Abstract
BackgroundMolecular adaptation to the severe environments present during the uplift of the Qinghai-Tibet Plateau has attracted the attention of researchers. The divergence of the three specialization groups of schizothoracins (Primitive, Specialized and Highly Specialized) may correspond to the three phases of plateau uplift. Based on the transcripts of representative species of the three specialized groups and an outgroup, genes in schizothoracins that may have played important roles during the adaptation to new environments were investigated.ResultsThe contigs of Gymnodiptychus dybowskii and Schizothorax pseudaksaiensis were compared with those of Gymnocypris przewalskii ganzihonensis and the outgroup Sinocyclocheilus angustiporus, and 5,894 ortholog groups with an alignment length longer than 90 nt after deleting gaps were retained. Evolutionary analyses indicated that the average evolutionary rate of the branch leading to the Specialized group was faster than that of the branch leading to the Highly Specialized group. Moreover, the numbers of gene categories in which more than half of the genes evolved faster than the average values of the genome were 117 and 15 along the branches leading to the Specialized and Highly Specialized groups, respectively. A total of 40, 36, and 55 genes were likely subject to positive selection along the branches leading to the Primitive, Specialized and Highly Specialized groups, respectively, and many of these genes are likely relevant to adaptation to the cold temperatures, low oxygen concentrations, and strong ultraviolet radiation that result from elevation.ConclusionsBy selecting representative species of the three groups of schizothoracins and applying next-generation sequencing technology, several candidate genes corresponding to adaptation to the three phases of plateau uplift were identified. Some of the genes identified in this report that were likely subject to positive selection are good candidates for subsequent evolutionary and functional analyses of adaptation to high altitude.
Highlights
Molecular adaptation to the severe environments present during the uplift of the Qinghai-Tibet Plateau has attracted the attention of researchers
Based on the combined data generated from different sequencing platforms, a total of 139,382 and 114,997 contigs with N50 lengths of 2407 nt and 2283 nt were obtained for G. dybowskii and S. pseudaksaiensis, respectively
In previous projects sequencing the transcriptomes of polyploid cyprinids, the amounts of data generated for the two species were larger than that for G. pachycheilus [12] but were smaller than those for S. angustiporus and G. przewalskii [32, 33]
Summary
Molecular adaptation to the severe environments present during the uplift of the Qinghai-Tibet Plateau has attracted the attention of researchers. Based on the transcripts of representative species of the three specialized groups and an outgroup, genes in schizothoracins that may have played important roles during the adaptation to new environments were investigated. Molecular events underlying adaptation to extreme environments, such as high altitude, have attracted widespread attention. Genomic studies targeting Tibetan populations have shown that the genes EGLN1 and PPARA, which are significantly associated with the decreased hemoglobin phenotype, were positively selected in the highland population [3]. In Ethiopian highlanders, genomic analysis revealed that a number of candidate loci were associated with hemoglobin levels relating to high-altitude adaptation [6]
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