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Davidović PG, Blagojević DJ, Lazić GG, Simeunović JB. Gene expression changes in Daphnia magna following waterborne exposure to cyanobacterial strains from the genus Nostoc. HARMFUL ALGAE 2022; 115:102232. [PMID: 35623688 DOI: 10.1016/j.hal.2022.102232] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/17/2022] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
Cyanobacteria can produce highly potent cyanotoxins, however, limited information is provided about their toxicity mechanisms in exposed aquatic invertebrates at the molecular level. In the present study, the effects of cyanobacterial strains from the genus Nostoc (Nostoc Z1 and Nostoc 2S3B) in Daphnia magna after waterborne exposure were investigated. Examined endpoints included immobilization (survival) in acute toxicity tests and selected gene expression changes (cyp314, cyp360A8, gst, p-gp, vtg) analyzed by the quantitative real-time polymerase chain reaction (RT-PCR). In addition, enzyme-linked immunosorbent assay (ELISA) was performed to determine whether the observed changes could be due to the presence of microcystins, the most widespread group of cyanotoxins. The results of acute toxicity tests have shown only minor changes in survival rates, which have not exceeded 20% after 48 h of exposure to either strain. On the other hand, significant changes were recorded in molecular responses of Daphnia to tested strains. Treatment with the aquatic strain Nostoc Z1 altered the expression levels of all analyzed genes. Both strains caused a significant p-glycoprotein (p-gp) induction at 75 µg ml-1 which suggests the involvement of p-gp mediated multixenobiotic resistance mechanism (MXR) in facilitating excretion of toxic cyanobacterial compounds in daphnids. Additionally, these strains caused an increase in the expression levels of cyp360A8, indicating that genes related to detoxification processes could be sensitive indicators of cyanobacterial toxicity. Statistically significant induction of cyp314, as well as increases in expression of gst and vtg, were observed only after exposure to Nostoc Z1. This study indicates the potential of certain cyanobacterial metabolites to modify the expression of toxicant responsive genes involved in phase I and phase III of the xenobiotic metabolism, as well as possible interference with growth and reproduction in D. magna. Low microcystin concentrations found in both samples suggest that these cyanotoxins were not responsible for the detected toxic effects.
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Affiliation(s)
- Petar G Davidović
- University of Novi Sad, Faculty of Sciences, Department of Biology and Ecology, Trg Dositeja Obradovića 2, Novi Sad 21000, Republic of Serbia
| | - Dajana J Blagojević
- University of Novi Sad, Faculty of Sciences, Department of Biology and Ecology, Trg Dositeja Obradovića 2, Novi Sad 21000, Republic of Serbia
| | - Gospava G Lazić
- Scientific Veterinary Institute "Novi Sad", Rumenački put 20, Novi Sad 21000, Republic of Serbia
| | - Jelica B Simeunović
- University of Novi Sad, Faculty of Sciences, Department of Biology and Ecology, Trg Dositeja Obradovića 2, Novi Sad 21000, Republic of Serbia.
