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DOI10.1371/journal.pone.0114178
Natural Variation in Fish Transcriptomes: Comparative Analysis of the Fathead Minnow (Pimephales promelas) and Zebrafish (Danio rerio)
Wang, Rong-Lin1,4; Bencic, David C.1; Garcia-Reyero, Natalia2; Perkins, Edward J.3; Villeneuve, Daniel L.4; Ankley, Gerald T.4; Biales, Adam D.1
发表日期2014-12-10
ISSN1932-6203
卷号9期号:12
英文摘要

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, better characterization and understanding are needed for natural variation in gene expression among fish individuals from lab cultures. 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 differentially impact subsets of fish transcriptomes in a nonsystematic way. Temporally more closely spaced batches tended to share a greater transcriptomic similarity among one another. The overall level of within-batch variation was quite low in fish ovary tissue, making it a suitable system for studying chemical stressors with subtle biological effects. The observed differences in the within-batch variability of gene expression, at the levels of both individual genes and pathways, were probably both technical and biological. This suggests that biological interpretation and prioritization of genes and pathways targeted by experimental conditions should take into account both their intrinsic variability and the size of induced transcriptional changes. There was significant conservation of both the genomes and transcriptomes between fathead minnow and zebrafish. The high degree of conservation offers promising opportunities in not only studying fish molecular responses to environmental stressors by a comparative biology approach, but also effective sharing of a large amount of existing public transcriptomics data for developing toxicogenomics applications.


语种英语
WOS记录号WOS:000346611400034
来源期刊PLOS ONE
来源机构美国环保署
文献类型期刊论文
条目标识符http://gcip.llas.ac.cn/handle/2XKMVOVA/60447
作者单位1.US EPA, Ecol Exposure Res Div, Natl Exposure Res Lab, Cincinnati, OH 45268 USA;
2.Mississippi State Univ, Inst Genom Biocomp & Biotechnol, Starkville, MS USA;
3.US Army Corps Engn, US Army Engn Res & Dev Ctr, Environm Lab, Vicksburg, MS USA;
4.US EPA, Midcontinent Ecol Div, Natl Hlth & Environm Effects Res Lab, Duluth, MN USA
推荐引用方式
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Wang, Rong-Lin,Bencic, David C.,Garcia-Reyero, Natalia,et al. Natural Variation in Fish Transcriptomes: Comparative Analysis of the Fathead Minnow (Pimephales promelas) and Zebrafish (Danio rerio)[J]. 美国环保署,2014,9(12).
APA Wang, Rong-Lin.,Bencic, David C..,Garcia-Reyero, Natalia.,Perkins, Edward J..,Villeneuve, Daniel L..,...&Biales, Adam D..(2014).Natural Variation in Fish Transcriptomes: Comparative Analysis of the Fathead Minnow (Pimephales promelas) and Zebrafish (Danio rerio).PLOS ONE,9(12).
MLA Wang, Rong-Lin,et al."Natural Variation in Fish Transcriptomes: Comparative Analysis of the Fathead Minnow (Pimephales promelas) and Zebrafish (Danio rerio)".PLOS ONE 9.12(2014).
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