Abstract
Pelteobagrus vachelli is a well-known commercial species in Asia. However, a sudden lack of oxygen will result in mortality and eventually to pond turnover. Studying the molecular mechanisms of hypoxia adaptation in fishes will not only help us to understand fish speciation and the evolution of the hypoxia-signaling pathway, but will also guide us in the breeding of hypoxia-tolerant fish strains. Despite this, the genetic regulatory network for miRNA-mRNA and the signaling pathways involved in hypoxia responses in fish have remained unexamined. In the present study, we used next-generation sequencing technology to characterise mRNA-seq and miRNA-seq of control- and hypoxia-treated P. vachelli livers to elucidate the molecular mechanisms of hypoxia adaptation. We were able to find miRNA-mRNA pairs using bioinformatics analysis and miRNA prediction algorithms. Furthermore, we compared several key pathways which were identified as involved in the hypoxia response of P. vachelli. Our study is the first report on integrated analysis of mRNA-seq and miRNA-seq in fishes and offers a deeper insight into the molecular mechanisms of hypoxia adaptation. qRT-PCR analysis further confirmed the results of mRNA-Seq and miRNA-Seq analysis. We provide a good case study for analyzing mRNA/miRNA expression and profiling a non-model fish species using next-generation sequencing technology.
Highlights
Oxygen serves as the terminal electron acceptor in oxidative phosphorylation
Quantitative real-time PCR analysis demonstrated that let-7a, miR-122, and miR-9-3p were down-regulated in the liver and brain of a hypoxic female Oryzias melastigma, while miR-2184 was up-regulated in the testis of a hypoxic male[15]
A large number of mRNAs and miRNAs from P. vachelli involved in diverse biological pathways were identified
Summary
Oxygen serves as the terminal electron acceptor in oxidative phosphorylation. several enzymatic processes in vivo require molecular oxygen as the direct substrate[1]. It is not suitable for high-density pond farming because of the relatively high oxygen-consumption rate and low oxygen threshold; a sudden lack of oxygen will result in mortality among the fish and will eventually lead to pond turnover[5] These special characteristics of P. vachelli suggest that it is a significant aquaculture species and a potential model organism for study of the molecular mechanisms of acute hypoxia. No genomic and transcriptomic resources from this species have previously been available, and until now only about 150 EST and 105 protein sequences have been deposited in the NCBI GenBank This dearth of genetic resources hinders P. vachelli molecular breeding as well as further studies on the mechanisms of specific biological processes. We provide a good case study with which to analyse mRNA/miRNA expression and profile non-model fish species using NGST
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