Evidence of high-altitude adaptation in the glyptosternoid fish, Creteuchiloglanis macropterus from the Nujiang River obtained through transcriptome analysis

Abstract

BackgroundOrganisms living at high altitudes face low oxygen and temperature conditions; thus, the genetic mechanisms underlying the adaptations in these organisms merit investigation. The glyptosternoid fish, Creteuchiloglanis macropterus mainly inhabits regions with gradual increases in altitudes along the Nujiang River and might serve as an appropriate evolutionary model for detecting adaptation processes in environments with altitude changes.ResultsWe constructed eleven RNA-sequencing (RNA-seq) libraries of C. macropterus collected from five locations at different altitudes to identify the genetic signatures of high-altitude adaptation. The comparative genomic analysis indicated that C. macropterus has an accelerated evolutionary rate compared with that of fishes in the lowland, and fishes at higher altitudes might evolve faster. Functional enrichment analysis of the fast-evolving and positively selected genes, differentially expressed genes and highly expressed genes, showed that these genes were involved in many functions related to energy metabolism and hypoxia.ConclusionsOur study provides evidence of high-altitude adaptation in C. macropterus, and the detected adaptive genes might be a resource for future investigations of adaptations to high-altitude environments in other fishes.Electronic supplementary materialThe online version of this article (10.1186/s12862-017-1074-0) contains supplementary material, which is available to authorized users.

Comparative transcriptomics reveal that adaptive evolution in immune genes drives the local adaptation and speciation of schizothoracine fish

“…Specific pathways are 5 plotted along the y-axis, and the x-axis indicates the enrichment factor. The size each colored dot indicates 6 przewalskii (Tong et al 2017) but consistent with most recent comparative transcriptome 1 studies in fish (Yang et al 2014;Ma et al 2015;Kang et al 2017).…”

Transcriptome Analysis Provides Insights Into the Adaptive Responses to Hypoxia of a Schizothoracine Fish (Gymnocypris eckloni)

“…Limited oxygen availability (hypoxia) is an important environmental stressor that has a profound impact on the survival, reproduction, growth, and development of aquatic life, and thus the aquatic ecosystem as a whole ( Shang and Wu, 2004 ; Storz et al, 2010 ). Many fish species are able to cope with or adapt to hypoxia via a complex suite of molecular strategies that operate at the transcriptional level ( Gracey et al, 2001 ; van der Meer et al, 2005 ; Zhong et al, 2009 ; Kang et al, 2017 ; Liu et al, 2018 ). Here, we describe the transcriptomic response of five G. eckloni tissues to hypoxia, affording new insights into the adaptive mechanisms employed by fish subjected to hypoxic conditions.…”

Genomic signature of ongoing alkaline adaptation in a Schizothoracine fish (Cyprinidae) inhabiting soda lake on the Tibetan Plateau

“…Comparative genomics has begun to elucidate the genomic basis of harsh environment adaptation in Tibetan fish species, but insight into the alkaline adaptation in Schizothoracine fishes has lagged behind. Building on previous comparative genomic or transcriptomic studies specifically focused on hypoxia and cold adaptation of Tibetan fishes (Yang et al 2014;Chi et al 2017;Kang et al 2017;Wang et al 2015;Zhang et al 2017;Tong, Tian, et al 2017;Ma et al 2015), we performed one of the first comparative genomics studies to identify the signature of ongoing alkaline adaptation in Schizothoracine fishes on the Tibetan Plateau. These putative genomic signatures included expansions of lineage-specific genes associated with ion transport and transmembrane functions, genome-wide elevated rate of molecular evolution in Schizothoracine fishes relative to other model teleost fish species.…”

“…In addition, genes associated with energy metabolism function, such as ATP synthase F1 subunit gamma (ATP5F1C) and ATP synthase subunit beta (ATP5b), had been detected the signature of positive selection in Tibetan naked carp that dwelt in Lake Qinghai with long-term of low temperature (Tong, Fei, et al 2017). The main focus of the genetic mechanism of highland adaptation in Tibetan fish are still on hypoxia and chronic cold response (Yang et al 2014;Wang et al 2015;Kang et al 2017;Guan et al 2014;Xu et al 2016). Notably, an increasing number of lakes on the Tibetan Plateau are existing or towards saline and alkaline due to the global climate changes and human activities (Zheng 1997;Yang et al 2010).…”