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Wang Y, Guo J, Jia X, Luo X, Zhou Y, Mao X, Fan X, Hu H, Zhu H, Jia C, Guo X, Cheng L, Li X, Zhang Z. Genome and transcriptome of Chinese medaka (Oryzias sinensis) and its uses as a model fish for evaluating estrogenicity of surface water. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120724. [PMID: 36427818 DOI: 10.1016/j.envpol.2022.120724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/13/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
Ecological toxicity assessments of contaminants in aquatic environments are of great concern. However, a dilemma in ecological toxicity assessments often arises when linking the effects found in model animals in the laboratory and the phenomena observed in wild fishes in the field due to species differences. Chinese medaka (Oryzias sinensis), widely distributed in East Asia, is a satisfactory model animal to assess aquatic environment in China. Here, we domesticated this species and assembled its genome (814 Mb) using next-generation sequencing (NGS). A total of 21,922 high-confidence genes with 41,306 transcripts were obtained and annotated, and their expression patterns in tissues were determined by RNA-sequencing. Six mostly sensitive biomarker genes, including vtg1, vtg3, vtg6, zp3a.2, zp2l1, and zp2.3 to estrogen exposure were screened and validated in the fish exposed to concentrations of estrone (E1), 17β-estradiol (E2), and estriol (E3) under laboratory condition. Field investigations were then performed to evaluating the gene expression of biomarkers in wild Chinese medaka and levels of E1, E2, and E3 in the fish habitats. It was found that in 40 sampling sites, the biomarker genes were obviously highly expressed in the wild fish from about half sites, and the detection frequencies of E1, E2, and E3, were 97.5%, 42.5%, and 45% with mean concentrations of 82.48, 43.17, 52.69 ng/L, respectively. Correlation analyses of the biomarker gene expressions in the fish with the estrogens levels which were converted to EEQs showed good correlation, indicating that the environmental estrogens and estrogenicity of the surface water might adversely affect wild fishes. Finally, histologic examination of gonads in male wild Chinese medaka was performed and found the presence of intersex in the fish. This study facilitated the uses of Chinese medaka as a model animal for ecotoxicological studies.
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Affiliation(s)
- Yue Wang
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China
| | - Jilong Guo
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China
| | - Xiaojing Jia
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China
| | - Xiaozhe Luo
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China
| | - Ying Zhou
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China
| | - Xingtai Mao
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China
| | - Xiaolin Fan
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China
| | - Hongxia Hu
- Fisheries Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100068, China
| | - Hua Zhu
- Fisheries Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100068, China
| | - Chengxia Jia
- Fisheries Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100068, China
| | - Xuan Guo
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China
| | - Lan Cheng
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China
| | - Xiqing Li
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China
| | - Zhaobin Zhang
- College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, 100871, China.
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Mohamed AR, Naval-Sanchez M, Menzies M, Evans B, King H, Reverter A, Kijas JW. Leveraging transcriptome and epigenome landscapes to infer regulatory networks during the onset of sexual maturation. BMC Genomics 2022; 23:413. [PMID: 35650521 PMCID: PMC9158274 DOI: 10.1186/s12864-022-08514-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/29/2022] [Indexed: 12/03/2022] Open
Abstract
Background Despite sexual development being ubiquitous to vertebrates, the molecular mechanisms underpinning this fundamental transition remain largely undocumented in many organisms. We designed a time course experiment that successfully sampled the period when Atlantic salmon commence their trajectory towards sexual maturation. Results Through deep RNA sequencing, we discovered key genes and pathways associated with maturation in the pituitary-ovarian axis. Analyzing DNA methylomes revealed a bias towards hypermethylation in ovary that implicated maturation-related genes. Co-analysis of DNA methylome and gene expression changes revealed chromatin remodeling genes and key transcription factors were both significantly hypermethylated and upregulated in the ovary during the onset of maturation. We also observed changes in chromatin state landscapes that were strongly correlated with fundamental remodeling of gene expression in liver. Finally, a multiomic integrated analysis revealed regulatory networks and identified hub genes including TRIM25 gene (encoding the estrogen-responsive finger protein) as a putative key regulator in the pituitary that underwent a 60-fold change in connectivity during the transition to maturation. Conclusion The study successfully documented transcriptome and epigenome changes that involved key genes and pathways acting in the pituitary – ovarian axis. Using a Systems Biology approach, we identified hub genes and their associated networks deemed crucial for onset of maturation. The results provide a comprehensive view of the spatiotemporal changes involved in a complex trait and opens the door to future efforts aiming to manipulate puberty in an economically important aquaculture species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08514-8.
