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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

Percentage of transcripts in the top 20 KEGG annotations for significantly downregulated transcripts in the general response and nutrient stress categories. The only shared KEGG annotation between these two categories was calmodulin.
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Figure 6: Percentage of transcripts in the top 20 KEGG annotations for significantly downregulated transcripts in the general response and nutrient stress categories. The only shared KEGG annotation between these two categories was calmodulin.

Mentions: There were relatively very few transcripts upregulated in all three treatments or shared across two treatments, as compared to significantly downregulated transcripts overlapping between treatments (Figure 5). Two of the six shared upregulated transcripts encode for putative WLM domains and the other four transcripts share homology to an ADP-ribosylation factor. The majority of the 2166 shared downregulated transcripts encode protein kinases, DNA polymerase subunits, and proteins involved in signal transduction (such as calmodulin), falling into KEGG pathways like DNA replication, ribosome biogenesis, and purine and pyrimidine metabolism (Figure 6). During nutrient stress (low N and low P), the most numerous categories of KEGG classified downregulated transcripts include metabolic pathways, biosynthesis of secondary metabolites, purine synthesis and cell cycle regulation proteins (Figure 6). The most numerous general response downregulated transcripts in these KEGG categories were involved with signal transduction, protein phosphorylation, and transcripts involved in transcription or translation (Figure 6). The downregulation of the transcripts in these categories could also point to decreases in growth rate that accompany the onset of stationary phase when treatment cultures were harvested.


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)

Percentage of transcripts in the top 20 KEGG annotations for significantly downregulated transcripts in the general response and nutrient stress categories. The only shared KEGG annotation between these two categories was calmodulin.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Percentage of transcripts in the top 20 KEGG annotations for significantly downregulated transcripts in the general response and nutrient stress categories. The only shared KEGG annotation between these two categories was calmodulin.
Mentions: There were relatively very few transcripts upregulated in all three treatments or shared across two treatments, as compared to significantly downregulated transcripts overlapping between treatments (Figure 5). Two of the six shared upregulated transcripts encode for putative WLM domains and the other four transcripts share homology to an ADP-ribosylation factor. The majority of the 2166 shared downregulated transcripts encode protein kinases, DNA polymerase subunits, and proteins involved in signal transduction (such as calmodulin), falling into KEGG pathways like DNA replication, ribosome biogenesis, and purine and pyrimidine metabolism (Figure 6). During nutrient stress (low N and low P), the most numerous categories of KEGG classified downregulated transcripts include metabolic pathways, biosynthesis of secondary metabolites, purine synthesis and cell cycle regulation proteins (Figure 6). The most numerous general response downregulated transcripts in these KEGG categories were involved with signal transduction, protein phosphorylation, and transcripts involved in transcription or translation (Figure 6). The downregulation of the transcripts in these categories could also point to decreases in growth rate that accompany the onset of stationary phase when treatment cultures were harvested.

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