Copious copies keep out the cold

Renn, S. C P; Lunt, Dave; Lunt, D. H.; Renn, S. C. P.

Abstract

ife in the sub-zero temperatures of the Southern Ocean requires special adaptation to extreme cold, and the notothenioid fish radiation—which dominates the biomass and species diversity of Antarctic fish—has provided textbook examples of molecular evolution and adaptation to thermal challenge. Previous studies have typically investigated single genes or phenotypes, such as antifreeze proteins, but in an exciting new survey, Chen et al. (2008) take a novel approach to characterizing the genome-wide changes in gene duplication and transcription, relating these to adaptation to the cold Antarctic waters. The broad implications and excitement generated by this research are because of its tripartite approach.

First, the authors investigated the transcriptome of the cold-adapted fish Dissostichus mawsoni by sequencing cDNA libraries made from multiple tissues. Chen et al. (2008) used unnormalized libraries in order to quantify EST (expressed sequence tag) abundance, and this revealed a highly biased transcription pattern, beyond ordinary expectations for simple tissue specificity. They identified a small number of dominant transcripts in each tissue, and a transcriptional shift towards a functional theme that suggests an elevated stress response.

Second, the frequency of recovery of gene transcripts was compared with published high-volume EST data sets for similar tissues in five model fish species (zebrafish, salmon, stickleback, mummichog and medaka). Over the 11 possible comparisons, 177 genes were found to be upregulated in D. mawsoni, of which 85 (48%) were already known to be upregulated with cold response in carp (Gracey et al., 2004). This result suggests that, not surprisingly, evolutionary adaptation to the Southern Ocean has co-opted some of the mechanisms that underlie typical physiological response to cold.

Third, and importantly, the authors investigated the contribution of gene duplication to transcriptional upregulation, using a D. mawsoni cDNA microarray based on the EST data. They employed array comparative genomic hybridizations (aCGH) to compare gene copy number at 10 700 loci in three Antarctic and two non-Antarctic notothenioid fishes. Using a hybridization threshold ratio set for a single, known, gene duplication event between two of these species, Chen et al. (2008) identified 101 protein-coding genes for which the average hybridization ratio across the cold-adapted species was above this threshold—indicating likely gene duplication. These candidate loci include 15 with potential activity in cold response, and many that were also among those upregulated in D. mawsoni relative to temperate species according to the EST analysis (Figure 1). It is perhaps unusual to apply a threshold analysis technique to this experiment, as Chen et al. (2008) do, rather than a statistical analysis that is more appropriate to the hybridization design. A more rigorous statistical analysis of aCGH results would help to quantify hybridization variation within and between species and ecotypes (for example, Emerson et al., 2008). Even so, successful identification of copy number variation (CNV) here supports the microarray technique as a rapid, sensitive and cost-effective method to assay genome-wide CNV in less traditional model organisms. Together these experiments provide a tantalizing glimpse of the genome-wide changes accompanying adaptation and radiation in an extreme environment.

Citation

Lunt, D. H., & Renn, S. C. P. (2009). Copious copies keep out the cold. Heredity, 103(4), 281-282. https://doi.org/10.1038/hdy.2009.59

• Journal Article Type: Article
• Online Publication Date: May 27, 2009
• Publication Date: Oct 1, 2009
• Journal: HEREDITY
• Print ISSN: 0018-067X
• Electronic ISSN: 1365-2540
• Publisher: Nature Publishing Group
• Peer Reviewed: Peer Reviewed
• Volume: 103
• Issue: 4
• Pages: 281-282
• DOI: https://doi.org/10.1038/hdy.2009.59
• Keywords: Genetics(clinical); Genetics
• Public URL: https://hull-repository.worktribe.com/output/396085
• Publisher URL: https://www.nature.com/articles/hdy200959