Original Research ARTICLE

Front. Microbiol., 09 November 2012 | doi: 10.3389/fmicb.2012.00385

Identifying reference genes with stable expression from high throughput sequence data

  • 1MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Cambridge, MA, USA
  • 2Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
  • 3Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
  • 4Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA
  • 5Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA

Genes that are constitutively expressed across multiple environmental stimuli are crucial to quantifying differentially expressed genes, particularly when employing quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) assays. However, the identification of these potential reference genes in non-model organisms is challenging and is often guided by expression patterns in distantly related organisms. Here, transcriptome datasets from the diatom Thalassiosira pseudonana grown under replete, phosphorus-limited, iron-limited, and phosphorus and iron co-limited nutrient regimes were analyzed through literature-based searches for homologous reference genes, k-means clustering, and analysis of sequence counts (ASC) to identify putative reference genes. A total of 9759 genes were identified and screened for stable expression. Literature-based searches surveyed 18 generally accepted reference genes, revealing 101 homologs in T. pseudonana with variable expression and a wide range of mean tags per million. k-means analysis parsed the whole transcriptome into 15 clusters. The two most stable clusters contained 709 genes, but still had distinct patterns in expression. ASC analyses identified 179 genes that were stably expressed (posterior probability < 0.1 for 1.25 fold change). Genes known to have a stable expression pattern across the test treatments, like actin, were identified in this pool of 179 candidate genes. ASC can be employed on data without biological replicates and was more robust than the k-means approach in isolating genes with stable expression. The intersection of the genes identified through ASC with commonly used reference genes from the literature suggests that actin and ubiquitin ligase may be useful reference genes for T. pseudonana and potentially other diatoms. With the wealth of transcriptome sequence data becoming available, ASC can be easily applied to transcriptome datasets from other phytoplankton to identify reference genes.

Keywords: Thalassiosira pseudonana, diatom, phytoplankton, housekeeping genes, RT-qPCR, transcriptome, relative gene expression, reference gene

Citation: Alexander H, Jenkins BD, Rynearson TA, Saito MA, Mercier ML and Dyhrman ST (2012) Identifying reference genes with stable expression from high throughput sequence data. Front. Microbio. 3:385. doi: 10.3389/fmicb.2012.00385

Received: 07 June 2012; Accepted: 16 October 2012;
Published online: 09 November 2012.

Edited by:

Peter R. Girguis, Harvard University, USA

Reviewed by:

Martin W. Hahn, Austrian Academy of Sciences, Austria
Xiang Xiao, Shanghai JiaoTong University, China

Copyright © 2012 Alexander, Jenkins, Rynearson, Saito, Mercier and Dyhrman. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.

*Correspondence: Sonya T. Dyhrman, Biology Department MS #33, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA. e-mail: sdyhrman@whoi.edu

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