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Transcriptome profiling of a toxic dinoflagellate reveals a gene-rich protist and a potential impact on gene expression due to bacterial presence.

Moustafa A, Evans AN, Kulis DM, Hackett JD, Erdner DL, Anderson DM, Bhattacharya D - PLoS ONE (2010)

Bottom Line: Of these, about 11,000 signatures did not display detectable differential expression patterns.Among microbial eukaryotes, dinoflagellates contain the largest number of genes in their nuclear genomes.These genes occur in complex families, many of which have evolved via recent gene duplication events.

View Article: PubMed Central - PubMed

Affiliation: Ecology, Evolution and Natural Resources, Institute of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America.

ABSTRACT

Background: Dinoflagellates are unicellular, often photosynthetic protists that play a major role in the dynamics of the Earth's oceans and climate. Sequencing of dinoflagellate nuclear DNA is thwarted by their massive genome sizes that are often several times that in humans. However, modern transcriptomic methods offer promising approaches to tackle this challenging system. Here, we used massively parallel signature sequencing (MPSS) to understand global transcriptional regulation patterns in Alexandrium tamarense cultures that were grown under four different conditions.

Methodology/principal findings: We generated more than 40,000 unique short expression signatures gathered from the four conditions. Of these, about 11,000 signatures did not display detectable differential expression patterns. At a p-value < 1E-10, 1,124 signatures were differentially expressed in the three treatments, xenic, nitrogen-limited, and phosphorus-limited, compared to the nutrient-replete control, with the presence of bacteria explaining the largest set of these differentially expressed signatures.

Conclusions/significance: Among microbial eukaryotes, dinoflagellates contain the largest number of genes in their nuclear genomes. These genes occur in complex families, many of which have evolved via recent gene duplication events. Our expression data suggest that about 73% of the Alexandrium transcriptome shows no significant change in gene expression under the experimental conditions used here and may comprise a "core" component for this species. We report a fundamental shift in expression patterns in response to the presence of bacteria, highlighting the impact of biotic interaction on gene expression in dinoflagellates.

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Differentially expressed signatures in response to three different culture treatments when compared to the control.Heatmap of the differentially expressed signatures under the three treatments (N, P, and X) compared to the control (F). The intersection between the treatments indicates signatures that showed significant differential expression patterns in two conditions out of the three or in the three conditions compared to the control.
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pone-0009688-g003: Differentially expressed signatures in response to three different culture treatments when compared to the control.Heatmap of the differentially expressed signatures under the three treatments (N, P, and X) compared to the control (F). The intersection between the treatments indicates signatures that showed significant differential expression patterns in two conditions out of the three or in the three conditions compared to the control.

Mentions: Although complex and multi-species bacterial assemblages have been shown to be associated with dinoflagellates both in extra- and intra-cellular environments [28], [29], taxa appear to be limited to the Cytophaga-Flavobacterium-Bacteroides (CFB) group and the α- and γ- classes of Proteobacteria. In this study, we did not attempt to identify the prokaryotes present in the bacterized Alexandrium culture. Previous studies have shown however that members of the genera Roseobacter (α-Proteobacteria) and Alteromonas (γ-Proteobacteria) are the dominant bacterial groups associated with Alexandrium sp. [30]. Here, we focused on the effect of the presence of bacteria in the culture on gene expression in the dinoflagellate. To identify transcriptionally regulated genes, we used the nutrient-replete culture as the control condition and identified signatures that were significantly up or down regulated in the other conditions using Fisher's test. At p-value < 1E-10, we found 1,124 signatures that were differentially expressed among the three (xenic, N-limited, P-limited) treatments compared to the control (Figure 3). By relaxing the p-value to a relatively more permissive threshold of 0.05 to detect even slight changes in expression among treatments, we identified ca. 11,000 differentially expressed signatures, indicating that about 29,000 signatures are consistently expressed with non-significant differences under the culture conditions used here. In dramatic contrast to a recent study which showed that about 6% of the expressed genes in rice are uniformly expressed, housekeeping genes [31], our results suggest that about 73% of the Alexandrium transcriptome comprises a “core” component and 27% comprises the regulated component, under differing cellular or environmental conditions. Of the 1,124 signatures, 307 (27%) were differentially expressed in the xenic culture, of which 119 and 188 were up- and down-regulated, respectively. Of these differentially regulated transcripts, two sets of genes stand out because they are collectively involved in the regulation of two important cellular processes, the methionine-homocysteine cycle and photosynthesis.


