1
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Drozdova P, Kizenko A, Saranchina A, Gurkov A, Firulyova M, Govorukhina E, Timofeyev M. The diversity of opsins in Lake Baikal amphipods (Amphipoda: Gammaridae). BMC Ecol Evol 2021; 21:81. [PMID: 33971810 PMCID: PMC8108468 DOI: 10.1186/s12862-021-01806-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/20/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Vision is a crucial sense for the evolutionary success of many animal groups. Here we explore the diversity of visual pigments (opsins) in the transcriptomes of amphipods (Crustacea: Amphipoda) and conclude that it is restricted to middle (MWS) and long wavelength-sensitive (LWS) opsins in the overwhelming majority of examined species. RESULTS We evidenced (i) parallel loss of MWS opsin expression in multiple species (including two independently evolved lineages from the deep and ancient Lake Baikal) and (ii) LWS opsin amplification (up to five transcripts) in both Baikal lineages. The number of LWS opsins negatively correlated with habitat depth in Baikal amphipods. Some LWS opsins in Baikal amphipods contained MWS-like substitutions, suggesting that they might have undergone spectral tuning. CONCLUSIONS This repeating two-step evolutionary scenario suggests common triggers, possibly the lack of light during the periods when Baikal was permanently covered with thick ice and its subsequent melting. Overall, this observation demonstrates the possibility of revealing climate history by following the evolutionary changes in protein families.
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Affiliation(s)
- Polina Drozdova
- Irkutsk State University, Irkutsk, Russia
- Baikal Research Centre, Irkutsk, Russia
| | | | | | - Anton Gurkov
- Irkutsk State University, Irkutsk, Russia
- Baikal Research Centre, Irkutsk, Russia
| | - Maria Firulyova
- Computer Technologies Department, ITMO University, St. Petersburg, Russia
| | | | - Maxim Timofeyev
- Irkutsk State University, Irkutsk, Russia
- Baikal Research Centre, Irkutsk, Russia
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2
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Artal MC, Pereira KD, Luchessi AD, Okura VK, Henry TB, Marques-Souza H, de Aragão Umbuzeiro G. Transcriptome analysis in Parhyale hawaiensis reveal sex-specific responses to AgNP and AgCl exposure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 260:113963. [PMID: 32004961 DOI: 10.1016/j.envpol.2020.113963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/09/2019] [Accepted: 01/09/2020] [Indexed: 06/10/2023]
Abstract
Analysis of the transcriptome of organisms exposed to toxicants offers new insights for ecotoxicology, but further research is needed to enhance interpretation of results and effectively incorporate them into useful environmental risk assessments. Factors that must be clarified to improve use of transcriptomics include assessment of the effect of organism sex within the context of toxicant exposure. Amphipods are well recognized as model organisms for toxicity evaluation because of their sensitivity and amenability to laboratory conditions. To investigate whether response to metals in crustaceans differs according to sex we analyzed the amphipod Parhyale hawaiensis after exposure to AgCl and Ag nanoparticles (AgNP) via contaminated food. Gene specific analysis and whole genome transcriptional profile of male and female organisms were performed by both RT-qPCR and RNA-seq. We observed that expression of transcripts of genes glutathione transferase (GST) did not differ among AgCl and AgNP treatments. Significant differences between males and females were observed after exposure to AgCl and AgNP. Males presented twice the number of differentially expressed genes in comparison to females, and more differentially expressed were observed after exposure to AgNP than AgCl treatments in both sexes. The genes that had the greatest change in expression relative to control were those genes related to peptidase and catalytic activity and chitin and carbohydrate metabolic processes. Our study is the first to demonstrate sex specific differences in the transcriptomes of amphipods upon exposure to toxicants and emphasizes the importance of considering gender in ecotoxicology.
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Affiliation(s)
- Mariana Coletty Artal
- School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, 05508-000, Brazil; School of Technology, University of Campinas, Limeira, São Paulo, 13484-332, Brazil
| | - Karina Danielle Pereira
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas, Limeira, São Paulo, 13484-350, Brazil; Institute of Biosciences, São Paulo State University, Rio Claro, São Paulo, 13506-900, Brazil
| | - Augusto Ducati Luchessi
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas, Limeira, São Paulo, 13484-350, Brazil; Institute of Biosciences, São Paulo State University, Rio Claro, São Paulo, 13506-900, Brazil
| | - Vagner Katsumi Okura
- Life Sciences Core Facility (LaCTAD), University of Campinas, Campinas, São Paulo, 13083-886, Brazil
| | - Theodore Burdick Henry
- Institute of Life and Earth Sciences, School of Energy, Geoscience, Infrastructure, and Society, Heriot-Watt University, EH14 4AS, Edinburgh, Scotland, UK; Center for Environmental Biotechnology, The University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN, 37996-1605, United States
| | - Henrique Marques-Souza
- Department of Biochemistry and Tissue Biology, University of Campinas, Campinas, São Paulo, 13083-970, Brazil.
| | - Gisela de Aragão Umbuzeiro
- School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, 05508-000, Brazil; School of Technology, University of Campinas, Limeira, São Paulo, 13484-332, Brazil.
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3
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De Novo assembly and characterisation of the greentail prawn (Metapenaeus bennettae) hepatopancreas transcriptome – identification of stress response and detoxification transcripts. Mar Genomics 2019; 47:100677. [DOI: 10.1016/j.margen.2019.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/15/2019] [Accepted: 04/05/2019] [Indexed: 11/19/2022]
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4
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Hiki K, Nakajima F, Tobino T, Watanabe H, Yamamoto H. Whole transcriptome analysis of an estuarine amphipod exposed to highway road dust. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 675:141-150. [PMID: 31026638 DOI: 10.1016/j.scitotenv.2019.04.201] [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: 02/19/2019] [Revised: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 06/09/2023]
Abstract
Urban road dust can potentially have adverse effects on aquatic and benthic ecosystems if discharged into receiving waters; however, little is known about the mode of action of road dust toxicity within aquatic organisms. With an aim to reveal the biological effects of road dust on benthic crustacean species, we performed a de novo transcriptome analysis of the estuarine amphipod Grandidierella japonica exposed to road dust collected from highways around Tokyo. A transcriptome analysis by Illumina HiSeq 2500 identified differentially expressed genes related to the gamma-aminobutyric acid (GABA) signaling pathway, oxidative damage, and cuticle metabolism. Among these, a GABAB receptor subunit showed down-regulation in the road dust treatment, but a constant expression in the treatment of road dust with a carbonaceous resin XAD-4, which can reduce the acute toxicity of road dust to G. japonica. These results and the time course expressions of the related genes were partially confirmed by quantitative PCR (qPCR) experiments. Although the linkage between acute lethal toxicity and the molecular initiating events induced by road dust was still unclear, our findings provide lines of evidence to identify the causative toxicants in urban road dust.