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Suppa A, Kvist J, Li X, Dhandapani V, Almulla H, Tian AY, Kissane S, Zhou J, Perotti A, Mangelson H, Langford K, Rossi V, Brown JB, Orsini L. Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target species. MICROBIOME 2020; 8:170. [PMID: 33339542 PMCID: PMC7780628 DOI: 10.1186/s40168-020-00943-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 11/09/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Research around the weedkiller Roundup is among the most contentious of the twenty-first century. Scientists have provided inconclusive evidence that the weedkiller causes cancer and other life-threatening diseases, while industry-paid research reports that the weedkiller has no adverse effect on humans or animals. Much of the controversial evidence on Roundup is rooted in the approach used to determine safe use of chemicals, defined by outdated toxicity tests. We apply a system biology approach to the biomedical and ecological model species Daphnia to quantify the impact of glyphosate and of its commercial formula, Roundup, on fitness, genome-wide transcription and gut microbiota, taking full advantage of clonal reproduction in Daphnia. We then apply machine learning-based statistical analysis to identify and prioritize correlations between genome-wide transcriptional and microbiota changes. RESULTS We demonstrate that chronic exposure to ecologically relevant concentrations of glyphosate and Roundup at the approved regulatory threshold for drinking water in the US induce embryonic developmental failure, induce significant DNA damage (genotoxicity), and interfere with signaling. Furthermore, chronic exposure to the weedkiller alters the gut microbiota functionality and composition interfering with carbon and fat metabolism, as well as homeostasis. Using the "Reactome," we identify conserved pathways across the Tree of Life, which are potential targets for Roundup in other species, including liver metabolism, inflammation pathways, and collagen degradation, responsible for the repair of wounds and tissue remodeling. CONCLUSIONS Our results show that chronic exposure to concentrations of Roundup and glyphosate at the approved regulatory threshold for drinking water causes embryonic development failure and alteration of key metabolic functions via direct effect on the host molecular processes and indirect effect on the gut microbiota. The ecological model species Daphnia occupies a central position in the food web of aquatic ecosystems, being the preferred food of small vertebrates and invertebrates as well as a grazer of algae and bacteria. The impact of the weedkiller on this keystone species has cascading effects on aquatic food webs, affecting their ability to deliver critical ecosystem services. Video Abstract.
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Affiliation(s)
- Antonio Suppa
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT UK
- Department of Chemistry, Life Sciences and Environmental Sustainability University of Parma, Department of Life Sciences, Viale Usberti, 11/A, Parma, Italy
| | - Jouni Kvist
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Xiaojing Li
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT UK
| | - Vignesh Dhandapani
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT UK
| | - Hanan Almulla
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT UK
| | | | - Stephen Kissane
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT UK
| | - Jiarui Zhou
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT UK
| | - Alessio Perotti
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT UK
| | | | | | - Valeria Rossi
- Department of Chemistry, Life Sciences and Environmental Sustainability University of Parma, Department of Life Sciences, Viale Usberti, 11/A, Parma, Italy
| | - James B. Brown
- Environmental Bioinformatics, Centre for Computational Biology, School of Biosciences, University of Birmingham Edgbaston, Birmingham, B15 2TT UK
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Statistics Department, University of California, Berkeley, Berkeley, CA, 94720 USA, Preminon LLC, Rodeo, CA 94572 USA
| | - Luisa Orsini
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT UK
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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Asselman J, Semmouri I, Jackson CE, Keith N, Van Nieuwerburgh F, Deforce D, Shaw JR, De Schamphelaere KAC. Genome-Wide Stress Responses to Copper and Arsenic in a Field Population of Daphnia. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:3850-3859. [PMID: 30817885 DOI: 10.1021/acs.est.8b06720] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Over the past decade, significant advances have been made to unravel molecular mechanisms of stress response in different ecotoxicological model species. Within this study, we focus on population level transcriptomic responses of a natural population of Daphnia magna Straus, (1820), to heavy metals. We aim to characterize the population level transcriptomic responses, which include standing genetic variation, and improve our understanding on how populations respond to environmental stress at a molecular level. We studied population level responses to two heavy metals, copper and arsenic, and their binary mixture across time. Transcriptomic patterns identified significantly regulated gene families and genes at the population level including cuticle proteins and resilins. Furthermore, some of these differentially regulated gene families, such as cuticle proteins, were also significantly enriched for genetic variations including SNPs and MNPs. In general, genetic variation was observed in specific gene families, many of which are known to be involved in stress response. Overall, our results indicate that molecular stress responses can be identified within natural populations and that linking molecular mechanisms with genetic variation at the population level could contribute significantly to adverse outcome frameworks.