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Comprehensive Characterization of Multitissue Expression Landscape, Co-Expression Networks and Positive Selection in Pikeperch. Cells 2021; 10:cells10092289. [PMID: 34571938 PMCID: PMC8471114 DOI: 10.3390/cells10092289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 11/19/2022] Open
Abstract
Promising efforts are ongoing to extend genomics resources for pikeperch (Sander lucioperca), a species of high interest for the sustainable European aquaculture sector. Although previous work, including reference genome assembly, transcriptome sequence, and single-nucleotide polymorphism genotyping, added a great wealth of genomic tools, a comprehensive characterization of gene expression across major tissues in pikeperch still remains an unmet research need. Here, we used deep RNA-Sequencing of ten vital tissues collected in eight animals to build a high-confident and annotated trancriptome atlas, to detect the tissue-specificity of gene expression and co-expression network modules, and to investigate genome-wide selective signatures in the Percidae fish family. Pathway enrichment and protein–protein interaction network analyses were performed to characterize the unique biological functions of tissue-specific genes and co-expression modules. We detected strong functional correlations and similarities of tissues with respect to their expression patterns—but also significant differences in the complexity and composition of their transcriptomes. Moreover, functional analyses revealed that tissue-specific genes essentially play key roles in the specific physiological functions of the respective tissues. Identified network modules were also functionally coherent with tissues’ main physiological functions. Although tissue specificity was not associated with positive selection, several genes under selection were found to be involved in hypoxia, immunity, and gene regulation processes, that are crucial for fish adaption and welfare. Overall, these new resources and insights will not only enhance the understanding of mechanisms of organ biology in pikeperch, but also complement the amount of genomic resources for this commercial species.
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Botwright NA, Mohamed AR, Slinger J, Lima PC, Wynne JW. Host-Parasite Interaction of Atlantic salmon ( Salmo salar) and the Ectoparasite Neoparamoeba perurans in Amoebic Gill Disease. Front Immunol 2021; 12:672700. [PMID: 34135900 PMCID: PMC8202022 DOI: 10.3389/fimmu.2021.672700] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/05/2021] [Indexed: 12/13/2022] Open
Abstract
Marine farmed Atlantic salmon (Salmo salar) are susceptible to recurrent amoebic gill disease (AGD) caused by the ectoparasite Neoparamoeba perurans over the growout production cycle. The parasite elicits a highly localized response within the gill epithelium resulting in multifocal mucoid patches at the site of parasite attachment. This host-parasite response drives a complex immune reaction, which remains poorly understood. To generate a model for host-parasite interaction during pathogenesis of AGD in Atlantic salmon the local (gill) and systemic transcriptomic response in the host, and the parasite during AGD pathogenesis was explored. A dual RNA-seq approach together with differential gene expression and system-wide statistical analyses of gene and transcription factor networks was employed. A multi-tissue transcriptomic data set was generated from the gill (including both lesioned and non-lesioned tissue), head kidney and spleen tissues naïve and AGD-affected Atlantic salmon sourced from an in vivo AGD challenge trial. Differential gene expression of the salmon host indicates local and systemic upregulation of defense and immune responses. Two transcription factors, znfOZF-like and znf70-like, and their associated gene networks significantly altered with disease state. The majority of genes in these networks are candidates for mediators of the immune response, cellular proliferation and invasion. These include Aurora kinase B-like, rho guanine nucleotide exchange factor 25-like and protein NDNF-like inhibited. Analysis of the N. perurans transcriptome during AGD pathology compared to in vitro cultured N. perurans trophozoites, as a proxy for wild type trophozoites, identified multiple gene candidates for virulence and indicates a potential master regulatory gene system analogous to the two-component PhoP/Q system. Candidate genes identified are associated with invasion of host tissue, evasion of host defense mechanisms and formation of the mucoid lesion. We generated a novel model for host-parasite interaction during AGD pathogenesis through integration of host and parasite functional profiles. Collectively, this dual transcriptomic study provides novel molecular insights into the pathology of AGD and provides alternative theories for future research in a step towards improved management of AGD.