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Affiliation(s)
- Kyoshiro Hiki
- Center for Environmental Risk Research, National Institute for Environmental Studies, Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan; Department of Urban Engineering, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Fumiyuki Nakajima
- Environmental Science Center, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tomohiro Tobino
- Department of Urban Engineering, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Haruna Watanabe
- Center for Environmental Risk Research, National Institute for Environmental Studies, Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan
| | - Hiroshi Yamamoto
- Center for Environmental Risk Research, National Institute for Environmental Studies, Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan
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5
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Zhou S, Wei Z, Chu T, Yu H, Li S, Zhang W, Gui W. Transcriptomic analysis of zebrafish (Danio rerio) embryos to assess integrated biotoxicity of Xitiaoxi River waters. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 242:42-53. [PMID: 29958174 DOI: 10.1016/j.envpol.2018.06.060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 05/22/2018] [Accepted: 06/19/2018] [Indexed: 06/08/2023]
Abstract
Assessing the toxicity posed by mixtures of unknown chemicals to aquatic organisms is challenging. In this study, water samples from six cross-sections along the Xitiaoxi River Basin (XRB) were monthly or bimonthly collected in 2014. The year-period physiochemical parameters as well as one-month-water sample based acute biotoxicity tests showed that the river water quality of the year was generally in a good status. High performance liquid chromatography (HPLC) screening based on one-month-water samples suggested that the organic pollutants might be non-to-moderately-polar chemicals in very low concentrations. One-month-water sample based RNA-seq was performed to measure the mRNA differential expression profile of zebrafish larvae to furtherly explore the potential bioeffect and the spatial water quality change of the river. Result indicated that the number of deferentially expressed genes (DEGs) tended to increase along the downstream direction of the river. Gene ontology (GO) enrichment analysis implied that the key pollutants might mainly be the function disruptors of biological processes. Principle components analysis (PCA) combining with transcripts and one-month-water sample based physiochemical parameters indicated that the pollution might be similar at TP, DP and CTB sites while pollution homology existed on some extent between YBQ and JW sites. Although the water quality of the river had a complex time-space alternation during the year, and the one-month-data based RNA-seq could not reflex the whole year-water quality of a watershed, the gene expression profile via RNA-seq provided an alternative way for assessing integrated biotoxicity of surface water, and it was relatively fit for early-warning of water quality of a watershed with unobservable acute toxicity. However, the identification of detail toxicants and the links between DEGs and pollution level as well as physiological-biochemical toxicity needed further investigation.
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Affiliation(s)
- Shengli Zhou
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, 310058, PR China; Zhejiang Province Environmental Monitoring Center, Hangzhou, 310012, PR China
| | - Zheng Wei
- Zhejiang Province Environmental Monitoring Center, Hangzhou, 310012, PR China
| | - Tianyi Chu
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, 310058, PR China
| | - Haiyan Yu
- Zhejiang Province Environmental Monitoring Center, Hangzhou, 310012, PR China
| | - Shuying Li
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, 310058, PR China
| | - Wei Zhang
- Department of Plant, Soil and Microbial Sciences, Environmental Science and Policy Program, Michigan State University, East Lansing, 48824, USA
| | - Wenjun Gui
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, 310058, PR China.
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6
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Hook SE, Mondon J, Revill AT, Greenfield PA, Stephenson SA, Strzelecki J, Corbett P, Armstrong E, Song J, Doan H, Barrett S. Monitoring sublethal changes in fish physiology following exposure to a light, unweathered crude oil. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 204:27-45. [PMID: 30173120 DOI: 10.1016/j.aquatox.2018.08.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 08/14/2018] [Accepted: 08/16/2018] [Indexed: 06/08/2023]
Abstract
Biomarkers are frequently used to determine the exposure of fish to petroleum hydrocarbons following an oil spill. These biomarkers must be chosen carefully if they are to be used to determine sublethal toxic impacts as well as oil exposure. Many commonly used biomarkers relate to the metabolism of high molecular weight, typically pyrogenic, polycyclic aromatic hydrocarbons (PAHs), which are not abundant in unweathered crude oil. The goal of this study was to compare the efficacy of different biomarkers, including histological examination and transcriptomic profiling, in showing exposure to oil and the potential for sublethal toxic impacts. To achieve these goals, subadults/adults of the spotted dragonet (Repomucenus calcaratus) were exposed to a representative light, unweathered Australian oil for 96 h, so that the physiological changes that occur with exposure could be documented. Fish were then transferred to clean sediment for 90 h to quantify recovery. Biomarker changes, including PAH metabolites, 7-ethoxyresorufin O-deethylase (EROD), and histopathology, are presented in this work. In addition, a de novo transcriptome for the spotted dragonet was assembled, and differential transcript abundance was determined for the gill and liver of petroleum-exposed fish relative to a control. Increased levels of some biliary phenanthrene metabolites were seen throughout the exposure period. EROD levels showed modest, but not significant, increases. Transcriptomic differences were noted in the abundances of transcripts with a role in inflammation, primary metabolism and cardiac function. The patterns of transcript abundance in the gill and the liver changed in a manner that reflected exposure and recovery. The histology showed elevated prevalence of lesions, most notably vacuolization in liver and heart tissue, multi-organ necrosis, and lamellar epithelial lifting and telangiectasia in the gill. These findings suggest that short-term exposures to low molecular weight PAHs could elicit changes in the health of fish that are well predicted by the transcriptome. Furthermore, when light oil is released into the environment, exposure and subsequent risk would be better estimated using phenanthrene metabolite levels rather than EROD. This study also adds to the weight of evidence that exposure to low molecular weight PAHs may cause cardiac problems in fish. Further study is needed to determine the impact of these changes on reproductive capacity, long-term survival, and other population specific parameters.