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Affiliation(s)
- Jana Asselman
- Laboratory of Environmental Toxicology and Aquatic Ecology, Environmental Toxicology Unit - GhEnToxLab , Ghent University , Campus Coupure, Coupure Links 653, Building F, Second Floor , 9000 Gent , Belgium
| | - Ilias Semmouri
- Laboratory of Environmental Toxicology and Aquatic Ecology, Environmental Toxicology Unit - GhEnToxLab , Ghent University , Campus Coupure, Coupure Links 653, Building F, Second Floor , 9000 Gent , Belgium
| | - Craig E Jackson
- School of Public and Environmental Affairs , Indiana University , 1315 E 10th Sreett , Bloomington , Indiana 47405 , United States
| | - Nathan Keith
- School of Public and Environmental Affairs , Indiana University , 1315 E 10th Sreett , Bloomington , Indiana 47405 , United States
| | - Filip Van Nieuwerburgh
- Laboratory for Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences , Ghent University , Campus UZ, Ottergemse Steenweg 460 , 9000 Ghent , Belgium
| | - Dieter Deforce
- Laboratory for Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences , Ghent University , Campus UZ, Ottergemse Steenweg 460 , 9000 Ghent , Belgium
| | - Joseph R Shaw
- School of Public and Environmental Affairs , Indiana University , 1315 E 10th Sreett , Bloomington , Indiana 47405 , United States
- School of Biosciences , University of Birmingham , Birmingham B15 2TT , United Kingdom
| | - Karel A C De Schamphelaere
- Laboratory of Environmental Toxicology and Aquatic Ecology, Environmental Toxicology Unit - GhEnToxLab , Ghent University , Campus Coupure, Coupure Links 653, Building F, Second Floor , 9000 Gent , Belgium
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Semmouri I, Asselman J, Van Nieuwerburgh F, Deforce D, Janssen CR, De Schamphelaere KAC. The transcriptome of the marine calanoid copepod Temora longicornis under heat stress and recovery. MARINE ENVIRONMENTAL RESEARCH 2019; 143:10-23. [PMID: 30415781 DOI: 10.1016/j.marenvres.2018.10.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/10/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
Understanding the impacts of global change in zooplankton communities is crucial, as alterations in the zooplankton communities can affect entire marine ecosystems. Despite the economic and ecological importance of the calanoid copepod Temora longicornis in the Belgian part of the North Sea, molecular data is still very limited for this species. Using HiSeq Illumina sequencing, we sequenced the whole transcriptome of T. longicornis, after being exposed to realistic temperatures of 14 and 17 °C. After both an acute (1 day) and a more sustained (5 days) thermal exposure to 17 °C, we investigated gene expression differences with animals exposed to 14 °C, which may be critical for the thermal acclimation and resilience of this copepod species. We also studied the possibility of a short term stress recovery of a heat shock. A total of 179,569 transcripts were yielded, of which 44,985 putative ORF transcripts were identified. These transcripts were subsequently annotated into roughly 22,000 genes based on known sequences using Gene Ontology (GO) and KEGG databases. Temora only showed a mild response to both the temperature and the duration of the exposure. We found that the expression of 27 transcripts varied significantly with an increase in temperature of 3 °C, of which eight transcripts were differentially expressed after acute exposure only. Gene set enrichment analysis revealed that, overall, T. longicornis was more impacted by a sustained thermal exposure, rather than an immediate (acute) exposure, with two times as many enriched GO terms in the sustained treatment. We also identified several general stress responses independent of exposure time, such as modified protein synthesis, energy mobilisation, cuticle and chaperone proteins. Finally, we highlighted candidate genes of a possible recovery from heat exposure, identifying similar terms as those enriched in the heat treatments, i.e. related to for example energy metabolism, cuticle genes and extracellular matrix. The data presented in this study provides the first transcriptome available for T. longicornis which can be used for future genomic studies.
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Affiliation(s)
- Ilias Semmouri
- Ghent University, Laboratory of Environmental Toxicology and Aquatic Ecology, Faculty of Bioscience Engineering, 9000, Ghent, Belgium.
