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

BMC Genomics

Research Article

Yin Qi¹  Jinzhong Fu²  Weizhao Yang³  Ke Bi⁴ 

[1] Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China;Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China;Department of Integrative Biology, University of Guelph, N1G 2W1, Guelph, Ontario, Canada;Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China;Graduate University of Chinese Academy of Sciences, 100049, Beijing, China;Museum of Vertebrate Zoology, University of California, 94720-3160, Berkeley, CA, USA;

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

DOI  :  10.1186/1471-2164-13-588

 received in 2012-08-15, accepted in 2012-10-30,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundUnderstanding 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.ResultsOver 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.ConclusionsWe 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.

【 授权许可】

Unknown   
© Yang et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.