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Affiliation(s)
- Sharon E Hook
- CSIRO Oceans and Atmosphere, Lucas Heights, NSW, 2234, Australia.
| | - Julie Mondon
- School of Life and Environmental Sciences, Deakin University, Warrnambool, VIC, 3280, Australia
| | | | | | | | - Joanna Strzelecki
- CSIRO Oceans and Atmosphere, Indian Ocean Marine Research Centre, Crawley, WA, 6009, Australia
| | - Patricia Corbett
- School of Life and Environmental Sciences, Deakin University, Warrnambool, VIC, 3280, Australia
| | - Emily Armstrong
- CSIRO Oceans and Atmosphere, Lucas Heights, NSW, 2234, Australia; School of Life and Environmental Sciences, Deakin University, Warrnambool, VIC, 3280, Australia
| | - Jing Song
- School of Life and Environmental Sciences, Deakin University, Warrnambool, VIC, 3280, Australia; Graduate School of Fisheries Science and Environmental Studies, Nagasaki University, Nagasaki, Japan
| | - Hai Doan
- CSIRO Land and Water, Glen Osmond, SA, 5064, Australia
| | - Skye Barrett
- South Australian Research and Development Institute Aquatic Sciences, West Beach, SA, 5024, Australia
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7
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Christie AE, Pascual MG, Yu A. Peptidergic signaling in the tadpole shrimp Triops newberryi: A potential model for investigating the roles played by peptide paracrines/hormones in adaptation to environmental change. Mar Genomics 2018. [DOI: 10.1016/j.margen.2018.01.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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8
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Poynton HC, Hasenbein S, Benoit JB, Sepulveda MS, Poelchau MF, Hughes DST, Murali SC, Chen S, Glastad KM, Goodisman MAD, Werren JH, Vineis JH, Bowen JL, Friedrich M, Jones J, Robertson HM, Feyereisen R, Mechler-Hickson A, Mathers N, Lee CE, Colbourne JK, Biales A, Johnston JS, Wellborn GA, Rosendale AJ, Cridge AG, Munoz-Torres MC, Bain PA, Manny AR, Major KM, Lambert FN, Vulpe CD, Tuck P, Blalock BJ, Lin YY, Smith ME, Ochoa-Acuña H, Chen MJM, Childers CP, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni H, Worley KC, Muzny DM, Gibbs RA, Richards S. The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:6009-6022. [PMID: 29634279 DOI: 10.15482/usda.adc/1415994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Hyalella azteca is a cryptic species complex of epibenthic amphipods of interest to ecotoxicology and evolutionary biology. It is the primary crustacean used in North America for sediment toxicity testing and an emerging model for molecular ecotoxicology. To provide molecular resources for sediment quality assessments and evolutionary studies, we sequenced, assembled, and annotated the genome of the H. azteca U.S. Lab Strain. The genome quality and completeness is comparable with other ecotoxicological model species. Through targeted investigation and use of gene expression data sets of H. azteca exposed to pesticides, metals, and other emerging contaminants, we annotated and characterized the major gene families involved in sequestration, detoxification, oxidative stress, and toxicant response. Our results revealed gene loss related to light sensing, but a large expansion in chemoreceptors, likely underlying sensory shifts necessary in their low light habitats. Gene family expansions were also noted for cytochrome P450 genes, cuticle proteins, ion transporters, and include recent gene duplications in the metal sequestration protein, metallothionein. Mapping of differentially expressed transcripts to the genome significantly increased the ability to functionally annotate toxicant responsive genes. The H. azteca genome will greatly facilitate development of genomic tools for environmental assessments and promote an understanding of how evolution shapes toxicological pathways with implications for environmental and human health.
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Affiliation(s)
- Helen C Poynton
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Simone Hasenbein
- Aquatic Systems Biology Unit , Technical University of Munich , D-85354 Freising , Germany
| | - Joshua B Benoit
- Department of Biological Sciences , University of Cincinnati , Cincinnati , Ohio 45221 United States
| | - Maria S Sepulveda
- Forestry and Natural Resources , Purdue University , West Lafayette , Indiana 47907 United States
| | - Monica F Poelchau
- Agricultural Research Service, National Agricultural Library , U.S. Department of Agriculture , Beltsville , Maryland 20705 United States
| | - Daniel S T Hughes
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Shwetha C Murali
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Shuai Chen
- Forestry and Natural Resources , Purdue University , West Lafayette , Indiana 47907 United States
- OmicSoft Corporation, Cary , North Carolina 27513 United States
| | - Karl M Glastad
- Perelman School of Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 United States
| | - Michael A D Goodisman
- School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 United States
| | - John H Werren
- Biology Department , University of Rochester , Rochester , New York 14627 United States
| | - Joseph H Vineis
- Department of Marine and Environmental Sciences, Marine Science Center , Northeastern University , Nahant , Massachusetts 01908 United States
| | - Jennifer L Bowen
- Department of Marine and Environmental Sciences, Marine Science Center , Northeastern University , Nahant , Massachusetts 01908 United States
| | - Markus Friedrich
- Department of Biological Sciences , Wayne State University , Detroit Michigan 48202 United States
| | - Jeffery Jones
- Department of Biological Sciences , Wayne State University , Detroit Michigan 48202 United States
| | - Hugh M Robertson
- Department of Entomology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 United States
| | - René Feyereisen
- Department of Plant and Environmental Sciences , University of Copenhagen , DK-1871 Frederiksberg , Denmark
| | - Alexandra Mechler-Hickson
- Center of Rapid Evolution (CORE) and Department of Integrative Biology , University of Wisconsin , Madison , Wisconsin 53706 United States
| | - Nicholas Mathers
- Center of Rapid Evolution (CORE) and Department of Integrative Biology , University of Wisconsin , Madison , Wisconsin 53706 United States
| | - Carol Eunmi Lee
- Center of Rapid Evolution (CORE) and Department of Integrative Biology , University of Wisconsin , Madison , Wisconsin 53706 United States
| | - John K Colbourne
- School of Biosciences , University of Birmingham , Birmingham B15 2TT U.K
| | - Adam Biales
- National Exposure Research Laboratory , United States Environmental Protection Agency , Cincinnati , Ohio 45268 United States
| | - J Spencer Johnston
- Department of Entomology , Texas A&M University , College Station , Texas 77843 United States
| | - Gary A Wellborn
- Department of Biology , University of Oklahoma , Norman , Oklahoma 73019 United States
| | - Andrew J Rosendale
- Department of Biological Sciences , University of Cincinnati , Cincinnati , Ohio 45221 United States
| | - Andrew G Cridge
- Laboratory for Evolution and Development, Department of Biochemistry , University of Otago , Dunedin , 9054 New Zealand
| | - Monica C Munoz-Torres
- Environmental Genomics and Systems Biology Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 United States
| | - Peter A Bain
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Urrbrae SA 5064 Australia
