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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

Expression patterns of light harvesting complex (LHC) transcripts between treatments. The notation on the x-axis refers to the phylogenetic groups of different LHC genes identified in the A. anophagefferens CCMP 1984 genome (Gobler et al., 2011). Filled circles indicate LHC groups with significantly differentially expressed contigs in the LHC group. Open circles indicate a lack of significant differentially expressed contigs in the LHC group. Error bars denote standard deviation.
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Figure 7: Expression patterns of light harvesting complex (LHC) transcripts between treatments. The notation on the x-axis refers to the phylogenetic groups of different LHC genes identified in the A. anophagefferens CCMP 1984 genome (Gobler et al., 2011). Filled circles indicate LHC groups with significantly differentially expressed contigs in the LHC group. Open circles indicate a lack of significant differentially expressed contigs in the LHC group. Error bars denote standard deviation.

Mentions: Transcripts involved with photosynthetic processes were dynamically expressed across all treatments. There were different transcripts identified as encoding photosystem I and II proteins upregulated under all three treatments. In addition to these photosystem-encoding transcripts, a large number of significantly responsive transcripts in all treatments were identified as encoding light harvesting complex (LHC) proteins. CCMP 1984 genome analysis identified 62 LHC proteins, which fell into 16 distinct groups based on phylogenetic similarity to LHCs from other phytoplankton (Gobler et al., 2011). Significantly upregulated LHC contigs spanned 15 of the 16 LHC groups during low P and 10 groups during low light, while significantly downregulated contigs during low N spanned 7 groups (Figure 7). The downregulation of LHC transcripts is supported by the noted decrease in photosynthetic efficiency at the time of culture harvest in the low N sample (Table 1).


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)

Expression patterns of light harvesting complex (LHC) transcripts between treatments. The notation on the x-axis refers to the phylogenetic groups of different LHC genes identified in the A. anophagefferens CCMP 1984 genome (Gobler et al., 2011). Filled circles indicate LHC groups with significantly differentially expressed contigs in the LHC group. Open circles indicate a lack of significant differentially expressed contigs in the LHC group. Error bars denote standard deviation.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 7: Expression patterns of light harvesting complex (LHC) transcripts between treatments. The notation on the x-axis refers to the phylogenetic groups of different LHC genes identified in the A. anophagefferens CCMP 1984 genome (Gobler et al., 2011). Filled circles indicate LHC groups with significantly differentially expressed contigs in the LHC group. Open circles indicate a lack of significant differentially expressed contigs in the LHC group. Error bars denote standard deviation.
Mentions: Transcripts involved with photosynthetic processes were dynamically expressed across all treatments. There were different transcripts identified as encoding photosystem I and II proteins upregulated under all three treatments. In addition to these photosystem-encoding transcripts, a large number of significantly responsive transcripts in all treatments were identified as encoding light harvesting complex (LHC) proteins. CCMP 1984 genome analysis identified 62 LHC proteins, which fell into 16 distinct groups based on phylogenetic similarity to LHCs from other phytoplankton (Gobler et al., 2011). Significantly upregulated LHC contigs spanned 15 of the 16 LHC groups during low P and 10 groups during low light, while significantly downregulated contigs during low N spanned 7 groups (Figure 7). The downregulation of LHC transcripts is supported by the noted decrease in photosynthetic efficiency at the time of culture harvest in the low N sample (Table 1).

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