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Open Access Highly Accessed Research article

Toward understanding the genetic basis of adaptation to high-elevation life in poikilothermic species: A comparative transcriptomic analysis of two ranid frogs, Rana chensinensis and R. kukunoris

Weizhao Yang12, Yin Qi1, Ke Bi3 and Jinzhong Fu14*

Author Affiliations

1 Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China

2 Graduate University of Chinese Academy of Sciences, Beijing, 100049, China

3 Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720-3160, USA

4 Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada

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BMC Genomics 2012, 13:588  doi:10.1186/1471-2164-13-588

Published: 1 November 2012

Abstract

Background

Understanding how organisms adapt to high-elevation environments at a genome scale provides novel insights into the process of adaptive evolution. Previous studies have mainly focused on endothermic organisms, while poikilothermic species may have evolved different mechanisms to cope with high-elevation environments. In this context, we sequenced transcriptomes of a pair of closely related anuran species, Rana chensinensis and R. kukunoris, which inhabit respective low- and high-elevation habitats. By comparing the two transcriptomes, we identified candidate genes that may be involved in high-elevation adaption in poikilothermic species.

Results

Over 66 million sequence reads from each transcriptome were generated. A total of 41,858 and 39,293 transcripts for each species were obtained by de novo assembly. By comparing the orthologous transcripts, we identified 125 protein-coding genes that have likely experienced strong positive selection (Ka/Ks>1). In addition, 335 genes that may bear a signature of positive selection (1≥Ka/Ks>0.5) were also recognized. By considering their functions, fourteen candidate genes were determined to be likely involved in high-elevation adaptation, including two CYP genes, USP-1, and several others.

Conclusions

We identified a set of candidate genes that may have promoted adaptation of R. kukunoris to its high-elevation environment. These include several genes that have previously been associated with oxygen binding, response to UV radiation, and repair of free radical injury. Detailed molecular, physiological, and phenotypic studies are required to better understand the roles of these genes in improving the performance of R. kukunoris in a high-elevation environment. We have evidence for both convergent and divergent evolution between endothermic and poikilothemic species, but additional research across a wide range of organisms will be necessary to comprehend the complexity of high-elevation adaptation.

Keywords:
Adaptation; High elevation; Transcriptome; Amphibian; Positive selection; Ka/Ks ratio; Candidate gene; Oxygen binding; UV radiation