| | - Jana Asselman
- Ghent University, Laboratory of Environmental Toxicology and Aquatic Ecology, Faculty of Bioscience Engineering, 9000, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Ghent University, Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, 9000, Ghent, Belgium
| | - Dieter Deforce
- Ghent University, Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, 9000, Ghent, Belgium
| | - Colin R Janssen
- Ghent University, Laboratory of Environmental Toxicology and Aquatic Ecology, Faculty of Bioscience Engineering, 9000, Ghent, Belgium
| | - Karel A C De Schamphelaere
- Ghent University, Laboratory of Environmental Toxicology and Aquatic Ecology, Faculty of Bioscience Engineering, 9000, Ghent, Belgium
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Asselman J, Pfrender ME, Lopez JA, Shaw JR, De Schamphelaere KAC. Gene Coexpression Networks Drive and Predict Reproductive Effects in Daphnia in Response to Environmental Disturbances. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:317-326. [PMID: 29211465 DOI: 10.1021/acs.est.7b05256] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Increasing effects of anthropogenic stressors and those of natural origin on aquatic ecosystems have intensified the need for predictive and functional models of their effects. Here, we use gene expression patterns in combination with weighted gene coexpression networks and generalized additive models to predict effects on reproduction in the aquatic microcrustacean Daphnia. We developed models to predict effects on reproduction upon exposure to different cyanobacteria, different insecticides and binary mixtures of cyanobacteria and insecticides. Models developed specifically for groups of stressors (e.g., either cyanobacteria or insecticides) performed better than general models developed on all data. Furthermore, models developed using in silico generated mixture gene expression profiles from single stressor data were able to better predict effects on reproduction compared to models derived from the mixture exposures themselves. Our results highlight the potential of gene expression data to quantify effects of complex exposures at higher level organismal effects without prior mechanistic knowledge or complex exposure data.
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Affiliation(s)
- J Asselman
- Laboratory of Environmental Toxicology and Aquatic Ecology, Environmental Toxicology Unit (GhEnToxLab), Ghent University , Ghent, B-9000, Belgium
| | - M E Pfrender
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame , Indiana 46556, United States
- Genomics & Bioinformatics Core, University of Notre Dame , Indiana 46556, United States
| | - J A Lopez
- Genomics & Bioinformatics Core, University of Notre Dame , Indiana 46556, United States
| | - J R Shaw
- The School of Public and Environmental Affairs and The Center for Genomics and Bioinformatics, Indiana University , Bloomington, Indiana, United States
- Environmental Genomics Group, School of Biosciences, University of Birmingham , Birmingham, U.K
| | - K A C De Schamphelaere
- Laboratory of Environmental Toxicology and Aquatic Ecology, Environmental Toxicology Unit (GhEnToxLab), Ghent University , Ghent, B-9000, Belgium
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Zhao JS, Wang AY, Zhao HB, Chen YH. Transcriptome sequencing and differential gene expression analysis of the schistosome-transmitting snail Oncomelania hupensis inhabiting hilly and marshland regions. Sci Rep 2017; 7:15809. [PMID: 29150650 PMCID: PMC5693929 DOI: 10.1038/s41598-017-16084-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 11/07/2017] [Indexed: 12/18/2022] Open
Abstract
The freshwater snail Oncomelania hupensis is the unique intermediate host of the blood fluke Schistosoma japonicum, which is the major cause of schistosomiasis. The snail inhabits two contrasting environments: the hilly and marshland regions. The hilly snails are smaller in size and have the typical smooth shell, whereas the marshland snails are larger and possess the ribbed shell. To reveal the differences in gene expression between the hilly and marshland snails, a total of six snails, three per environment, were individually examined by RNA sequencing technology. All paired-end reads were assembled into contigs from which 34,760 unigenes were predicted. Based on single nucleotide polymorphisms, principal component analysis and neighbor-joining clustering revealed two distinct clusters of hilly and marshland snails. Analysis of expression changes between environments showed that upregulated genes relating to immunity and development were enriched in hilly snails, while those associated with reproduction were over-represented in marshland snails. Eight differentially expressed genes between the two types of snails were validated by qRT-PCR. Our study identified candidate genes that could be targets for future functional studies, and provided a link between expression profiling and ecological adaptation of the snail that may have implications for schistosomiasis control.