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Affiliation(s)
- Natasha A Botwright
- Livestock and Aquaculture, CSIRO Agriculture and Food, St Lucia, QLD, Australia
| | - Amin R Mohamed
- Livestock and Aquaculture, CSIRO Agriculture and Food, St Lucia, QLD, Australia
| | - Joel Slinger
- Livestock and Aquaculture, CSIRO Agriculture and Food, Woorim, QLD, Australia
| | - Paula C Lima
- Livestock and Aquaculture, CSIRO Agriculture and Food, St Lucia, QLD, Australia
| | - James W Wynne
- Livestock and Aquaculture, CSIRO Agriculture and Food, Hobart, TAS, Australia
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Alcaraz AJG, Potěšil D, Mikulášek K, Green D, Park B, Burbridge C, Bluhm K, Soufan O, Lane T, Pipal M, Brinkmann M, Xia J, Zdráhal Z, Schneider D, Crump D, Basu N, Hogan N, Hecker M. Development of a Comprehensive Toxicity Pathway Model for 17α-Ethinylestradiol in Early Life Stage Fathead Minnows ( Pimephales promelas). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:5024-5036. [PMID: 33755441 DOI: 10.1021/acs.est.0c05942] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
There is increasing pressure to develop alternative ecotoxicological risk assessment approaches that do not rely on expensive, time-consuming, and ethically questionable live animal testing. This study aimed to develop a comprehensive early life stage toxicity pathway model for the exposure of fish to estrogenic chemicals that is rooted in mechanistic toxicology. Embryo-larval fathead minnows (FHM; Pimephales promelas) were exposed to graded concentrations of 17α-ethinylestradiol (water control, 0.01% DMSO, 4, 20, and 100 ng/L) for 32 days. Fish were assessed for transcriptomic and proteomic responses at 4 days post-hatch (dph), and for histological and apical end points at 28 dph. Molecular analyses revealed core responses that were indicative of observed apical outcomes, including biological processes resulting in overproduction of vitellogenin and impairment of visual development. Histological observations indicated accumulation of proteinaceous fluid in liver and kidney tissues, energy depletion, and delayed or suppressed gonad development. Additionally, fish in the 100 ng/L treatment group were smaller than controls. Integration of omics data improved the interpretation of perturbations in early life stage FHM, providing evidence of conservation of toxicity pathways across levels of biological organization. Overall, the mechanism-based embryo-larval FHM model showed promise as a replacement for standard adult live animal tests.
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Affiliation(s)
- Alper James G Alcaraz
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Kamil Mikulášek
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Derek Green
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada
| | - Bradley Park
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada
| | - Connor Burbridge
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Kerstin Bluhm
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada
| | - Othman Soufan
- Computer Science Department, St. Francis Xavier University, Antigonish, Nova Scotia B2G 2W5, Canada
| | - Taylor Lane
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada
- Department of Environment and Geography, York University, York YO10 5NG, United Kingdom
| | - Marek Pipal
- RECETOX, Masaryk University, Brno 625 00, Czech Republic
| | - Markus Brinkmann
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada
- School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C8, Canada
- Global Institute for Water Security, University of Saskatchewan, Saskatoon, Saskatchewan S7N 3H5, Canada
| | - Jianguo Xia
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec H9X 3V9, Canada
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - David Schneider
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan S7N 0W9, Canada
- School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C8, Canada
| | - Doug Crump
- Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa, Ontario K1A 0H3, Canada
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec H9X 3V9, Canada
| | - Natacha Hogan
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada
- Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Markus Hecker
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada
- School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C8, Canada
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Transcriptome Response of Atlantic Salmon ( Salmo salar) to a New Piscine Orthomyxovirus. Pathogens 2020; 9:pathogens9100807. [PMID: 33007914 PMCID: PMC7600774 DOI: 10.3390/pathogens9100807] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 01/12/2023] Open
Abstract
Pilchard orthomyxovirus (POMV) is an emerging pathogen of concern to the salmon industry in Australia. To explore the molecular events that underpin POMV infection, we challenged Atlantic salmon (Salmo salar) post-smolts in seawater via cohabitation. Tissue samples of the head kidney and liver were collected from moribund and surviving individuals and analyzed using transcriptome sequencing. Viral loads were higher in the head kidney compared to the liver, yet the liver presented more upregulated genes. Fish infected with POMV showed a strong innate immune response that included the upregulation of pathogen recognition receptors such as RIG-I and Toll-like receptors as well as the induction of interferon-stimulated genes (MX, ISG15). Moribund fish also presented a dramatic induction of pro-inflammatory cytokines, contributing to severe tissue damage and morbidity. An induction of major histocompatibility complex (MHC) class I genes (B2M) and markers of T cell-mediated immunity (CD8-alpha, CD8-beta, Perforin-1, Granzyme-A) was observed in both moribund fish and survivors. In addition, differential connectivity analysis showed that three key regulators (RELA/p65, PRDM1, and HLF) related to cell-mediated immunity had significant differences in connectivity in "clinically healthy" versus "clinically affected" or moribund fish. Collectively, our results show that T cell-mediated immunity plays a central role in the response of Atlantic salmon to the infection with POMV.