| | - Austin R Manny
- Department of Microbiology & Cell Science , University of Florida , Gainesville , Florida 32611 United States
| | - Kaley M Major
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Faith N Lambert
- Center for Environmental and Human Toxicology, Department of Physiological Sciences , University of Florida , Gainesville , Florida 32611 United States
| | - Chris D Vulpe
- Center for Environmental and Human Toxicology, Department of Physiological Sciences , University of Florida , Gainesville , Florida 32611 United States
| | - Padrig Tuck
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Bonnie J Blalock
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Yu-Yu Lin
- Graduate Institute of Biomedical Electronics and Bioinformatics , National Taiwan University , Taipei , 10617 Taiwan
| | - Mark E Smith
- McConnell Group, Cincinnati , Ohio 45268 , United States
| | - Hugo Ochoa-Acuña
- Forestry and Natural Resources , Purdue University , West Lafayette , Indiana 47907 United States
| | - Mei-Ju May Chen
- Graduate Institute of Biomedical Electronics and Bioinformatics , National Taiwan University , Taipei , 10617 Taiwan
| | - Christopher P Childers
- Agricultural Research Service, National Agricultural Library , U.S. Department of Agriculture , Beltsville , Maryland 20705 United States
| | - Jiaxin Qu
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Shannon Dugan
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Sandra L Lee
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Hsu Chao
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Huyen Dinh
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Yi Han
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | | | - Kim C Worley
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
- Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Donna M Muzny
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Richard A Gibbs
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Stephen Richards
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
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9
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Poynton HC, Hasenbein S, Benoit JB, Sepulveda MS, Poelchau MF, Hughes DST, Murali SC, Chen S, Glastad KM, Goodisman MAD, Werren JH, Vineis JH, Bowen JL, Friedrich M, Jones J, Robertson HM, Feyereisen R, Mechler-Hickson A, Mathers N, Lee CE, Colbourne JK, Biales A, Johnston JS, Wellborn GA, Rosendale AJ, Cridge AG, Munoz-Torres MC, Bain PA, Manny AR, Major KM, Lambert FN, Vulpe CD, Tuck P, Blalock BJ, Lin YY, Smith ME, Ochoa-Acuña H, Chen MJM, Childers CP, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni H, Worley KC, Muzny DM, Gibbs RA, Richards S. The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:6009-6022. [PMID: 29634279 PMCID: PMC6091588 DOI: 10.1021/acs.est.8b00837] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Hyalella azteca is a cryptic species complex of epibenthic amphipods of interest to ecotoxicology and evolutionary biology. It is the primary crustacean used in North America for sediment toxicity testing and an emerging model for molecular ecotoxicology. To provide molecular resources for sediment quality assessments and evolutionary studies, we sequenced, assembled, and annotated the genome of the H. azteca U.S. Lab Strain. The genome quality and completeness is comparable with other ecotoxicological model species. Through targeted investigation and use of gene expression data sets of H. azteca exposed to pesticides, metals, and other emerging contaminants, we annotated and characterized the major gene families involved in sequestration, detoxification, oxidative stress, and toxicant response. Our results revealed gene loss related to light sensing, but a large expansion in chemoreceptors, likely underlying sensory shifts necessary in their low light habitats. Gene family expansions were also noted for cytochrome P450 genes, cuticle proteins, ion transporters, and include recent gene duplications in the metal sequestration protein, metallothionein. Mapping of differentially expressed transcripts to the genome significantly increased the ability to functionally annotate toxicant responsive genes. The H. azteca genome will greatly facilitate development of genomic tools for environmental assessments and promote an understanding of how evolution shapes toxicological pathways with implications for environmental and human health.
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Affiliation(s)
- Helen C Poynton
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Simone Hasenbein
- Aquatic Systems Biology Unit , Technical University of Munich , D-85354 Freising , Germany
| | - Joshua B Benoit
- Department of Biological Sciences , University of Cincinnati , Cincinnati , Ohio 45221 United States
| | - Maria S Sepulveda
- Forestry and Natural Resources , Purdue University , West Lafayette , Indiana 47907 United States
| | - Monica F Poelchau
- Agricultural Research Service, National Agricultural Library , U.S. Department of Agriculture , Beltsville , Maryland 20705 United States
| | - Daniel S T Hughes
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Shwetha C Murali
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Shuai Chen
- Forestry and Natural Resources , Purdue University , West Lafayette , Indiana 47907 United States
- OmicSoft Corporation, Cary , North Carolina 27513 United States
| | - Karl M Glastad
- Perelman School of Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 United States
| | - Michael A D Goodisman
- School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 United States
| | - John H Werren
- Biology Department , University of Rochester , Rochester , New York 14627 United States
| | - Joseph H Vineis
- Department of Marine and Environmental Sciences, Marine Science Center , Northeastern University , Nahant , Massachusetts 01908 United States
| | - Jennifer L Bowen
- Department of Marine and Environmental Sciences, Marine Science Center , Northeastern University , Nahant , Massachusetts 01908 United States
| | - Markus Friedrich
- Department of Biological Sciences , Wayne State University , Detroit Michigan 48202 United States
| | - Jeffery Jones
- Department of Biological Sciences , Wayne State University , Detroit Michigan 48202 United States
| | - Hugh M Robertson
- Department of Entomology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 United States
| | - René Feyereisen
- Department of Plant and Environmental Sciences , University of Copenhagen , DK-1871 Frederiksberg , Denmark
| | - Alexandra Mechler-Hickson
- Center of Rapid Evolution (CORE) and Department of Integrative Biology , University of Wisconsin , Madison , Wisconsin 53706 United States
| | - Nicholas Mathers
- Center of Rapid Evolution (CORE) and Department of Integrative Biology , University of Wisconsin , Madison , Wisconsin 53706 United States
| | - Carol Eunmi Lee
- Center of Rapid Evolution (CORE) and Department of Integrative Biology , University of Wisconsin , Madison , Wisconsin 53706 United States
| | - John K Colbourne
- School of Biosciences , University of Birmingham , Birmingham B15 2TT U.K
| | - Adam Biales
- National Exposure Research Laboratory , United States Environmental Protection Agency , Cincinnati , Ohio 45268 United States
| | - J Spencer Johnston
- Department of Entomology , Texas A&M University , College Station , Texas 77843 United States
| | - Gary A Wellborn
- Department of Biology , University of Oklahoma , Norman , Oklahoma 73019 United States
