Guosong Zhang

Integrated analysis of mRNA-seq and miRNA-seq in the liver of Pelteobagrus vachelli in response to hypoxia

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.

Complete mitochondrial genome and phylogenic analysis of Odontobutis yaluensis, Perciformes, Odontobutidae

Abstract The complete mitochondrial genome of Odontobutis yaluensis was sequenced as to be 16,909 bp in length with (A + T) content of 55.73%, and it contained 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a control region. The gene order and orientation are similar to some typical fish species. The data will provide the useful molecular information for phylogenetic relationships of O. yaluensis with Odontobutis potamophila first clustered into a small branch, and then with Odontobutis platycephala clade, and finally with Odontobutis sinensis clade. Odontobutidae and Rhyacichthyidae formed the sister group, and Eleotridae and Gobiidae formed the sister group.

Genetic diversity of Odontobutis potamophila from different geographic populations inferred from mtDNA control region

Abstract Odontobutis potamophila is a Chinese endemic species and an economically important fishery resource in the Yangtze River. The genetic variability of O. potamophila was studied based on the sequence analysis of mitochondrial DNA control region from 150 individuals of five geographical populations including from Dangtu (n = 30), Sheyang (n = 30), Yuyao (n = 30), Tai Lake nearby Dongxishan (n = 30) and Minjiang (n = 30). Among five populations, the genetic distance between Minjiang population and other populations (0.1186–0.1223) was larger than that among four populations except for Minjiang (0.0015–0.0198). In addition, 23 haplotypes were obtained and each population had special haplotypes. The samples from five sites had high haplotype diversity (0.80510) and low nucleotide diversity (0.04028). Through Tajima’s D and Fu’s F neutral testing and mismatch distribution test among all geographical populations, O. potamophila did not undergo recent population expansion. During the population evolution, O. potamophila experienced a balanced selection function and maintained a stable state and population size. Moreover, the haplotype Neighbor-Joining (NJ) tree was separated two haplotype groups. The NJ tree, TCS network and median-joining network could clearly separate the haplotypes of the specimens from different areas. Analysis of molecular variance and pairwise FST revealed an obvious genetic differentiation among different geographical populations, suggesting that O. potamophila in different geographical populations should be managed and conserved separately.

The complete mitochondrial genome of the hybrid of Pelteobagrus fulvidraco (♀) × Pelteobagrus vachelli (♂).

Abstract In the present of study, we have reported the complete mitochondrial DNA sequence of the hybrid of Pelteobagrus fulvidraco (♀) × Pelteobagrus vachelli (♂) that is obtained by artificial hybridization. The total length of the mitochondrial genome is 16,527 bp, with the base compositions of 30.84% A, 25.54% T, 28.22% C, and 15.40% G. It contains two ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes, and a major non-coding control region (D-loop region). The arrangement of these genes is same as that observed in the teleosts. All protein initiation codons are ATG, except for COX1 that begins with GTG. The complete mitogenome of the hybrid of P. fulvidraco (♀) × P. vachelli (♂) provides an important data set for the exploration of mitochondrial inheritance mechanism. The termination-associated sequence and critical central conserved sequences (CSB-D, CSB-E and CSB-F) are also detected.

Development of 39 novel polymorphic microsatellite markers for the giant mottled eel Anguilla marmorata and cross-amplification in other eel species

In this study, we have developed microsatellite markers for the giant mottled eel (Anguilla marmorata) from expressed sequence tag (EST) sequences using next-generation sequencing. Consequently, a total of 39 novel polymorphic microsatellite markers were identified in 32 individuals from Wangquan River wild population area. The range of observed heterozygosity, expected heterozygosity and polymorphism information content were 0.044–1.000, 0.285–0.946 and 0.3783–0.9016, respectively. In addition, eight loci were deviated from Hardy–Weinberg equilibrium and modified by Bonferroni correction, and the results showed no significant linkage disequilibrium between the locus pair. The amplification of cross-species was conducted in Anguilla bicolor pacifica and Anguilla japonica, which revealed the applicability of EST-SSR primers. These EST-SSR markers can provide sufficient polymorphism for population genetic studies, pedigree and genome mapping of these three kinds of closely related eels.

Comparative iTRAQ‐Based Quantitative Proteomic Analysis of Pelteobagrus vachelli Liver under Acute Hypoxia: Implications in Metabolic Responses

More and more frequently these days, aquatic ecosystems are being stressed by nutrient enrichment, pollutants, and global warming, leading to a serious depletion in oxygen concentrations. Although a sudden, significant lack of oxygen will result in mortality, fishes can have an acute behavior (e.g., an increase in breathing rate, reduction in swimming frequency) and physiology responses (e.g., increase in oxygen delivery, and reduction in oxygen consumption) to hypoxia, which allows them to maintain normal physical activity. Therefore, in order to shed further light on the molecular mechanisms of hypoxia adaptation in fishes, the authors conduct comparative quantitative proteomics on Pelteobagrus vachelli livers using iTRAQ. The research identifies 511 acute hypoxia‐responsive proteins in P. vachelli. Furthermore, comparison of several of the diverse key pathways studied (e.g., peroxisome pathway, PPAR signaling pathway, lipid metabolism, glycolysis/gluco‐neogenesis, and amino acid metabolism) help to articulate the different mechanisms involved in the hypoxia response of P. vachelli. Data from proteome analysis shows that P. vachelli can have an acute reaction to hypoxia, including detoxification of metabolic by‐products and oxidative stress in light of continued metabolic activity (e.g., peroxisomes), an activation in the capacity of catabolism to get more energy (e.g., lipolysis and amino acid catabolism), a depression in the capacity of biosynthesis to reduce energy consumption (e.g., biosynthesis of amino acids and lipids), and a shift in the aerobic and anaerobic contributions to total metabolism. The observed hypoxia‐related changes in the liver proteome of the fish can help to understand or can be related to the hypoxia‐related response that takes place in similar conditions in the liver or other proteomes of mammals.

