensitivity genomics technology (qPCR) to search for siderophore biosynthesis genes related to the production of photoactive siderophores. In this way one can access their “biochemical potential” and utilize this information as a proxy for the presence of these siderophores in the marine environment. In this report we studied the correlation of the presence of bacteria producing one of the three photoactive siderophores relative to total bacterial and dinoflagellate numbers from surface water at the Scripps Pier before, during, and after fall bloom of the dinoflagellate Lingulodinium polyedrum. We believe that these findings will aid us in gauging the importance of photoactive siderophores in the marine environment and in harmful algal bloom dynamics in particular.

PMID: 24760287 [PubMed – as supplied by publisher]

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Ycf93 (Orf105), a Small Apicoplast-Encoded Membrane Protein in the Relict Plastid of the Malaria Parasite Plasmodium falciparum That Is Conserved in Apicomplexa.
PLoS One. 2014;9(4):e91178
Authors: …

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Accommodating the load: The transposable element content of very large genomes.
Mob Genet Elements. 2013 Mar 1;3(2):e24775
Authors: Metcalfe CJ, Casane D
Abstract
Very large genomes, that is, …

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Photophysiology of kleptoplasts: photosynthetic use of light by chloroplasts living in animal cells.

Philos Trans R Soc Lond B Biol Sci. 2014;369(1640):20130242

Authors: Serôdio J, Cruz S, Cartaxana P, Calado R

Abstract
Kleptoplasty is a remarkable type of photosynthetic association, resulting from the maintenance of functional chloroplasts-the ‘kleptoplasts’-in the tissues of a non-photosynthetic host. It represents a biologically unique condition for chloroplast and photosynthesis functioning, occurring in different phylogenetic lineages, namely dinoflagellates, ciliates, foraminiferans and, most interestingly, a single taxon of metazoans, the sacoglossan sea slugs. In the case of sea slugs, chloroplasts from macroalgae are often maintained as intracellular organelles in cells of these marine gastropods, structurally intact and photosynthetically competent for extended periods of time. Kleptoplasty has long attracted interest owing to the longevity of functional kleptoplasts in the absence of the original algal nucleus and the limited number of proteins encoded by the chloroplast genome. This review updates the state-of-the-art on kleptoplast photophysiology, focusing on the comparative analysis of the responses to light of the chloroplasts when in their original, macroalgal cells, and when sequestered in animal cells and functioning as kleptoplasts. It covers fundamental but ecologically relevant aspects of kleptoplast light responses, such as the occurrence of photoacclimation in hospite, operation of photoprotective processes and susceptibility to photoinhibition. Emphasis is given to host-mediated processes unique to kleptoplastic associations, reviewing current hypotheses on behavioural photoprotection and host-mediated enhancement of photosynthetic performance, and identifying current gaps in sacoglossan kleptoplast photophysiology research.

PMID: 24591722 [PubMed – in process]

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Chromera velia, Endosymbioses and the Rhodoplex Hypothesis – Plastid Evolution in Cryptophytes, Alveolates, Stramenopiles and Haptophytes (CASH Lineages).
Genome Biol Evol. 2014 Feb 25;
Authors: Petersen J, L…