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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

Pairwise comparison of transcriptional responses across 37,314 contigs generated by a 90% clustering of the Trinity assembly in each treatment relative to the replete control. Transcriptome-side gene expression patterns are shown in low N (A), low P (B), and low light (C). Transcripts were normalized to total library size in tags per million (TPM). Gray points represent transcripts that were not significantly differentially regulated. Significance (colored points) was determined with ASC using a fold change greater than or equal to 2 and a posterior probability greater than 0.95 (Wu et al., 2010). The average significant fold change and maximum fold change value of up and downregulated transcripts is noted.
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Figure 2: Pairwise comparison of transcriptional responses across 37,314 contigs generated by a 90% clustering of the Trinity assembly in each treatment relative to the replete control. Transcriptome-side gene expression patterns are shown in low N (A), low P (B), and low light (C). Transcripts were normalized to total library size in tags per million (TPM). Gray points represent transcripts that were not significantly differentially regulated. Significance (colored points) was determined with ASC using a fold change greater than or equal to 2 and a posterior probability greater than 0.95 (Wu et al., 2010). The average significant fold change and maximum fold change value of up and downregulated transcripts is noted.

Mentions: ASC was used to determine significant differential expression in the treatments relative to the replete condition control using the 90% clustered Trinity assembly (Wu et al., 2010). The low P condition elicited the strongest overall response, with more transcripts (1205) significantly upregulated than the other treatments and the largest fold changes (Figure 2; Table 4). The transcriptomic response to low N was the weakest overall, relative to the other treatments (Figure 2; Table 4). The Trinity and ABySS methods yielded similar numbers of differentially upregulated transcripts (Table 4). Although the genome mapping method recovered fewer significantly differentially regulated transcripts, this disparity is due to the difference in the number of gene models (11,501) vs. the number of contigs generated by the two de novo assemblies (>30,000). The percentage of differentially expressed transcripts relative to the total were comparable across all methods, with ~2.5% of all gene models or contigs significantly upregulated.


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)

Pairwise comparison of transcriptional responses across 37,314 contigs generated by a 90% clustering of the Trinity assembly in each treatment relative to the replete control. Transcriptome-side gene expression patterns are shown in low N (A), low P (B), and low light (C). Transcripts were normalized to total library size in tags per million (TPM). Gray points represent transcripts that were not significantly differentially regulated. Significance (colored points) was determined with ASC using a fold change greater than or equal to 2 and a posterior probability greater than 0.95 (Wu et al., 2010). The average significant fold change and maximum fold change value of up and downregulated transcripts is noted.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Pairwise comparison of transcriptional responses across 37,314 contigs generated by a 90% clustering of the Trinity assembly in each treatment relative to the replete control. Transcriptome-side gene expression patterns are shown in low N (A), low P (B), and low light (C). Transcripts were normalized to total library size in tags per million (TPM). Gray points represent transcripts that were not significantly differentially regulated. Significance (colored points) was determined with ASC using a fold change greater than or equal to 2 and a posterior probability greater than 0.95 (Wu et al., 2010). The average significant fold change and maximum fold change value of up and downregulated transcripts is noted.
Mentions: ASC was used to determine significant differential expression in the treatments relative to the replete condition control using the 90% clustered Trinity assembly (Wu et al., 2010). The low P condition elicited the strongest overall response, with more transcripts (1205) significantly upregulated than the other treatments and the largest fold changes (Figure 2; Table 4). The transcriptomic response to low N was the weakest overall, relative to the other treatments (Figure 2; Table 4). The Trinity and ABySS methods yielded similar numbers of differentially upregulated transcripts (Table 4). Although the genome mapping method recovered fewer significantly differentially regulated transcripts, this disparity is due to the difference in the number of gene models (11,501) vs. the number of contigs generated by the two de novo assemblies (>30,000). The percentage of differentially expressed transcripts relative to the total were comparable across all methods, with ~2.5% of all gene models or contigs significantly upregulated.

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