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

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0925-z) contains supplementary material, which is available to authorized users.

Genomic signature of accelerated evolution in a saline-alkaline lake-dwelling Schizothoracine fish

“…Over the past few years, transcriptome-based assembly approach enables comparative genomics studies widely employed in many Tibetan endemic organisms to provide insights of highland adaptation [15][16][17]23,40,41]. Unlike whole genome data, although transcriptome sequencing is an effective and accessible approach to initiate comparative genomic analyses on non-model organisms [28], it still can not cover the whole protein coding gene repertoire of one species.…”

“…Comparative genomics approaches have the power to facilitate investigation of the genomic basis of evolution and adaptation [14]. Recent comparative genomics studies based on transcriptomic data of several Schizothoracine species have identified a number of candidate genes that underwent positive selection during the longterm adaptive processes to harsh environments on the Tibetan Plateau, such as hypoxia [15] and low temperature [16,17]. Notably, an increasing number of lakes are existing or towards saline and alkaline due to the geological evolution and global climate changes on the Tibetan Plateau [3,18].…”

Comparative genomics identifies putative signatures of sociality in spiders

“…Only RNA with high quality (RNA Integrity Number > 7) were used for cDNA synthesis and amplification. Libraries were prepared with the Nextera XT DNA Library Prep Kit (Illumina, CA, USA) using ~350-bp inserted fragments for transcriptome sequencing as previously described (Tong, Tian, et al 2017;Tong, Fei, et al 2017). Libraries were individually barcoded and run on a single lane of an Illumina NovaSeq (Novogene, CA, USA) yielding 150-bp paired-end reads.…”

Transcriptomic signature of rapidly evolving immune genes in a highland fish

“…An increasing number of transcriptome targeted to identify abundant immune genes in fish by sampling immune-relevant tissues, such as head-kidney and spleen [21][22][23]25]. To maximize the information content of immune gene sequences, we collected two immune relevant tissues, head-kidney and spleen, plus two less relevant tissues (gills and skin) transcriptome data for assembly, which generated much more unigenes than our previous assembly versions of G. przewalskii [7,23]. In addition, compared with our previous comparative genomics study in G. przewalskii [7], we identified more immune genes…”

“…Understanding how fish species adapt to the aquatic life at high altitude is an interest for both ichthyologists and evolutionary biologists [1]. As the largest and highest highland in the world with the average elevation above 4000m [2], the Tibetan Plateau imposes extremely harsh aquatic environments on endemic fish fauna [3], including hypoxia [4], chronic cold [5,6] and high salinity and alkalinity [7,8].…”