Transcriptome profiling of a toxic dinoflagellate reveals a gene-rich protist and a potential impact on gene expression due to bacterial presence.

Moustafa A, Evans AN, Kulis DM, Hackett JD, Erdner DL, Anderson DM, Bhattacharya D - PLoS ONE (2010)

Differentially expressed signatures in response to three different culture treatments when compared to the control.Heatmap of the differentially expressed signatures under the three treatments (N, P, and X) compared to the control (F). The intersection between the treatments indicates signatures that showed significant differential expression patterns in two conditions out of the three or in the three conditions compared to the control.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2837391&req=5

pone-0009688-g003: Differentially expressed signatures in response to three different culture treatments when compared to the control.Heatmap of the differentially expressed signatures under the three treatments (N, P, and X) compared to the control (F). The intersection between the treatments indicates signatures that showed significant differential expression patterns in two conditions out of the three or in the three conditions compared to the control.
Mentions: Although complex and multi-species bacterial assemblages have been shown to be associated with dinoflagellates both in extra- and intra-cellular environments [28], [29], taxa appear to be limited to the Cytophaga-Flavobacterium-Bacteroides (CFB) group and the α- and γ- classes of Proteobacteria. In this study, we did not attempt to identify the prokaryotes present in the bacterized Alexandrium culture. Previous studies have shown however that members of the genera Roseobacter (α-Proteobacteria) and Alteromonas (γ-Proteobacteria) are the dominant bacterial groups associated with Alexandrium sp. [30]. Here, we focused on the effect of the presence of bacteria in the culture on gene expression in the dinoflagellate. To identify transcriptionally regulated genes, we used the nutrient-replete culture as the control condition and identified signatures that were significantly up or down regulated in the other conditions using Fisher's test. At p-value < 1E-10, we found 1,124 signatures that were differentially expressed among the three (xenic, N-limited, P-limited) treatments compared to the control (Figure 3). By relaxing the p-value to a relatively more permissive threshold of 0.05 to detect even slight changes in expression among treatments, we identified ca. 11,000 differentially expressed signatures, indicating that about 29,000 signatures are consistently expressed with non-significant differences under the culture conditions used here. In dramatic contrast to a recent study which showed that about 6% of the expressed genes in rice are uniformly expressed, housekeeping genes [31], our results suggest that about 73% of the Alexandrium transcriptome comprises a “core” component and 27% comprises the regulated component, under differing cellular or environmental conditions. Of the 1,124 signatures, 307 (27%) were differentially expressed in the xenic culture, of which 119 and 188 were up- and down-regulated, respectively. Of these differentially regulated transcripts, two sets of genes stand out because they are collectively involved in the regulation of two important cellular processes, the methionine-homocysteine cycle and photosynthesis.

Bottom Line: Of these, about 11,000 signatures did not display detectable differential expression patterns.Among microbial eukaryotes, dinoflagellates contain the largest number of genes in their nuclear genomes.These genes occur in complex families, many of which have evolved via recent gene duplication events.

View Article: PubMed Central - PubMed

Affiliation: Ecology, Evolution and Natural Resources, Institute of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America.

ABSTRACT

Background: Dinoflagellates are unicellular, often photosynthetic protists that play a major role in the dynamics of the Earth's oceans and climate. Sequencing of dinoflagellate nuclear DNA is thwarted by their massive genome sizes that are often several times that in humans. However, modern transcriptomic methods offer promising approaches to tackle this challenging system. Here, we used massively parallel signature sequencing (MPSS) to understand global transcriptional regulation patterns in Alexandrium tamarense cultures that were grown under four different conditions.

Methodology/principal findings: We generated more than 40,000 unique short expression signatures gathered from the four conditions. Of these, about 11,000 signatures did not display detectable differential expression patterns. At a p-value < 1E-10, 1,124 signatures were differentially expressed in the three treatments, xenic, nitrogen-limited, and phosphorus-limited, compared to the nutrient-replete control, with the presence of bacteria explaining the largest set of these differentially expressed signatures.

Conclusions/significance: Among microbial eukaryotes, dinoflagellates contain the largest number of genes in their nuclear genomes. These genes occur in complex families, many of which have evolved via recent gene duplication events. Our expression data suggest that about 73% of the Alexandrium transcriptome shows no significant change in gene expression under the experimental conditions used here and may comprise a "core" component for this species. We report a fundamental shift in expression patterns in response to the presence of bacteria, highlighting the impact of biotic interaction on gene expression in dinoflagellates.

Show MeSH
Related in: MedlinePlus