The complete mitochondrial genome and phylogenic analysis of Pseudobagrus vachelli

Abstract The complete mitochondrial genome of Pseudobagrus vachelli has been sequenced. The mitochondrial genome is 16 529 bp in length, with the base composition of 31.61% A, 26.88% T, 26.55% C, and 14.96% G, containing 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and a major non-coding control region (D-loop region). The gene order and orientation are similar with some typical fish species. The data will provide useful molecular information for phylogenetic studies concerning P. vachelli and its related species.

The complete mitochondrial genome of the hybrid of Leiocassis longirostris (♂)×Pelteobagrus fulvidraco (♀)

Abstract In this work, we reported the complete mitochondrial DNA sequence of the hybrid of Leiocassis longirostris (♂)×Pelteobagrus fulvidraco (♀), which was obtained by artificial hybridization. The total length of the mitochondrial genome is 16,527 bp, with the base composition of 30.86% for A, 25.56% for T, 28.20% for C, and 15.38% for G. It contains two ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes, and a major non-coding control region (D-loop region). The arrangement of these genes is the same as that found in the teleosts. All the protein initiation codons are ATG, except for COX1 that begins with GTG. The complete mitogenome of the hybrid provides an important data set for the study in mitochondrial inheritance mechanism. Both the termination-associated sequence and critical central conserved sequences (CSB-D, CSB-E, and CSB-F) were also detected.

Identification of HIF-1 signaling pathway in Pelteobagrus vachelli using RNA-Seq: effects of acute hypoxia and reoxygenation on oxygen sensors, respiratory metabolism, and hematology indices

Oxygen is a vital element in aquatic environments. The concentration of oxygen to which aquatic organisms are exposed is influenced by salinity, water temperature, weather, and surface water runoff. Hypoxia has a serious effect on fish populations, and can lead to the loss of habitat and die-offs. Therefore, in the present study we used next-generation sequencing technology to characterize the transcriptomes of Pelteobagrus vachelli and identified 70 candidate genes in the HIF-1 signaling pathway that are important for the hypoxic response in all metazoan species. For the first time, the present study reported the effects of acute hypoxia and reoxygenation on oxygen sensors, respiratory metabolism, and hematology indices in P. vachelli. The predicted physiological adjustments show that P. vachelli’s blood oxygen-carrying capacity was increased through increased RBC, HB, and SI after hypoxia exposure. Glycolysis-related enzyme activities (PFK, HK, and PK) and LDH in the brain and liver also increased, indicating a rise in anaerobic metabolism. The observed reduction in oxidative enzyme level (CS) in the liver during hypoxia suggests a concomitant depression in aerobic metabolism. There were significant increases in oxygen sensor mRNA expression and HIF-1α protein expression during hypoxia and reoxygenation exposure, suggesting that the HIF-1 signaling pathway was activated in the liver and brain of P. vachelli in response to acute hypoxia and reoxygenation. Our findings suggest that oxygen sensors (e.g., HIF-1α) of P. vachelli are potentially useful biomarkers of environmental hypoxic exposure. These data contribute to a better understanding of the molecular mechanisms of the hypoxia signaling pathway in fish under hypoxia and reoxygenation.

Integrated analysis of mRNA-seq and miRNA-seq reveals the potential roles of sex-biased miRNA-mRNA pairs in gonad tissue of dark sleeper (Odontobutis potamophila)

BackgroundThe dark sleeper (Odontobutis potamophila) is an important commercial fish species which shows a sexually dimorphic growth pattern. However, the lack of sex transcriptomic data is hindering further research and genetically selective breeding of the dark sleeper. In this study, integrated analysis of mRNA and miRNA was performed on gonad tissue to elucidate the molecular mechanisms of sex determination and differentiation in the dark sleeper.ResultsA total of 143 differentially expressed miRNAs and 16,540 differentially expressed genes were identified. Of these, 8103 mRNAs and 75 miRNAs were upregulated in testes, and 8437 mRNAs and 68 miRNAs were upregulated in ovaries. Integrated analysis of miRNA and mRNA expression profiles predicted more than 50,000 miRNA-mRNA interaction sites, and among them 27,583 negative miRNA-mRNA interactions. A number of sex related genes were targeted by sex-biased miRNAs. The relationship between 15 sex-biased genes and 15 sex-biased miRNAs verified by using qRT-PCR were described. Additionally, a number of SNPs were revealed through the transcriptome data.ConclusionsThe overall results of this study facilitate our understanding of the molecular mechanism underlying sex determination and differentiation and provide valuable genomic information for selective breeding of the dark sleeper.