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A de novo Assembly of the Common Frog (Rana temporaria) Transcriptome and Comparison of Transcription Following Exposure to Ranavirus and Batrachochytrium dendrobatidis.

Price SJ, Garner TW, Balloux F, Ruis C, Paszkiewicz KH, Moore K, Griffiths AG - PLoS ONE (2015)

Bottom Line: We found strong up-regulation of a gene involved in the adaptive immune response (AP4S1) at four days post-exposure to both pathogens.We detected a significant transcriptional response to Bd, covering the immune response (innate and adaptive immunity, complement activation, and general inflammatory responses), but relatively little transcriptional response to Ranavirus.This may reflect the higher mortality rates found in wild common frogs infected with Ranavirus as opposed to Bd.

View Article: PubMed Central - PubMed

Affiliation: UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, United Kingdom; Institute of Zoology, Zoological Society of London, London, United Kingdom.

ABSTRACT
Amphibians are experiencing global declines and extinctions, with infectious diseases representing a major factor. In this study we examined the transcriptional response of metamorphic hosts (common frog, Rana temporaria) to the two most important amphibian pathogens: Batrachochytrium dendrobatidis (Bd) and Ranavirus. We found strong up-regulation of a gene involved in the adaptive immune response (AP4S1) at four days post-exposure to both pathogens. We detected a significant transcriptional response to Bd, covering the immune response (innate and adaptive immunity, complement activation, and general inflammatory responses), but relatively little transcriptional response to Ranavirus. This may reflect the higher mortality rates found in wild common frogs infected with Ranavirus as opposed to Bd. These data provide a valuable genomic resource for the amphibians, contribute insight into gene expression changes after pathogen exposure, and suggest potential candidate genes for future host-pathogen research.

No MeSH data available.


Related in: MedlinePlus

Comparison of transcriptional profiles across all samples.Heatmap visualizing the hierarchically clustered Spearman correlation matrix resulting from a comparison of the transcript expression values (TMM-normalized FPKM) for each pair of samples; Bd = Batrachochytrium dendrobatidis, Con = control, Rv = Ranavirus.
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pone.0130500.g001: Comparison of transcriptional profiles across all samples.Heatmap visualizing the hierarchically clustered Spearman correlation matrix resulting from a comparison of the transcript expression values (TMM-normalized FPKM) for each pair of samples; Bd = Batrachochytrium dendrobatidis, Con = control, Rv = Ranavirus.

Mentions: Transcriptional profiles of replicates were consistent within treatments, clustering together within treatments when expression values were compared for each pair of samples (Fig 1). Expression values were more similar within the Ranavirus and control treatments than in the more divergent Bd treatment. The total number of differentially expressed transcripts that we report was affected by the False Discovery Rate (FDR), as well as our procedure for re-allocating some differentially expressed transcripts from the Bd vs. Ranavirus comparisons to the other comparisons (Table 2; Fig 2). Increasing the FDR increased the number of differentially expressed transcripts in our output. Classifying some of the Bd vs. Ranavirus transcripts to Bd or Ranavirus vs. control (S1 Text) also increased the number of transcripts for each pathogen vs. control comparison but reduced the total number of unique differentially expressed transcripts because, for example, some of these transcripts were due to small but opposite effects of the two pathogens compared to controls.


A de novo Assembly of the Common Frog (Rana temporaria) Transcriptome and Comparison of Transcription Following Exposure to Ranavirus and Batrachochytrium dendrobatidis.

Price SJ, Garner TW, Balloux F, Ruis C, Paszkiewicz KH, Moore K, Griffiths AG - PLoS ONE (2015)

Comparison of transcriptional profiles across all samples.Heatmap visualizing the hierarchically clustered Spearman correlation matrix resulting from a comparison of the transcript expression values (TMM-normalized FPKM) for each pair of samples; Bd = Batrachochytrium dendrobatidis, Con = control, Rv = Ranavirus.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4481470&req=5

pone.0130500.g001: Comparison of transcriptional profiles across all samples.Heatmap visualizing the hierarchically clustered Spearman correlation matrix resulting from a comparison of the transcript expression values (TMM-normalized FPKM) for each pair of samples; Bd = Batrachochytrium dendrobatidis, Con = control, Rv = Ranavirus.
Mentions: Transcriptional profiles of replicates were consistent within treatments, clustering together within treatments when expression values were compared for each pair of samples (Fig 1). Expression values were more similar within the Ranavirus and control treatments than in the more divergent Bd treatment. The total number of differentially expressed transcripts that we report was affected by the False Discovery Rate (FDR), as well as our procedure for re-allocating some differentially expressed transcripts from the Bd vs. Ranavirus comparisons to the other comparisons (Table 2; Fig 2). Increasing the FDR increased the number of differentially expressed transcripts in our output. Classifying some of the Bd vs. Ranavirus transcripts to Bd or Ranavirus vs. control (S1 Text) also increased the number of transcripts for each pathogen vs. control comparison but reduced the total number of unique differentially expressed transcripts because, for example, some of these transcripts were due to small but opposite effects of the two pathogens compared to controls.

Bottom Line: We found strong up-regulation of a gene involved in the adaptive immune response (AP4S1) at four days post-exposure to both pathogens.We detected a significant transcriptional response to Bd, covering the immune response (innate and adaptive immunity, complement activation, and general inflammatory responses), but relatively little transcriptional response to Ranavirus.This may reflect the higher mortality rates found in wild common frogs infected with Ranavirus as opposed to Bd.

View Article: PubMed Central - PubMed

Affiliation: UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, United Kingdom; Institute of Zoology, Zoological Society of London, London, United Kingdom.

ABSTRACT
Amphibians are experiencing global declines and extinctions, with infectious diseases representing a major factor. In this study we examined the transcriptional response of metamorphic hosts (common frog, Rana temporaria) to the two most important amphibian pathogens: Batrachochytrium dendrobatidis (Bd) and Ranavirus. We found strong up-regulation of a gene involved in the adaptive immune response (AP4S1) at four days post-exposure to both pathogens. We detected a significant transcriptional response to Bd, covering the immune response (innate and adaptive immunity, complement activation, and general inflammatory responses), but relatively little transcriptional response to Ranavirus. This may reflect the higher mortality rates found in wild common frogs infected with Ranavirus as opposed to Bd. These data provide a valuable genomic resource for the amphibians, contribute insight into gene expression changes after pathogen exposure, and suggest potential candidate genes for future host-pathogen research.

No MeSH data available.


Related in: MedlinePlus