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Affiliation(s)
- Jin-Song Zhao
- School of Basic Medicine, Wannan Medical College, Wuhu, 241002, China
| | - An-Yun Wang
- School of Public Health, Wannan Medical College, Wuhu, 241002, China
| | - Hua-Bin Zhao
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yan-Hong Chen
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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Kim HY, Asselman J, Jeong TY, Yu S, De Schamphelaere KAC, Kim SD. Multigenerational Effects of the Antibiotic Tetracycline on Transcriptional Responses of Daphnia magna and Its Relationship to Higher Levels of Biological Organizations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:12898-12907. [PMID: 29023098 DOI: 10.1021/acs.est.7b05050] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Given the risk of environmental pollution by pharmaceutical compounds and the effects of these compounds on exposed ecosystems, ecologically relevant and realistic assessments are required. However, many studies have been mostly focused on individual responses in a single generation exposed to one-effect concentrations. Here, transcriptional responses of the crustacean Daphnia magna to the antibiotic tetracycline across multiple generations and effect concentrations were investigated. The results demonstrated that tetracycline induced different transcriptional responses of daphnids that were dependent on dose and generation. For example, reproduction-related expressed sequence tags (ESTs), including vitellogenin, were distinctly related to the dose-dependent tetracycline exposure, whereas multigenerational exposure induced significant change of molting-related ESTs such as cuticle protein. A total of 65 ESTs were shared in all contrasts, suggesting a conserved mechanism of tetracycline toxicity regardless of exposure concentration or time. Most of them were associated with general stress responses including translation, protein and carbohydrate metabolism, and oxidative phosphorylation. In addition, effects across the dose-response curve showed higher correlative connections among transcriptional, physiological, and individual responses than multigenerational effects. In the multigenerational exposure, the connectivity between adjacent generations decreased with increasing generation number. The results clearly highlight that exposure concentration and time trigger different mechanisms and functions, providing further evidence that multigenerational and dose-response effects cannot be neglected in environmental risk assessment.
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Affiliation(s)
- Hyun Young Kim
- Research and Development Division, Korea Institute of Nuclear Nonproliferation and Control (KINAC) , 1534 Yuseong-daero, Yuseong-gu, Daejeon, 34054 Republic of Korea
| | - Jana Asselman
- Laboratory of Environmental Toxicology and Aquatic Ecology (GhEnToxLab), Ghent University , Ghent, B-9000 Belgium
| | - Tae-Yong Jeong
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST) , 123 Cheomdan-gwagiro, Buk-gu, Gwangju, 61005 Republic of Korea
| | - Seungho Yu
- Radiation Research Division for Industry and Environment, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute , Jeongeup-Si, Jeollabuk-Do, 56212 Republic of Korea
| | - Karel A C De Schamphelaere
- Laboratory of Environmental Toxicology and Aquatic Ecology (GhEnToxLab), Ghent University , Ghent, B-9000 Belgium
| | - Sang Don Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST) , 123 Cheomdan-gwagiro, Buk-gu, Gwangju, 61005 Republic of Korea
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Abstract
Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact of effective population size on genome evolution. For this purpose, we present a high quality genome assembly of Daphnia pulex (PA42), and compare this with the first sequenced genome of this species (TCO), which was derived from an isolate from a population with >90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at the gene level, with an average amino acid sequence identity of 98.8 and >60% of orthologous proteins identical. Nonetheless, there is a highly elevated number of genes in the TCO genome annotation, with ∼7000 excess genes appearing to be false positives. This view is supported by the high GC content, lack of introns, and short length of these suspicious gene annotations. Consistent with the view that reduced effective population size can facilitate the accumulation of slightly deleterious genomic features, we observe more proliferation of transposable elements (TEs) and a higher frequency of gained introns in the TCO genome.