| | - Andrew J Rosendale
- Department of Biological Sciences , University of Cincinnati , Cincinnati , Ohio 45221 United States
| | - Andrew G Cridge
- Laboratory for Evolution and Development, Department of Biochemistry , University of Otago , Dunedin , 9054 New Zealand
| | - Monica C Munoz-Torres
- Environmental Genomics and Systems Biology Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 United States
| | - Peter A Bain
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Urrbrae SA 5064 Australia
| | - Austin R Manny
- Department of Microbiology & Cell Science , University of Florida , Gainesville , Florida 32611 United States
| | - Kaley M Major
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Faith N Lambert
- Center for Environmental and Human Toxicology, Department of Physiological Sciences , University of Florida , Gainesville , Florida 32611 United States
| | - Chris D Vulpe
- Center for Environmental and Human Toxicology, Department of Physiological Sciences , University of Florida , Gainesville , Florida 32611 United States
| | - Padrig Tuck
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Bonnie J Blalock
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Yu-Yu Lin
- Graduate Institute of Biomedical Electronics and Bioinformatics , National Taiwan University , Taipei , 10617 Taiwan
| | - Mark E Smith
- McConnell Group, Cincinnati , Ohio 45268 , United States
| | - Hugo Ochoa-Acuña
- Forestry and Natural Resources , Purdue University , West Lafayette , Indiana 47907 United States
| | - Mei-Ju May Chen
- Graduate Institute of Biomedical Electronics and Bioinformatics , National Taiwan University , Taipei , 10617 Taiwan
| | - Christopher P Childers
- Agricultural Research Service, National Agricultural Library , U.S. Department of Agriculture , Beltsville , Maryland 20705 United States
| | - Jiaxin Qu
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Shannon Dugan
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Sandra L Lee
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Hsu Chao
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Huyen Dinh
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Yi Han
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | | | - Kim C Worley
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
- Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Donna M Muzny
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Richard A Gibbs
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Stephen Richards
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
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10
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Krivoshiev BV, Beemster GTS, Sprangers K, Cuypers B, Laukens K, Blust R, Husson SJ. Transcriptome profiling of HepG2 cells exposed to the flame retardant 9,10-dihydro-9-oxa-10-phosphaphenanthrene 10-oxide (DOPO). Toxicol Res (Camb) 2018; 7:492-502. [PMID: 30090599 PMCID: PMC6060682 DOI: 10.1039/c8tx00006a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/09/2018] [Indexed: 12/31/2022] Open
Abstract
The flame retardant, 9,10-dihydro-9-oxa-10-phosphaphenanthrene 10-oxide (DOPO), has been receiving great interest given its superior fire protection properties, and its predicted low level of persistence, bioaccumulation, and toxicity. However, empirical toxicological data that are essential for a complete hazard assessment are severely lacking. In this study, we attempted to identify the potential toxicological modes of action by transcriptome (RNA-seq) profiling of the human liver hepatocellular carcinoma cell line, HepG2. Such insight may help in identifying compounds of concern and potential toxicological phenotypes. DOPO was found to have little cytotoxic potential, with lower effective concentrations compared to other flame retardants studied in the same cell line. Differentially expressed genes revealed a wide range of molecular effects including changes in protein, energy, DNA, and lipid metabolism, along with changes in cellular stress response pathways. In response to 250 μM DOPO, the most perturbed biological processes were fatty acid metabolism, androgen metabolism, glucose transport, and renal function and development, which is in agreement with other studies that observed similar effects of other flame retardants in other species. However, treatment with 2.5 μM DOPO resulted in very few differentially expressed genes and failed to indicate any potential effects on biology, despite such concentrations likely being orders of magnitude greater than would be encountered in the environment. This, together with the low levels of cytotoxicity, supports the potential replacement of the current flame retardants by DOPO, although further studies are needed to establish the nephrotoxicity and endocrine disruption of DOPO.
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Affiliation(s)
- Boris V Krivoshiev
- Department of Biology , Systemic Physiological & Ecotoxicological Research , University of Antwerp , Antwerp , Belgium .
| | - Gerrit T S Beemster
- Department of Biology , Integrated Molecular Plant Physiology Research , University of Antwerp , Antwerp , Belgium
| | - Katrien Sprangers
- Department of Biology , Integrated Molecular Plant Physiology Research , University of Antwerp , Antwerp , Belgium
| | - Bart Cuypers
- Department of Mathematics and Computer Science , Advanced Database Research and Modelling (ADReM) , University of Antwerp , Antwerp , Belgium
- Department of Biomedical Sciences , Unit of Molecular Parasitology , Institute of Tropical Medicine , Antwerp , Belgium
| | - Kris Laukens
- Department of Mathematics and Computer Science , Advanced Database Research and Modelling (ADReM) , University of Antwerp , Antwerp , Belgium
| | - Ronny Blust
- Department of Biology , Systemic Physiological & Ecotoxicological Research , University of Antwerp , Antwerp , Belgium .
| | - Steven J Husson
- Department of Biology , Systemic Physiological & Ecotoxicological Research , University of Antwerp , Antwerp , Belgium .
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11
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Das S, Shyamal S, Durica DS. Analysis of Annotation and Differential Expression Methods used in RNA-seq Studies in Crustacean Systems. Integr Comp Biol 2018; 56:1067-1079. [PMID: 27940611 DOI: 10.1093/icb/icw117] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In the field of crustacean biology, usage of RNA-seq to study gene expression is rapidly growing. Major advances in sequencing technology have contributed to the ability to examine complex patterns of genome activity in a wide range of organisms that are extensively used for comparative physiology, ecology and evolution, environmental monitoring, and commercial aquaculture. Relative to insect and vertebrate model organisms, however, information on the organization of crustacean genomes is virtually nonexistent, making de novo transcriptome assembly, annotation and quantification problematic and challenging. We present here a summary of the methodologies and software analyses employed in 23 recent publications, which describe de novo transcriptome assembly, annotation, and differential gene expression in a variety of crustacean experimental systems. We focus on establishing a series of best practices that will allow for investigators to produce datasets that are understandable, reproducible, and of general utility for related analyses and cross-study comparisons.
