Comprehensive transcriptomic analysis of Tibetan Schizothoracinae fish Gymnocypris przewalskii reveals how it adapts to a high altitude aquatic life

Chao Tong,Tian Fei,Kai Zhao,Cunfang Zhang

doi:10.1186/s12862-017-0925-z

Abstract

BackgroundUnderstanding the genetic basis of adaptation to high altitude life is of paramount importance for preserving and managing genetic diversity in highland animals. This objective has been addressed mainly in terrestrial fauna but rarely in aquatic animals. Tibetan Schizothoracinae fish is the ideal model system in evolutionary biology, carrying key insights into evolutionary genetics of speciation and adaptation at high altitude. Gymnocypris przewalskii is the newly formed Schizothoracinae fish species in the Tibetan Plateau, inhabits chronic cold, extreme saline and alkaline aquatic environment in Lake Qinghai, thus evolving the unique genomic signatures to adapt extremely severe environments.ResultsTo characterize its genomic features, we assembled de novo transcriptome of G. przewalskii from Lake Qinghai. Intriguingly, by comparative genomic analyses of G. przewalskii and 8 other fish species, we identified potential expansions in gene families related to energy metabolism, transport and developmental functions, possibly underlying the adaptation to these environmental stresses. Through comprehensive molecular evolution analyses, we found that sets of genes controlling mitochondrion, ion homoeostasis, acid-base balance and innate immunity show significant signals of positive selection. Compared to previous studies on highland fishes, we failed to identify any positively selected genes related to hypoxia response.ConclusionsOur findings provide comprehensive insights into the genetic basis of teleost fish that underlie their adaptation to extreme high altitude aquatic life on the Tibetan Plateau.

Highlights

Understanding the genetic basis of adaptation to high altitude life is of paramount importance for preserving and managing genetic diversity in highland animals
By conducting the comparative transcriptomic analysis, we treated G. przewalskii as a genomic resource to improve our understanding of the genetic makeup of fish species in the TP and to identify candidate genes underlying adaptation to the Tibetan Plateau of Schizothoracinae fishes
Our study identified positively selected genes (PSGs) in SLC family, including SLC4A1, SLC9A3 and SLC19A3, which may acquire functional shift of transport to cope with the severe saline and alkaline stress in the Lake Qinghai

Summary

Introduction

Understanding the genetic basis of adaptation to high altitude life is of paramount importance for preserving and managing genetic diversity in highland animals This objective has been addressed mainly in terrestrial fauna but rarely in aquatic animals. Gymnocypris przewalskii is the newly formed Schizothoracinae fish species in the Tibetan Plateau, inhabits chronic cold, extreme saline and alkaline aquatic environment in Lake Qinghai, evolving the unique genomic signatures to adapt extremely severe environments. It is an interest for both evolutionary biologists and ecologists to understand how wildlife adapts to environment at high attitude [1, 2].

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Conclusion