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Asselman J, De Coninck DI, Beert E, Janssen CR, Orsini L, Pfrender ME, Decaestecker E, De Schamphelaere KA. Bisulfite Sequencing with Daphnia Highlights a Role for Epigenetics in Regulating Stress Response to Microcystis through Preferential Differential Methylation of Serine and Threonine Amino Acids. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:924-931. [PMID: 27983812 DOI: 10.1021/acs.est.6b03870] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Little is known about the influence that environmental stressors may have on genome-wide methylation patterns, and to what extent epigenetics may be involved in environmental stress response. Yet, studies of methylation patterns under stress could provide crucial insights on stress response and toxicity pathways. Here, we focus on genome-wide methylation patterns in the microcrustacean Daphnia magna, a model organism in ecotoxicology and risk assessment, exposed to the toxic cyanobacterium Microcystis aeruginosa. Bisulfite sequencing of exposed and control animals highlighted differential methylation patterns in Daphnia upon exposure to Microcystis primarily in exonic regions. These patterns are enriched for serine/threonine amino acid codons and genes related to protein synthesis, transport and degradation. Furthermore, we observed that genes with differential methylation corresponded well with genes susceptible to alternative splicing in response to Microcystis stress. Overall, our results suggest a complex mechanistic response in Daphnia characterized by interactions between DNA methylation and gene regulation mechanisms. These results underscore that DNA methylation is modulated by environmental stress and can also be an integral part of the toxicity response in our study species.
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Affiliation(s)
- Jana Asselman
- Laboratory for Environmental Toxicology and Aquatic Ecology (GhEnToxLab), Ghent University , Ghent, B-9000, Belgium
- Department of Biological Sciences, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Dieter Im De Coninck
- Laboratory for Environmental Toxicology and Aquatic Ecology (GhEnToxLab), Ghent University , Ghent, B-9000, Belgium
| | - Eline Beert
- Laboratory of Aquatic Biology, KU Leuven-Kulak , Kortrijk, B-8500, Belgium
| | - Colin R Janssen
- Laboratory for Environmental Toxicology and Aquatic Ecology (GhEnToxLab), Ghent University , Ghent, B-9000, Belgium
| | - Luisa Orsini
- Environmental Genomics Group, School of Biosciences, University of Birmingham , Birmingham, B15 2TT, United Kingdom
| | - Michael E Pfrender
- Department of Biological Sciences, University of Notre Dame , Notre Dame, Indiana 46556, United States
- Environmental Change Initiative, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Ellen Decaestecker
- Laboratory of Aquatic Biology, KU Leuven-Kulak , Kortrijk, B-8500, Belgium
| | - Karel Ac De Schamphelaere
- Laboratory for Environmental Toxicology and Aquatic Ecology (GhEnToxLab), Ghent University , Ghent, B-9000, Belgium
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Transcriptome Analysis of the Tadpole Shrimp (Triops longicaudatus) by Illumina Paired-End Sequencing: Assembly, Annotation, and Marker Discovery. Genes (Basel) 2016; 7:genes7120114. [PMID: 27918468 PMCID: PMC5192490 DOI: 10.3390/genes7120114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/19/2016] [Accepted: 11/24/2016] [Indexed: 11/17/2022] Open
Abstract
The tadpole shrimp (Triops longicaudatus) is an aquatic crustacean that helps control pest populations. It inhabits freshwater ponds and pools and has been described as a living fossil. T. longicaudatus was officially declared an endangered species South Korea in 2005; however, through subsequent protection and conservation management, it was removed from the endangered species list in 2012. The limited number of available genetic resources on T. longicaudatus makes it difficult to obtain valuable genetic information for marker-aided selection programs. In this study, whole-transcriptome sequencing of T. longicaudatus generated 39.74 GB of clean data and a total of 269,822 contigs using the Illumina HiSeq 2500 platform. After clustering, a total of 208,813 unigenes with an N50 length of 1089 bp were generated. A total of 95,105 unigenes were successfully annotated against Protostome (PANM), Unigene, Eukaryotic Orthologous Groups (KOG), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases using BLASTX with a cut-off of 1E−5. A total of 57,731 unigenes were assigned to GO terms, and 7247 unigenes were mapped to 129 KEGG pathways. Furthermore, 1595 simple sequence repeats (SSRs) were detected from the unigenes with 1387 potential SSR markers. This is the first report of high-throughput transcriptome analysis of T. longicaudatus, and it provides valuable insights for genetic research and molecular-assisted breeding of this important species.