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Transcriptome Profiling across Five Tissues of Giant Panda. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3852586. [PMID: 32851066 PMCID: PMC7436357 DOI: 10.1155/2020/3852586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/03/2020] [Accepted: 06/01/2020] [Indexed: 11/18/2022]
Abstract
Gene differential expression studies can serve to explore and understand the laws and characteristics of animal life activities, and the difference in gene expression between different animal tissues has been well demonstrated and studied. However, for the world-famous rare and protected species giant panda (Ailuropoda melanoleuca), only the transcriptome of the blood and spleen has been reported separately. Here, in order to explore the transcriptome differences between the different tissues of the giant panda, transcriptome profiles of the heart, liver, spleen, lung, and kidney from five captive giant pandas were constructed with Illumina HiSeq 2500 platform. The comparative analysis of the intertissue gene expression patterns was carried out based on the generated RNA sequencing datasets. Analyses of Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction (PPI) network were performed according to the identified differentially expressed genes (DEGs). We generated 194.52 GB clean base data from twenty-five sequencing libraries and identified 18,701 genes, including 3492 novel genes. With corrected p value <0.05 and |log2FoldChange| >2, we finally obtained 921, 553, 574, 457, and 638 tissue-specific DEGs in the heart, liver, spleen, lung, and kidney, respectively. In addition, we identified TTN, CAV3, LDB3, TRDN, and ACTN2 in the heart; FGA, AHSG, and SERPINC1 in the liver; CD19, CD79B, and IL21R in the spleen; NKX2-4 and SFTPB in the lung; GC and HRG in the kidney as hub genes in the PPI network. The results of the analyses showed a similar gene expression pattern between the spleen and lung. This study provided for the first time the heart, liver, lung, and kidney's transcriptome resources of the giant panda, and it provided a valuable resource for further genetic research or other potential research.
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Andrew SC, Primmer CR, Debes PV, Erkinaro J, Verta JP. The Atlantic salmon whole blood transcriptome and how it relates to major locus maturation genotypes and other tissues. Mar Genomics 2020; 56:100809. [PMID: 33632426 DOI: 10.1016/j.margen.2020.100809] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023]
Abstract
The Atlantic salmon (Salmo salar) is important to many ecosystems and local economies and has therefore become the focus of a broad range of research questions that have benefited from the availability of high-quality genomic resources. Albeit gene expression studies have been extensive for this species, the transcriptome information for Atlantic salmon whole blood has been lacking. A transcriptome of Atlantic salmon blood would be a valuable resource for future studies, especially those wishing to take non-lethal samples. Here, we report a whole blood transcriptome for Atlantic salmon constructed from twelve 8-month old salmon parr using RNA-seq. We identify transcriptomic proxies for the genotype at the major maturation timing locus vestigial-like 3 (vgll3). Differentially expressed genes between the early and late maturing genotypes showed overrepresented Gene Ontology (GO) terms with the strongest result linked to 13 ribosomal subunit genes. To assess how the whole blood gene expression profile relates to other tissues, we compare the blood transcriptome to the reference transcriptome of fourteen other tissue types using both a common PCA method and a novel method. The novel method compares transcriptomes when gene expression is visualised as a layer using thin-plate spline smoothers. Both methods found similar patterns with the blood transcriptome being quite unique compared to the transcription profiles of other tissues.
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Affiliation(s)
- Samuel C Andrew
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland
| | - Craig R Primmer
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland; Institute of Biotechnology, University of Helsinki, Finland
| | - Paul V Debes
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland; Department of Aquaculture and Fish Biology, Hólar University College, Sauðárkrókur, Iceland
| | | | - Jukka-Pekka Verta
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland.
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