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De novo assembly of Aureococcus anophagefferens transcriptomes reveals diverse responses to the low nutrient and low light conditions present during blooms.

Frischkorn KR, Harke MJ, Gobler CJ, Dyhrman ST - Front Microbiol (2014)

Bottom Line: On average, 93% of significantly upregulated transcripts recovered by genome mapping were present in the significantly upregulated pool from both de novo assembly methods.A comparison of this transcriptome to the nutrient regulated transcriptional response of CCMP 1984 identified conserved responses between these two strains.These analyses reveal the transcriptional underpinnings of physiological shifts that could contribute to the ecological success of this species in situ: organic matter processing, metal detoxification, lipid restructuring, and photosynthetic apparatus turnover.

View Article: PubMed Central - PubMed

Affiliation: Department of Earth and Environmental Sciences and the Lamont-Doherty Earth Observatory, Columbia University Palisades, NY, USA.

ABSTRACT
Transcriptome profiling was performed on the harmful algal bloom-forming pelagophyte Aureococcus anophagefferens strain CCMP 1850 to assess responses to common stressors for dense phytoplankton blooms: low inorganic nitrogen concentrations, low inorganic phosphorus concentrations, low light levels, and a replete control. The de novo assemblies of pooled reads from all treatments reconstructed ~54,000 transcripts using Trinity, and ~31,000 transcripts using ABySS. Comparison to the strain CCMP 1984 genome showed that the majority of the gene models were present in both de novo assemblies and that roughly 95% of contigs from both assemblies mapped to the genome, with Trinity capturing slightly more genome content. Sequence reads were mapped back to the de novo assemblies as well as the gene models and differential expression was analyzed using a Bayesian approach called Analysis of Sequence Counts (ASC). On average, 93% of significantly upregulated transcripts recovered by genome mapping were present in the significantly upregulated pool from both de novo assembly methods. Transcripts related to the transport and metabolism of nitrogen were upregulated in the low nitrogen treatment, transcripts encoding enzymes that hydrolyze organic phosphorus or relieve arsenic toxicity were upregulated in the low phosphorus treatment, and transcripts for enzymes that catabolize organic compounds, restructure lipid membranes, or are involved in sulfolipid biosynthesis were upregulated in the low light treatment. A comparison of this transcriptome to the nutrient regulated transcriptional response of CCMP 1984 identified conserved responses between these two strains. These analyses reveal the transcriptional underpinnings of physiological shifts that could contribute to the ecological success of this species in situ: organic matter processing, metal detoxification, lipid restructuring, and photosynthetic apparatus turnover.

No MeSH data available.


Related in: MedlinePlus

Broad categories of significant transcriptional responses. Diagrams illustrate the patterns of significantly differentially regulated genes across the treatments. Sections without overlap represent unique responses to each treatment. Overlapping sections are indicative of nutrient stress response transcripts [overlap between low nitrogen (N) and low phosphorus (P)], and shared low light and low N or P responses. The generally responsive category describes significantly up or downregulated transcripts shared across three treatments.
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Figure 5: Broad categories of significant transcriptional responses. Diagrams illustrate the patterns of significantly differentially regulated genes across the treatments. Sections without overlap represent unique responses to each treatment. Overlapping sections are indicative of nutrient stress response transcripts [overlap between low nitrogen (N) and low phosphorus (P)], and shared low light and low N or P responses. The generally responsive category describes significantly up or downregulated transcripts shared across three treatments.

Mentions: Response patterns are defined by identifying the overlap in significantly differentially regulated transcripts under the low nutrient and low light treatments (Figure 5). The overlap between significant transcripts from low N and low P conditions represents differential expression indicative of nutrient stress. The general response transcripts are defined here as those that are either upregulated or downregulated under all three treatments relative to the control (Figure 5). However, many of these general response transcripts could be jointly upregulated because they are responding to the switch to stationary phase and the cessation of exponential growth, rather than being a shared response to nutrient or light stress.