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Horn RL, Ramaraj T, Devitt NP, Schilkey FD, Cowley DE. De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis. Mol Ecol Resour 2016; 17:161-171. [PMID: 27292122 DOI: 10.1111/1755-0998.12555] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 06/05/2016] [Accepted: 06/07/2016] [Indexed: 01/16/2023]
Abstract
Next-generation sequencing techniques, such as RNA sequencing, have provided a wealth of genomic information for nonmodel species. Transcriptomic information can be used to quantify the patterns of gene expression, which can identify how environmental differences invoke organismal stress responses and provide a gauge in predicting species adaptability. In our study, we used RNA sequencing to characterize the first transcriptome from a naupliar tadpole shrimp (Triops newberryi) to identify the genes expressed during the early life history stages and which could be important for future genomic studies. RNA was extracted from naupliar T. newberryi that were reared in a laboratory-controlled setting and in two different water types, a native and a non-native condition. A total of six replicates, three per condition, were sequenced with the Illumina Hi-Seq 2000 achieving 365 M 50-nt reads. High-quality reads were produced and de novo assembly was used to construct a T. newberryi transcriptome that was approximately 24.8 M base pairs. More than 10 000 peptides were predicted from the assembly, and genes were sorted into gene ontology categories. The use of different water conditions allowed for a preliminary differential gene expression analysis in order to compare the changes in gene expression between conditions. There were 299 differentially expressed genes between water conditions that might serve as a focal point for future genomic studies of Triops acclimation to different environments. The Triops transcriptome could serve as vital genomic information for additional studies on Branchiopod crustaceans.
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Affiliation(s)
- Rebekah L Horn
- Biology Department, Trent University, 1600 West Bank Drive, Peterborough, ON, Canada, K9J 7B8
| | - Thiruvarangan Ramaraj
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA
| | - Nicholas P Devitt
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA
| | - Faye D Schilkey
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA
| | - David E Cowley
- Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Box 30003, MSC 4901, Las Cruces, NM, 88003, USA
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Lyu K, Meng Q, Zhu X, Dai D, Zhang L, Huang Y, Yang Z. Changes in iTRAQ-Based Proteomic Profiling of the Cladoceran Daphnia magna Exposed to Microcystin-Producing and Microcystin-Free Microcystis aeruginosa. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:4798-4807. [PMID: 27057760 DOI: 10.1021/acs.est.6b00101] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Global warming and increased nutrient fluxes cause cyanobacterial blooms in freshwater ecosystems. These phenomena have increased the concern for human health and ecosystem services. The mass occurrences of toxic cyanobacteria strongly affect freshwater zooplankton communities, especially the unselective filter feeder Daphnia. However, the molecular mechanisms of cyanobacterial toxicity remain poorly understood. This study is the first to combine the established body growth rate (BGR), which is an indicator of life-history fitness, with differential peptide labeling (iTRAQ)-based proteomics in Daphnia magna influenced by microcystin-producing (MP) and microcystin-free (MF) Microcystis aeruginosa. A significant decrease in BGR was detected when D. magna was exposed to MP or MF M. aeruginosa. Conducting iTRAQ proteomic analyses, we successfully identified and quantified 211 proteins with significant changes in expression. A cluster of orthologous groups revealed that M. aeruginosa-affected differential proteins were strongly associated with lipid, carbohydrate, amino acid, and energy metabolism. These parameters could potentially explain the reduced fitness based on the cost of the substance metabolism.
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Affiliation(s)
- Kai Lyu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University , 1 Wenyuan Road, Nanjing 210023, China
| | - Qingguo Meng
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University , 1 Wenyuan Road, Nanjing 210023, China
| | - Xuexia Zhu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University , 1 Wenyuan Road, Nanjing 210023, China
| | - Daoxin Dai
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University , 1 Wenyuan Road, Nanjing 210023, China
| | - Lu Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University , 1 Wenyuan Road, Nanjing 210023, China
| | - Yuan Huang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University , 1 Wenyuan Road, Nanjing 210023, China
| | - Zhou Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University , 1 Wenyuan Road, Nanjing 210023, China
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Asselman J, De Coninck DIM, Pfrender ME, De Schamphelaere KAC. Gene Body Methylation Patterns in Daphnia Are Associated with Gene Family Size. Genome Biol Evol 2016; 8:1185-96. [PMID: 27017526 PMCID: PMC4860698 DOI: 10.1093/gbe/evw069] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The relation between gene body methylation and gene function remains elusive. Yet, our understanding of this relationship can contribute significant knowledge on how and why organisms target specific gene bodies for methylation. Here, we studied gene body methylation patterns in two Daphnia species. We observed both highly methylated genes and genes devoid of methylation in a background of low global methylation levels. A small but highly significant number of genes was highly methylated in both species. Remarkably, functional analyses indicate that variation in methylation within and between Daphnia species is primarily targeted to small gene families whereas large gene families tend to lack variation. The degree of sequence similarity could not explain the observed pattern. Furthermore, a significant negative correlation between gene family size and the degree of methylation suggests that gene body methylation may help regulate gene family expansion and functional diversification of gene families leading to phenotypic variation.