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Affiliation(s)
- Sunetra Das
- *Department of Biology, Colorado State University, 1878 Campus Delivery Fort Collins, CO 80523, USA;
| | | | - David S Durica
- Department of Biology, University of Oklahoma, Norman, OK 73019, USA
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12
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Toxicogenomics of the flame retardant tris (2-butoxyethyl) phosphate in HepG2 cells using RNA-seq. Toxicol In Vitro 2018; 46:178-188. [DOI: 10.1016/j.tiv.2017.10.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/10/2017] [Accepted: 10/08/2017] [Indexed: 11/20/2022]
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13
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Brinke A, Reifferscheid G, Klein R, Feiler U, Buchinger S. Transcriptional changes measured in rice roots after exposure to arsenite-contaminated sediments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:2707-2717. [PMID: 29134529 PMCID: PMC5773613 DOI: 10.1007/s11356-017-0515-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 10/18/2017] [Indexed: 06/07/2023]
Abstract
Transcriptional analyses are discussed to provide a deeper understanding of the molecular mechanisms underlying toxic effects. Thus, they can complement classic ecotoxicological test methods and potentially allow the identification of biomarkers associated to the exposure of chemical stressors and or adverse biological effects. This feasibility study intended to identify a set of potential gene expression biomarkers for arsenite-exposure in rice roots that could complement the informative value of an existing sediment-contact test with rice. A sediment-contact test with Oryza sativa with the parameters inhibition of root and shoot elongation as phenotypic endpoints was used as basis. Rice plants were exposed to arsenite-spiked sediments. Transcriptomic changes in response to arsenite were observed by means of cDNA-microarray analysis regarding the whole-transcriptome at two sublethal arsenite concentrations. In order to identify candidate biomarker genes, differentially expressed genes were identified. Arsenite-induced differentially expressed genes were significantly associated with gene ontology (GO)-terms that indicated a general stress response. Of the differentially expressed genes, five genes were selected and their expression was measured at seven arsenite concentrations by means of qPCR in order to obtain their expression profiles. Three candidate biomarker genes showed a dose-dependent upregulation, while two showed no clear dose-dependent expression. The expression of all candidate biomarkers was also assessed in rice plants grown on two arsenic-contaminated natural sediments, but only one biomarker gene showed the expected upregulation.
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Affiliation(s)
- Alexandra Brinke
- German Federal Institute of Hydrology, Am Mainzer Tor 1, 56068, Koblenz, Germany.
| | - Georg Reifferscheid
- German Federal Institute of Hydrology, Am Mainzer Tor 1, 56068, Koblenz, Germany
| | - Roland Klein
- Department VI, Trier University, Biogeography, 54286, Trier, Germany
| | - Ute Feiler
- German Federal Institute of Hydrology, Am Mainzer Tor 1, 56068, Koblenz, Germany
| | - Sebastian Buchinger
- German Federal Institute of Hydrology, Am Mainzer Tor 1, 56068, Koblenz, Germany
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14
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A toxicogenomics approach to screen chlorinated flame retardants tris(2-chloroethyl) phosphate and tris(2-chloroisopropyl) phosphate for potential health effects. J Appl Toxicol 2017; 38:459-470. [DOI: 10.1002/jat.3553] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 09/25/2017] [Accepted: 09/26/2017] [Indexed: 12/26/2022]
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15
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Christie AE. Neuropeptide discovery in Proasellus cavaticus: Prediction of the first large-scale peptidome for a member of the Isopoda using a publicly accessible transcriptome. Peptides 2017; 97:29-45. [PMID: 28893643 DOI: 10.1016/j.peptides.2017.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/01/2017] [Accepted: 09/03/2017] [Indexed: 11/29/2022]
Abstract
In silico transcriptome mining is one of the most effective methods for neuropeptide discovery in crustaceans, particularly for species that are small, rare or from geographically inaccessible habitats that make obtaining the large pools of tissue needed for other peptide discovery platforms impractical. Via this approach, large peptidomes have recently been described for members of many of the higher crustacean taxa, one notable exception being the Isopoda; no peptidome has been predicted for any member of this malacostracan order. Using a publicly accessible transcriptome for the isopod Proasellus cavaticus, a subcentimeter subterranean ground water dweller, the first in silico-predicted peptidome for a member of the Isopoda is presented here. BLAST searches employing known arthropod neuropeptide pre/preprohormone queries identified 49 transcripts as encoding putative homologs within the P. cavaticus transcriptome. The proteins deduced from these transcripts allowed for the prediction of 171 distinct mature neuropeptides. The P. cavaticus peptidome includes members of the adipokinetic hormone-corazonin-like peptide, allatostatin A, allatostatin B, allatostatin C, allatotropin, bursicon α, bursicon β, CCHamide, crustacean cardioactive peptide, crustacean hyperglycemic hormone/molt-inhibiting hormone, diuretic hormone 31, eclosion hormone, elevenin, FMRFamide-like peptide, glycoprotein hormone α2, leucokinin, myosuppressin, neuroparsin, neuropeptide F, pigment dispersing hormone, pyrokinin, red pigment concentrating hormone, RYamide, short neuropeptide F, sulfakinin, tachykinin-related peptide and trissin families, as well as many linker/precursor-related sequences that may or may not represent additional bioactive molecules. Interestingly, many of the predicted P. cavaticus neuropeptides possess structures identical (or nearly so) to those previously described from members of several other malacostracan orders, i.e., the Decapoda, Amphipoda and Euphausiacea, a finding that suggests broad phylogenetic conservation of bioactive peptide structures, and possibly functions, may exist within the Malacostraca.
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Affiliation(s)
- Andrew E Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822 USA, USA.
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16
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Christie AE, Yu A, Pascual MG. Circadian signaling in the Northern krill Meganyctiphanes norvegica: In silico prediction of the protein components of a putative clock system using a publicly accessible transcriptome. Mar Genomics 2017; 37:97-113. [PMID: 28964713 DOI: 10.1016/j.margen.2017.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/01/2017] [Accepted: 09/02/2017] [Indexed: 11/25/2022]
Abstract
The Northern krill Meganyctiphanes norvegica is a significant component of the zooplankton community in many regions of the North Atlantic Ocean. In the areas it inhabits, M. norvegica is of great importance ecologically, as it is both a major consumer of phytoplankton/small zooplankton and is a primary food source for higher-level consumers. One behavior of significance for both feeding and predator avoidance in Meganyctiphanes is diel vertical migration (DVM), i.e., a rising from depth at dusk and a return to depth at dawn. In this and other euphausiids, an endogenous circadian pacemaker is thought, at least in part, to control DVM. Currently, there is no information concerning the identity of the genes/proteins that comprise the M. norvegica circadian system. In fact, there is little information concerning the molecular underpinnings of circadian rhythmicity in crustaceans generally. Here, a publicly accessible transcriptome was used to identify the molecular components of a putative Meganyctiphanes circadian system. A complete set of core clock proteins was deduced from the M. norvegica transcriptome (clock, cryptochrome 2, cycle, period and timeless), as was a large suite of proteins that likely function as modulators of the core clock (e.g., doubletime), or serves as inputs to it (cryptochrome 1) or outputs from it (pigment dispersing hormone). This is the first description of a "complete" (core clock through putative output pathway signals) euphausiid clock system, and as such, provides a foundation for initiating molecular investigations of circadian signaling in M. norvegica and other krill species, including how clock systems may regulate DVM and other behaviors.
