Genome-wide identification of genes probably relevant to the adaptation of schizothoracins (Teleostei: Cypriniformes) to the uplift of the Qinghai-Tibet Plateau

Abstract

Background: Molecular 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.

Results: The 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.

Conclusions: By 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.

Keywords: High-altitude adaptation; Polyploid; Positive selection; Schizothoracins.

Fig. 1

Phylogenetic relationships of the species used in this report. G. dybowskii and S. pseudoaksaiensis were collected from the Ili River, which is located in Sinkiang, northwestern China; G. p. ganzihonensis and the outgroup species S. angustiporus were respectively collected from the Ganzi River in Qinghai province and from the Huangnihe River in Yunnan province, previously [32, 33]. I, II and III represent branches leading to the Primitive, Specialized and Highly Specialized groups, respectively. Numbers below branches denote the number of fast-evolving gene categories with the same GO term or KEGG pathway assigned along branches II and III, respectively

Fig. 2

Venn diagram of the overlap between the candidate genes subject to positive selection along the branches leading to the Primitive, Specialized and Highly Specialized groups of Schizothoracins (branchesI, II and III in Fig. 1)