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Affiliation(s)
- Jana Asselman
- Laboratory for Environmental Toxicology and Aquatic Ecology, Environmental Toxicology Unit (GhEnToxLab), Ghent University, Ghent, Belgium Department of Biological Sciences, University of Notre Dame
| | - Dieter I M De Coninck
- Laboratory for Environmental Toxicology and Aquatic Ecology, Environmental Toxicology Unit (GhEnToxLab), Ghent University, Ghent, Belgium Laboratory of Pharmaceutical Biotechnology (labFBT), Ghent University, Ghent, Belgium
| | - Michael E Pfrender
- Department of Biological Sciences, University of Notre Dame Environmental Change Initiative, University of Notre Dame
| | - Karel A C De Schamphelaere
- Laboratory for Environmental Toxicology and Aquatic Ecology, Environmental Toxicology Unit (GhEnToxLab), Ghent University, Ghent, Belgium
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Drugă B, Turko P, Spaak P, Pomati F. Cyanobacteria Affect Fitness and Genetic Structure of Experimental Daphnia Populations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:3416-3424. [PMID: 26943751 DOI: 10.1021/acs.est.5b05973] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Zooplankton communities can be strongly affected by cyanobacterial blooms, especially species of genus Daphnia, which are key-species in lake ecosystems. Here, we explored the effect of microcystin/nonmicrocystin (MC/non-MC) producing cyanobacteria in the diet of experimental Daphnia galeata populations composed of eight genotypes. We used D. galeata clones hatched from ephippia 10 to 60 years old, which were first tested in monocultures, and then exposed for 10 weeks as mixed populations to three food treatments consisting of green algae combined with cyanobacteria able/unable of producing MC. We measured the expression of nine genes potentially involved in Daphnia acclimation to cyanobacteria: six protease genes, one ubiquitin-conjugating enzyme gene, and two rRNA genes, and then we tracked the dynamics of the genotypes in mixed populations. The expression pattern of one protease and the ubiquitin-conjugating enzyme genes was positively correlated with the increased fitness of competing clones in the presence of cyanobacteria, suggesting physiological plasticity. The genotype dynamics in mixed populations was only partially related to the growth rates of clones in monocultures and varied strongly with the food. Our results revealed strong intraspecific differences in the tolerance of D. galeata clones to MC/non-MC-producing cyanobacteria in their diet, suggesting microevolutionary effects.
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Affiliation(s)
- Bogdan Drugă
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , Department of Aquatic Ecology, 133 Überlandstrasse, 8600 Dübendorf, Switzerland
- Institute of Biological Research , Branch of the National Institute of Research and Development for Biological Sciences, 48 Republicii, 400015 Cluj-Napoca, Romania
| | - Patrick Turko
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , Department of Aquatic Ecology, 133 Überlandstrasse, 8600 Dübendorf, Switzerland
- Institute of Integrative Biology, ETH Zurich , Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Piet Spaak
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , Department of Aquatic Ecology, 133 Überlandstrasse, 8600 Dübendorf, Switzerland
- Institute of Integrative Biology, ETH Zurich , Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Francesco Pomati
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , Department of Aquatic Ecology, 133 Überlandstrasse, 8600 Dübendorf, Switzerland
- Institute of Integrative Biology, ETH Zurich , Universitätstrasse 16, 8092 Zürich, Switzerland
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