Abstract
BackgroundGenome-wide studies on highland adaptation mechanism in terrestrial animal have been widely reported with few available for aquatic animals. Tibetan Schizothoracinae species are ideal model systems to study speciation and adaptation of fish. The Schizothoracine fish, Gymnocypris przewalskii ganzihonensis had underwent the ecological niche shift from salt water to freshwater, and also experienced a recent split from Gymnocypris przewalskii przewalskii. In addition, G. p. ganzihonensis inhabited harsh aquatic environment including low temperature and hypoxia as well as other Schizothoracinae species, its genetic mechanism of highland adaptation have yet to be determined.ResultsOur study used comparative genomic analysis based on the transcriptomic data of G. p. ganzihonensis and other four fish genome datasets to investigate the genetic basis of highland adaptation in Schizothoracine fish. We found that Schizothoracine fish lineage on the terminal branch had an elevated dN/dS ratio than its ancestral branch. A total of 202 gene ontology (GO) categories involved into transport, energy metabolism and immune response had accelerated evolutionary rates than zebrafish. Interestingly, we also identified 162 genes showing signature of positive selection (PSG) involved into energy metabolism, transport and immune response in G. p. ganzihonesis. While, we failed to find any PSG related to hypoxia response as previous studies.ConclusionsComparative genomic analysis based on G. p. ganzihonensis transcriptome data revealed significant genomic signature of accelerated evolution ongoing within Tibetan Schizothoracinae species lineage. Molecular evolution analysis suggested that genes involved in energy metabolism, transport and immune response functions in Schizothoracine fish underwent positive selection, especially in innate immunity including toll-like receptor signaling pathway genes. Taken together, our result as a case study in Schizothoracinae species provides novel insights in understanding the aquatic animal adaptation to extreme environment on the Tibetan Plateau, and also provides valuable genomic resource for further functional verification studies.
Highlights
Genome-wide studies on highland adaptation mechanism in terrestrial animal have been widely reported with few available for aquatic animals
Transcriptome sequence analysis and assembly Two pooled cDNA libraries derived from gill and kidney tissues of Schizothoracine fish, G. p. ganzihonensis were prepared and sequenced, totally generated 85,371,306 and 88,787,918 raw 101-bp paired-end (PE) reads, respectively
Functional annotation To comprehensively annotate the transcriptome of G. p. ganzihonensis, all unigenes were queried against several public databases
Summary
Genome-wide studies on highland adaptation mechanism in terrestrial animal have been widely reported with few available for aquatic animals. Tibetan Schizothoracinae species are ideal model systems to study speciation and adaptation of fish. Ganzihonensis inhabited harsh aquatic environment including low temperature and hypoxia as well as other Schizothoracinae species, its genetic mechanism of highland adaptation have yet to be determined. Tong et al BMC Genomics (2017) 18:948 It may provide novel insights for understanding the mechanism of highland adaptation of Tibetan wildlife. Past research had revealed that Schizothoracinae species had well adapted to the harsh aquatic environment on the TP, including hypoxia, low temperature and even high salinity [9, 11,12,13], making them excellent models for investigating the genetic mechanism of aquatic animal adaptation to the extreme environment at high altitude. It is an interesting issue to investigate the highland adaptation in fish species using G. p. ganzihonesis as a case study in Schizothoracinae
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