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Natural Variation in Fish Transcriptomes: Comparative Analysis of the Fathead Minnow (Pimephales promelas) and Zebrafish (Danio rerio)
Citation:
Wang, R., D. Bencic, N. Garcia-Reyero, E. Perkins, Dan Villeneuve, G. Ankley, AND A. Biales. Natural Variation in Fish Transcriptomes: Comparative Analysis of the Fathead Minnow (Pimephales promelas) and Zebrafish (Danio rerio). PLOS ONE . Public Library of Science, San Francisco, CA, 9(12):e114178, (2014).
Impact/Purpose:
An assessment and basic understanding of the extent and scope of transcriptomic variations should be considered an important priority in order to improve interpretation of treatment effects caused by chemical stressors and their discrimination from background variability. Our research team has conducted a number of microarray studies focused on chemical effects on reproductive pathways in zebrafish and fathead minnows. This data set provides an opportunity to evaluate issues related to transcriptome variability. The objectives of the current analyses were to determine: 1) the extent of between-batch variation, namely, how much gene expression profiles of untreated lab fish change over time or experiments; 2) the extent of variation in gene expression among individuals within a batch and its partitioning across cellular hierarchy, from a whole transcriptome to molecular pathways and genes; and 3) inter-specific differences between fathead minnow and zebrafish with respect to their within- and between-batch variation.
Description:
Fathead minnow and zebrafish are among the most intensively studied fish species in environmental toxicogenomics. To aid the assessment and interpretation of subtle transcriptomic effects from treatment conditions of interest, there needs to be a better characterization and understanding of the natural variation in gene expression among fish individuals within populations. Little effort, however, has been made in this area. Leveraging the transcriptomics data from a number of our toxicogenomics studies conducted over the years, we conducted a meta-analysis of nearly 600 microarrays generated from the ovary tissue of untreated, reproductively mature fathead minnow and zebrafish samples. As expected, there was considerable batch-to-batch transcriptomic variation; this “batch-effect” appeared to impact the fish transcriptomes randomly. The overall level of variation within-batch was quite low in fish ovary tissue, making it a suitable system for studying chemical stressors with subtle biological effects. The within-batch variation, however, differed considerably among individual genes and molecular pathways. This difference in variability is probably both technical and biological, thus suggesting a need to take into account both the expression levels and variance in evaluating and interpreting the transcriptional impact on genes and pathways by experimental conditions. There was significant conservation of both the genomes and transcriptomes between fathead minnow and zebrafish. The conservation to such a degree would enable not only a comparative biology approach in studying the mechanisms of action underlying environmental stressors, but also effective sharing of a large amount of existing public data for future development of toxicogenomics applications.
