Characterization of EPO H131S as a Key Mutation Site in the Hypoxia-adaptive Evolution of Gymnocypris Dobula

Erythropoietin (EPO) is a glycoprotein hormone involved in proerythropoiesis, antioxidation and antiapoptosis. It also contributes to cellular immune function in high-altitude species, such as the schizothoracine fish Gymnocypris dobula (G. dobula). Six mutation sites previously identified in EPO from G. dobula (GD-EPO) were injected into zebrafish embryos and their effects were compared with EPO from the low-altitude schizothoracine Schizothorax prenanti (S. prenanti). The key mutation site in GD-EPO was identified as H131S. Under hypoxic conditions, the levels of superoxide dismutase and malondialdehyde were decreased, whereas that of nitric oxide was increased in zebrafish injected with GD-EPO compared with those injected with S. prenanti-EPO (SP-EPO). The results suggest that EPO in high-altitude schizothoracine species is both antioxidative and antiapoptotic, driven by the H131S mutation site. Thus, this enhanced the ability of this species to adapt to the high-altitude hypoxic environment. These results provide a basis for investigating further the hypoxia adaptation mechanisms of teleosts.

Comparative transcriptome analysis of scaled and scaleless skins in Gymnocypris eckloni provides insights into the molecular mechanism of scale degeneration

Background The scale degeneration is thought to be related to the adaptation to the extreme environment with cold climate and high-altitude in schizothoracine fishes. Gymnocypris eckloni, a schizothoracine fish living in plateau waters with the elevation above 2500 m, is nearly esquamate and only covered with shoulder scales and anal scales, making it a good model species to study the molecular mechanism of scale degeneration. Results The transcriptomes of shoulder scaled skins (SSS), anal scaled skins (ASS) and scaleless skins (NSS) were sequenced and analyzed in G. eckloni at the age of 1 year. Histological examination showed that shoulder scale had completed its differentiation and anal scale just initiated the differentiation. A total of 578,046 unigenes were obtained from the transcriptomes, with 407,799 unigenes annotated in public databases. A total of 428 and 142 differentially expressed unigenes (DEUs) were identified between SSS and NSS, and between ASS and NSS, respectively, with 45 DEUs that were overlapped. Annotation analysis indicated that these DEUs were mainly enriched in Gene Ontology (GO) terms and KEGG pathways associated with bone and muscle formation, such as myofibril, contractile fiber, cytoskeletal protein binding, muscle structure development, cardiac muscle contraction, hypertrophic cardiomyopathy (HCM) and calcium signaling pathway. Conclusions Our results would provide insights into the molecular mechanisms of scale degeneration in G. eckloni and other congeneric fishes. In addition, the transcriptome data provides candidate genes and markers for future studies.

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

Tibetan Plateau imposes extremely inhospitable environment on most wildlife. Besides the harsh aquatic environment including hypoxia and chronic cold, high salinity and alkalinity is an increasing threat to Tibetan endemic fishes. Previous genome-wide studies identified key genes contributed to highland fish adaptation to hypoxia and long-term cold, while our understanding of saline and alkaline adaptation in Tibetan fish remains limited. In this study, we performed a comparative genomics analysis in a saline lake-dwelling highland fish Gymnocypris przewalskii, aimed to identify candidate genes that contributed to saline and alkaline adaptation. We found elevated genome-wide rate of molecular evolution in G. przewalskii relative to lowland teleost fish species. In addition, we found nine genes encoding biological macromolecules associated with ion transport functions underwent accelerated evolution in G. przewalskii, which broadly expressed across kidney, gill, liver, spleen, brain and muscle tissues. Moreover, we found putative evidence of ion transport under selection were interacted by co-expression in G. przewalskii adaptation to high salinity and alkalinity environment of Lake Qinghai. Taken together, our comparative genomics study identified a set of rapidly evolving ion transport genes and transcriptomic signatures in Schizothoracine fish adaptation to saline and alkaline environment on the Tibetan Plateau.

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

Comparative genomics has elucidate the molecular footprints of adaptations to extreme environments at high altitude including hypoxia, but insight into the genomic basis of saline and alkaline adaptation in highland fish has rarely been provided. The increasing of water salinization is a growing threat to Tibetan endemic fish species. Here we performed one of the first comparative genomics studies and began to characterize genomic signature of alkaline adaptation in a Schizothoracine fish inhabiting soda lake on the Tibetan Plateau. We found that 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 lowland teleost fish species. In addition, we found specific changes in the rate of molecular evolution between G. p. kelukehuensis and other teleost fishes for ion transport-related genes. Furthermore, we identified a set of genes associated with ion transport and energy metabolism underwent positive selection. Using tissue-transcriptomics, we found that most REGs and PSGs in G. p. kelukehuensis were broadly expressed across three tissues and significantly enriched for ion transport functions. Finally, we identified a set of ion transport-related genes with evidences for both selection and co-expressed which contributed to alkaline tolerance in G. p. kelukehuensis. Altogether, our study identified putative genomic signature and potential candidate genes contributed to ongoing alkaline adaptation in Schizothoracine fish.

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

ABSTRACTTranscriptomic information can increase our understanding of the molecular processes underlying speciation. The schizothoracine fish, the largest and most diverse taxon within the Qinghai-Tibetan Plateau (QTP) ichthyofauna, are widespread in drainages throughout the QTP. These fish thus serve as an ideal model group with which to investigate how molecular evolution drives local adaptation during speciation. Here, we performed an interspecific comparative analysis of the transcriptomes of 13 schizothoracine fish species, and identified the key positively selected genes (PSGs) associated with significantly enriched functions and metabolite pathway acting on the specific lineages (or species) in the schizothoracine fish. We generated 64,637,602–83,968,472 sequence reads per schizothoracine fish species using Illumina sequencing, yielding 95,251–145,805 unigenes per species. We identified 52 out of 2,064 orthologous genes as candidate genes, which have probably been subject to positive selection along the whole schizothoracine fish lineage. Nine of these candidate genes were significantly enriched in key GO functions and metabolite pathways, all of which were associated with the immune system. The lineage-specific evolution test showed species-specific differences among the nine candidate PSGs, probably due to ecological differences among drainages, as well as among micro-habitats in the same drainage (e.g., benthic and pelagic). Here, we provide evidence that the adaptive evolution of immune genes, along with the uplift of the QTP, allowed new schizothoracine species to colonize ecologically novel environments or to exploit vacant ecological niches during speciation.Supplemental material available at FigShare: https://doi.org/10.25387/.