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Background  Organisms living at high altitudes must overcome three major environmental challenges: hypoxia, cold, and intense UV radiation. The molecular mechanisms that enable these challenges to be overcome have mainly been studied in endothermic organisms; relatively little attention has been paid to poikilothermic species. Here, we present deep transcriptome sequencing in two closely related lizards, the high altitude-dwelling  Phrynocephalus erythrurus  and the lowland-dwelling  P. putjatia , to identify candidate genes under positive selection and to explore the convergent evolutionary adaptation of poikilothermic animals to high altitude life.    Results  More than 70 million sequence reads were generated for each species via Illumina sequencing.  De novo  assembly produced 56,845 and 63,140 transcripts for  P. erythrurus  and  P. putjatia , respectively.  P. erythrurus  had higher Ka/Ks ratios than  P. putjatia , implying an accelerated evolutionary rate in the high altitude lizard lineage. 206 gene ontology (GO) categories with accelerated evolutionary rates and 43 candidate positively selected genes were detected along the  P. erythrurus  lineage. Some of these GO categories have functions associated with responses to hypoxia, energy metabolism and responses to UV damage. We also found that the high-altitude ranid frog  R. kukunoris  had higher Ka/Ks ratios than the closely related low-altitude frog  R. chensinensis , and that the functional categories with accelerated evolutionary rates in  R. kukunoris  overlapped extensively with those detected along the  P. erythrurus  lineage.    Conclusions  The mechanisms of high altitude adaptation in  P. erythrurus  were tentatively inferred. By comparing two pairs of low- and high-altitude poikilothermic species, we found that similar functional categories had undergone positive selection in high altitude-dwelling  Phrynocephalus  and  Rana  lineages, indicating that similar mechanisms of adaptation to high altitude might have evolved in both genera. Our findings provide important guidance for future functional studies on high altitude adaptation in poikilothermic animals.    Electronic supplementary material  The online version of this article (doi:10.1186/s12862-015-0371-8) contains supplementary material, which is available to authorized users.

bmc evolutionary biology

Comparative transcriptomic analysis revealed adaptation mechanism of Phrynocephalus erythrurus, the highest altitude Lizard living in the Qinghai-Tibet Plateau