Gene expression changes leading extreme alkaline tolerance in Amur ide (Leuciscus waleckii) inhabiting soda lake

Abstract

BackgroundAmur ide (Leuciscus waleckii) is an economically and ecologically important cyprinid species in Northern Asia. The Dali Nor population living in the soda lake Dali Nor can adapt the extremely high alkalinity, providing us a valuable material to understand the adaptation mechanism against extreme environmental stress in teleost.ResultsIn this study, we generated high-throughput RNA-Seq data from three tissues gill, liver and kidney of L. waleckii living in the soda lake Dali Nor and the fresh water lake Ganggeng Nor, then performed parallel comparisons of three tissues. Our results showed that out of assembled 64,603 transcript contigs, 28,391 contigs had been assigned with a known function, corresponding to 20,371 unique protein accessions. We found 477, 2,761 and 3,376 differentially expressed genes (DEGs) in the gill, kidney, and liver, respectively, of Dali Nor population compared to Ganggeng Nor population with FDR ≤ 0.01and fold-change ≥ 2. Further analysis revealed that well-known functional categories of genes and signaling pathway, which are associated with stress response and extreme environment adaptation, have been significantly enriched, including the functional categories of “response to stimulus”, “transferase activity”, “transporter activity” and “oxidoreductase activity”, and signaling pathways of “mTOR signaling”, “EIF2 signaling”, “superpathway of cholesterol biosynthesis”. We also identified significantly DEGs encoding important modulators on stress adaptation and tolerance, including carbonic anhydrases, heat shock proteins, superoxide dismutase, glutathione S-transferases, aminopeptidase N, and aminotransferases.ConclusionsOverall, this study demonstrated that transcriptome changes in L. waleckii played a role in adaptation to complicated environmental stress in the highly alkalized Dali Nor lake. The results set a foundation for further analyses on alkaline-responsive candidate genes, which help us understand teleost adaptation under extreme environmental stress and ultimately benefit future breeding for alkaline-tolerant fish strains.

Defining the role of omics in assessing ecosystem health: Perspectives from the Canadian environmental monitoring program

“…exposed to an extreme alkaline environment exhibited changes associated with stress response and extreme environment adaptation, including the functional categories of response to stimulus and oxidoreductase activity, among others [112]. In medaka gills, microarray analysis showed pH changes can impact gene groups related to processes such as acid-base and ion regulation, cellular stress response, and metabolism [75].…”

Transcriptomic responses to environmental change in fishes: Insights from RNA sequencing

“…An acclimation experiment comparing native freshwater to anadromous saltwater threespine stickleback (Gasterosteus aculeatus) also revealed many genes potentially underlying salinity adaptation . Finally, a rare study examining the effects of elevated pH on a fish transcriptome described how changes in gene expression played a key role in the relatively recent shift of Amur ide (Leuciscus waleckii) from freshwater to extreme alkalinity in a soda lake (Xu et al 2013). Further research is needed to determine whether the intraspecific variation in expression described for the wild-caught fish used in these studies has a genetic (as opposed to epigenetic) basis, thereby representing adaptive evolution.…”

“…Gill, liver, kidney 1 (9-10) Intraspecific pH (↑) Metabolism (↑), immune response (↑), response to stimulus (↑↓), oxidation-reduction (↑↓), signalling (Xu et al 2013) …”

Genomics of Adaptation to Multiple Concurrent Stresses: Insights from Comparative Transcriptomics of a Cichlid Fish from One of Earth’s Most Extreme Environments, the Hypersaline Soda Lake Magadi in Kenya, East Africa

“…Several studies using closely related tilapia and other euryhaline teleost species have provided some insights on the molecular responses to environmental stresses (Boutet et al 2006;Tine et al 2008;Xu et al 2013b;Lam et al 2014). However, most of these studies focused on molecular responses associated with single environmental variables and could therefore not always capture the complexity of all challenging variables experienced by natural populations (Oleksiak 2011).…”

“…Therefore, gills are an ideal tissue to use when examining the transcriptomic responses to water chemistry in fish (Oleksiak 2011;Xu et al 2013b;Lam et al 2014). In order to increase the robustness of our analysis (Kelley et al 2012;Xu et al 2013b), we compared the transcriptomes of A. grahami with corresponding data from O. leucostictus, a close relative freshwater species from Lake Victoria (Fig. 2).…”