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Affiliation(s)
- Andrew E Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA.
| | - Andy Yu
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA
| | - Micah G Pascual
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA
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17
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Hook SE, Kroon FJ, Greenfield PA, Warne MSJ, Smith RA, Turner RD. Hepatic transcriptomic profiles from barramundi, Lates calcarifer, as a means of assessing organism health and identifying stressors in rivers in northern Queensland. MARINE ENVIRONMENTAL RESEARCH 2017; 129:166-179. [PMID: 28601346 DOI: 10.1016/j.marenvres.2017.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 05/12/2017] [Accepted: 05/29/2017] [Indexed: 06/07/2023]
Abstract
Resource managers need to differentiate between sites with and without contaminants and those where contaminants cause impacts. Potentially, transcriptomes could be used to evaluate sites where contaminant-induced effects may occur, to identify causative stressors of effects and potential adverse outcomes. To test this hypothesis, the hepatic transcriptomes in Barramundi, a perciforme teleost fish, (Lates calcarifer) from two reference sites, two agriculturally impacted sites sampled during the dry season, and an impacted site sampled during the wet season were compared. The hepatic transcriptome was profiled using RNA-Seq. Multivariate analysis showed that transcriptomes were clustered based on site and by inference water quality, but not sampling time. The largest differences in transcriptomic profile were between reference sites and a site sampled during high run-off, showing that impacted sites can be identified via RNA-Seq. Transcripts with altered abundance were linked to xenobiotic metabolism, peroxisome proliferation and stress responses, indicating putative stressors with the potential for adverse outcomes in barramundi.
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Affiliation(s)
- Sharon E Hook
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Oceans and Atmosphere, Kirrawee, NSW 2232, Australia.
| | - Frederieke J Kroon
- Australian Institute of Marine Science, PMB 3, Townsville, Queensland 4810, Australia
| | - Paul A Greenfield
- CSIRO Oceans and Atmosphere North Ryde, New South Wales 2113, Australia
| | - Michael St J Warne
- Centre for Agroecology, Water and Resilience, Coventry University, United Kingdom; Queensland Department of Science, Information Technology, and Innovation, Brisbane, Queensland 4001, Australia; Australian Rivers Institute, Griffith University, Queensland 4111, Australia; National Research Centre for Environmental Toxicology (EnTox), University of Queensland, Queensland 4108, Australia
| | - Rachael A Smith
- Queensland Department of Science, Information Technology, and Innovation, Brisbane, Queensland 4001, Australia; Australian Rivers Institute, Griffith University, Queensland 4111, Australia
| | - Ryan D Turner
- Queensland Department of Science, Information Technology, and Innovation, Brisbane, Queensland 4001, Australia; Australian Rivers Institute, Griffith University, Queensland 4111, Australia
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18
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Remaili TM, Simpson SL, Jolley DF. Effects of enhanced bioturbation intensities on the toxicity assessment of legacy-contaminated sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 226:335-345. [PMID: 28365043 DOI: 10.1016/j.envpol.2016.11.038] [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: 08/23/2016] [Revised: 11/11/2016] [Accepted: 11/14/2016] [Indexed: 05/14/2023]
Abstract
Many benthic communities within estuarine ecosystems are highly degraded due to the close proximity of urban and industrial contamination sources. The maintenance of recolonised, healthy ecosystems following remediation is a challenge, and better techniques are required for monitoring their progressive recovery. Rates of ecosystem recovery are influenced by the changes in the concentrations and forms of contaminants, the sensitivity of recolonising organisms to bioavailable contaminants, and a range of abiotic and biotic factors influencing the exposure of organisms to the contamination. Here we investigate the influence of bioturbation by an active amphipod (Victoriopisa australiensis) on the bioavailability of metals and hydrocarbons in highly contaminated sediments. Changes in contaminant bioavailability were evaluated by assessing sublethal effects to a smaller cohabiting amphipod (Melita plumulosa). For predominantly metal-contaminated sediments, the presence of V. australiensis generally increased survival and reproduction of M. plumulosa when compared to treatments with only M. plumulosa present (from 42 to 93% survival and 3-61% reproduction). The decrease in toxic effects to M. plumulosa corresponded with lower dissolved copper and zinc concentrations in the overlying waters (14-9 μg Cu L-1, and 14 to 6 μg Zn L-1 for absence to presence of V. australiensis). For sediments contaminated with both hydrocarbons and metals, the increased bioturbation intensity by V. australiensis resulted in decreased reproduction of M. plumulosa, despite lower dissolved metal exposure, and indicated increased bioavailability of the hydrocarbon contaminants. Thus, the presence of a secondary active bioturbator can enhance or suppress toxicity to co-inhabiting organisms, and may depend on the contaminant class and form. The results highlight the need to consider both abiotic and biotic interactions when using laboratory studies to evaluate the ability of organisms to recolonise and reproduce within benthic environments degraded by contamination, or for more general extrapolation for sediment quality assessment purposes.
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Affiliation(s)
- Timothy M Remaili
- School of Chemistry, University of Wollongong, NSW 2522, Australia; Centre for Environmental Contaminants Research, CSIRO Land and Water, Sydney, NSW 2234, Australia.
| | - Stuart L Simpson
- Centre for Environmental Contaminants Research, CSIRO Land and Water, Sydney, NSW 2234, Australia.
| | - Dianne F Jolley
- School of Chemistry, University of Wollongong, NSW 2522, Australia
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19
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Lan Y, Sun J, Tian R, Bartlett DH, Li R, Wong YH, Zhang W, Qiu JW, Xu T, He LS, Tabata HG, Qian PY. Molecular adaptation in the world's deepest-living animal: Insights from transcriptome sequencing of the hadal amphipod Hirondellea gigas. Mol Ecol 2017; 26:3732-3743. [PMID: 28429829 DOI: 10.1111/mec.14149] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 03/30/2017] [Accepted: 04/05/2017] [Indexed: 12/17/2022]
Abstract
The Challenger Deep in the Mariana Trench is the deepest point in the oceans of our planet. Understanding how animals adapt to this harsh environment characterized by high hydrostatic pressure, food limitation, dark and cold is of great scientific interest. Of the animals dwelling in the Challenger Deep, amphipods have been captured using baited traps. In this study, we sequenced the transcriptome of the amphipod Hirondellea gigas collected at a depth of 10,929 m from the East Pond of the Challenger Deep. Assembly of these sequences resulted in 133,041 contigs and 22,046 translated proteins. Functional annotation of these contigs was made using the go and kegg databases. Comparison of these translated proteins with those of four shallow-water amphipods revealed 10,731 gene families, of which 5659 were single-copy orthologs. Base substitution analysis on these single-copy orthologs showed that 62 genes are positively selected in H. gigas, including genes related to β-alanine biosynthesis, energy metabolism and genetic information processing. For multiple-copy orthologous genes, gene family expansion analysis revealed that cold-inducible proteins (i.e., transcription factors II A and transcription elongation factor 1) as well as zinc finger domains are expanded in H. gigas. Overall, our results indicate that genetic adaptation to the hadal environment by H. gigas may be mediated by both gene family expansion and amino acid substitutions of specific proteins.
