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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 key nitrogen metabolism transcripts. The black hashed line denotes the mean variance in expression across treatments of transcripts significantly upregulated in the low N treatment. Significance 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 blue line denotes the average variance in expression of transcripts from this study with functional annotations previously determined to be significantly upregulated during low N conditions in A. anophagefferens CCMP 1984 (Berg et al., 2008; Wurch et al., 2011b) (See Table 5). The green line denotes the variance in expression of transcripts from this study with functional annotations identified as upregulated during low N conditions in diatoms or coccolithophores (Dyhrman et al., 2006, 2012; Allen et al., 2011; Bender et al., 2014) (See Table 5).
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Figure 3: Expression patterns of key nitrogen metabolism transcripts. The black hashed line denotes the mean variance in expression across treatments of transcripts significantly upregulated in the low N treatment. Significance 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 blue line denotes the average variance in expression of transcripts from this study with functional annotations previously determined to be significantly upregulated during low N conditions in A. anophagefferens CCMP 1984 (Berg et al., 2008; Wurch et al., 2011b) (See Table 5). The green line denotes the variance in expression of transcripts from this study with functional annotations identified as upregulated during low N conditions in diatoms or coccolithophores (Dyhrman et al., 2006, 2012; Allen et al., 2011; Bender et al., 2014) (See Table 5).

Mentions: The A. anophagefferens CCMP 1850 response to low N conditions was characterized by significantly upregulated transcripts encoding nitrate transporters, nitrate reductases and peptidases (Table 5). In addition to the transcripts that passed the stringent ASC significance cutoff, modeling of expression of N metabolism genes known to respond significantly to N limitation in A. anophagefferens CCMP 1984 (Berg et al., 2008; Wurch et al., 2011b) or other phytoplankton (Dyhrman et al., 2006; Allen et al., 2011; Bender et al., 2014) revealed that these transcripts mirror expression patterns in the significantly upregulated N-responsive set, with higher expression in the low N treatment relative to replete, low P and low light (Table 5; Figure 3).


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 key nitrogen metabolism transcripts. The black hashed line denotes the mean variance in expression across treatments of transcripts significantly upregulated in the low N treatment. Significance 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 blue line denotes the average variance in expression of transcripts from this study with functional annotations previously determined to be significantly upregulated during low N conditions in A. anophagefferens CCMP 1984 (Berg et al., 2008; Wurch et al., 2011b) (See Table 5). The green line denotes the variance in expression of transcripts from this study with functional annotations identified as upregulated during low N conditions in diatoms or coccolithophores (Dyhrman et al., 2006, 2012; Allen et al., 2011; Bender et al., 2014) (See Table 5).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Expression patterns of key nitrogen metabolism transcripts. The black hashed line denotes the mean variance in expression across treatments of transcripts significantly upregulated in the low N treatment. Significance 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 blue line denotes the average variance in expression of transcripts from this study with functional annotations previously determined to be significantly upregulated during low N conditions in A. anophagefferens CCMP 1984 (Berg et al., 2008; Wurch et al., 2011b) (See Table 5). The green line denotes the variance in expression of transcripts from this study with functional annotations identified as upregulated during low N conditions in diatoms or coccolithophores (Dyhrman et al., 2006, 2012; Allen et al., 2011; Bender et al., 2014) (See Table 5).
Mentions: The A. anophagefferens CCMP 1850 response to low N conditions was characterized by significantly upregulated transcripts encoding nitrate transporters, nitrate reductases and peptidases (Table 5). In addition to the transcripts that passed the stringent ASC significance cutoff, modeling of expression of N metabolism genes known to respond significantly to N limitation in A. anophagefferens CCMP 1984 (Berg et al., 2008; Wurch et al., 2011b) or other phytoplankton (Dyhrman et al., 2006; Allen et al., 2011; Bender et al., 2014) revealed that these transcripts mirror expression patterns in the significantly upregulated N-responsive set, with higher expression in the low N treatment relative to replete, low P and low light (Table 5; Figure 3).

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