De novo assembly of Aureococcus anophagefferens transcriptomes reveals diverse responses to the low nutrient and low light conditions present during blooms.

Frischkorn KR, Harke MJ, Gobler CJ, Dyhrman ST - Front Microbiol (2014)

Broad categories of significant transcriptional responses. Diagrams illustrate the patterns of significantly differentially regulated genes across the treatments. Sections without overlap represent unique responses to each treatment. Overlapping sections are indicative of nutrient stress response transcripts [overlap between low nitrogen (N) and low phosphorus (P)], and shared low light and low N or P responses. The generally responsive category describes significantly up or downregulated transcripts shared across three treatments.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4109616&req=5

Figure 5: Broad categories of significant transcriptional responses. Diagrams illustrate the patterns of significantly differentially regulated genes across the treatments. Sections without overlap represent unique responses to each treatment. Overlapping sections are indicative of nutrient stress response transcripts [overlap between low nitrogen (N) and low phosphorus (P)], and shared low light and low N or P responses. The generally responsive category describes significantly up or downregulated transcripts shared across three treatments.
Mentions: Response patterns are defined by identifying the overlap in significantly differentially regulated transcripts under the low nutrient and low light treatments (Figure 5). The overlap between significant transcripts from low N and low P conditions represents differential expression indicative of nutrient stress. The general response transcripts are defined here as those that are either upregulated or downregulated under all three treatments relative to the control (Figure 5). However, many of these general response transcripts could be jointly upregulated because they are responding to the switch to stationary phase and the cessation of exponential growth, rather than being a shared response to nutrient or light stress.

Bottom Line: On average, 93% of significantly upregulated transcripts recovered by genome mapping were present in the significantly upregulated pool from both de novo assembly methods.A comparison of this transcriptome to the nutrient regulated transcriptional response of CCMP 1984 identified conserved responses between these two strains.These analyses reveal the transcriptional underpinnings of physiological shifts that could contribute to the ecological success of this species in situ: organic matter processing, metal detoxification, lipid restructuring, and photosynthetic apparatus turnover.

View Article: PubMed Central - PubMed

Affiliation: Department of Earth and Environmental Sciences and the Lamont-Doherty Earth Observatory, Columbia University Palisades, NY, USA.

ABSTRACT
Transcriptome profiling was performed on the harmful algal bloom-forming pelagophyte Aureococcus anophagefferens strain CCMP 1850 to assess responses to common stressors for dense phytoplankton blooms: low inorganic nitrogen concentrations, low inorganic phosphorus concentrations, low light levels, and a replete control. The de novo assemblies of pooled reads from all treatments reconstructed ~54,000 transcripts using Trinity, and ~31,000 transcripts using ABySS. Comparison to the strain CCMP 1984 genome showed that the majority of the gene models were present in both de novo assemblies and that roughly 95% of contigs from both assemblies mapped to the genome, with Trinity capturing slightly more genome content. Sequence reads were mapped back to the de novo assemblies as well as the gene models and differential expression was analyzed using a Bayesian approach called Analysis of Sequence Counts (ASC). On average, 93% of significantly upregulated transcripts recovered by genome mapping were present in the significantly upregulated pool from both de novo assembly methods. Transcripts related to the transport and metabolism of nitrogen were upregulated in the low nitrogen treatment, transcripts encoding enzymes that hydrolyze organic phosphorus or relieve arsenic toxicity were upregulated in the low phosphorus treatment, and transcripts for enzymes that catabolize organic compounds, restructure lipid membranes, or are involved in sulfolipid biosynthesis were upregulated in the low light treatment. A comparison of this transcriptome to the nutrient regulated transcriptional response of CCMP 1984 identified conserved responses between these two strains. These analyses reveal the transcriptional underpinnings of physiological shifts that could contribute to the ecological success of this species in situ: organic matter processing, metal detoxification, lipid restructuring, and photosynthetic apparatus turnover.

No MeSH data available.


Related in: MedlinePlus