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Affiliation(s)
- Yi Lan
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Jin Sun
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Renmao Tian
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Douglas H Bartlett
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Runsheng Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yue Him Wong
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Weipeng Zhang
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Ting Xu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Li-Sheng He
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Harry G Tabata
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
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20
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Kim BM, Kang S, Ahn DH, Kim JH, Ahn I, Lee CW, Cho JL, Min GS, Park H. First Insights into the Subterranean Crustacean Bathynellacea Transcriptome: Transcriptionally Reduced Opsin Repertoire and Evidence of Conserved Homeostasis Regulatory Mechanisms. PLoS One 2017; 12:e0170424. [PMID: 28107438 PMCID: PMC5249073 DOI: 10.1371/journal.pone.0170424] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 01/04/2017] [Indexed: 11/25/2022] Open
Abstract
Bathynellacea (Crustacea, Syncarida, Parabathynellidae) are subterranean aquatic crustaceans that typically inhabit freshwater interstitial spaces (e.g., groundwater) and are occasionally found in caves and even hot springs. In this study, we sequenced the whole transcriptome of Allobathynella bangokensis using RNA-seq. De novo sequence assembly produced 74,866 contigs including 28,934 BLAST hits. Overall, the gene sequences were most similar to those of the waterflea Daphnia pulex. In the A. bangokensis transcriptome, no opsin or related sequences were identified, and no contig aligned to the crustacean visual opsins and non-visual opsins (i.e. arthropsins, peropsins, and melaopsins), suggesting potential regressive adaptation to the dark environment. However, A. bangokensis expressed conserved gene family sets, such as heat shock proteins and those related to key innate immunity pathways and antioxidant defense systems, at the transcriptional level, suggesting that this species has evolved adaptations involving molecular mechanisms of homeostasis. The transcriptomic information of A. bangokensis will be useful for investigating molecular adaptations and response mechanisms to subterranean environmental conditions.
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Affiliation(s)
- Bo-Mi Kim
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
| | - Seunghyun Kang
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
| | - Do-Hwan Ahn
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
| | - Jin-Hyoung Kim
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
| | - Inhye Ahn
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
- Polar Sciences, University of Science & Technology, Yuseong-gu, Daejeon, South Korea
| | - Chi-Woo Lee
- Department of Biological Sciences, Inha University, Incheon, South Korea
| | - Joo-Lae Cho
- Nakdonggang National Institute of Biological Resources, Sangju, South Korea
| | - Gi-Sik Min
- Department of Biological Sciences, Inha University, Incheon, South Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
- Polar Sciences, University of Science & Technology, Yuseong-gu, Daejeon, South Korea
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Hook SE, Kroon FJ, Metcalfe S, Greenfield PA, Moncuquet P, McGrath A, Smith R, Warne MSJ, Turner RD, McKeown A, Westcott DA. Global transcriptomic profiling in barramundi (Lates calcarifer) from rivers impacted by differing agricultural land uses. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2017; 36:103-112. [PMID: 27219023 DOI: 10.1002/etc.3505] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 11/23/2015] [Accepted: 05/22/2016] [Indexed: 06/05/2023]
Abstract
Most catchments discharging into the Great Barrier Reef lagoon have elevated loads of suspended sediment, nutrients, and pesticides, including photosystem II inhibiting herbicides, associated with upstream agricultural land use. To investigate potential impacts of declining water quality on fish physiology, RNA sequencing (RNASeq) was used to characterize and compare the hepatic transcriptomes of barramundi (Lates calcarifer) captured from 2 of these tropical river catchments in Queensland, Australia. The Daintree and Tully Rivers differ in upstream land uses, as well as sediment, nutrient, and pesticide loads, with the area of agricultural land use and contaminant loads lower in the Daintree. In fish collected from the Tully River, transcripts involved in fatty acid metabolism, amino acid metabolism, and citrate cycling were also more abundant, suggesting elevated circulating cortisol concentrations, whereas transcripts involved in immune responses were less abundant. Fish from the Tully also had an increased abundance of transcripts associated with xenobiotic metabolism. Previous laboratory-based studies observed similar patterns in fish and amphibians exposed to the agricultural herbicide atrazine. If these transcriptomic patterns are manifested at the whole organism level, the differences in water quality between the 2 rivers may alter fish growth and fitness. Environ Toxicol Chem 2017;36:103-112. © 2016 SETAC.
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Affiliation(s)
- Sharon E Hook
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Kirrawee, New South Wales, Australia
| | - Frederieke J Kroon
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Suzanne Metcalfe
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Dutton Park, Queensland, Australia
| | - Paul A Greenfield
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, New South Wales, Australia
| | - Philippe Moncuquet
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Acton, Australian Capital Territory, Australia
| | - Annette McGrath
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Acton, Australian Capital Territory, Australia
| | - Rachael Smith
- Queensland Department of Science, Information Technology, and Innovation, Brisbane, Queensland, Australia
| | - Michael St J Warne
- Queensland Department of Science, Information Technology, and Innovation, Brisbane, Queensland, Australia
| | - Ryan D Turner
- Queensland Department of Science, Information Technology, and Innovation, Brisbane, Queensland, Australia
| | - Adam McKeown
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Smithfield, Queensland, Australia
| | - David A Westcott
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Atherton, Queensland, Australia
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High-throughput proteome dynamics for discovery of key proteins in sentinel species: Unsuspected vitellogenins diversity in the crustacean Gammarus fossarum. J Proteomics 2016; 146:207-14. [DOI: 10.1016/j.jprot.2016.07.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 07/01/2016] [Accepted: 07/04/2016] [Indexed: 01/10/2023]
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Legrand E, Forget-Leray J, Duflot A, Olivier S, Thomé JP, Danger JM, Boulangé-Lecomte C. Transcriptome analysis of the copepod Eurytemora affinis upon exposure to endocrine disruptor pesticides: Focus on reproduction and development. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2016; 176:64-75. [PMID: 27111276 DOI: 10.1016/j.aquatox.2016.04.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 03/19/2016] [Accepted: 04/12/2016] [Indexed: 06/05/2023]
Abstract
Copepods-which include freshwater and marine species-represent the most abundant group of aquatic invertebrates. Among them, the calanoid copepod Eurytemora affinis is widely represented in the northern hemisphere estuaries and has become a species of interest in ecotoxicology. Like other non-target organisms, E. affinis may be exposed to a wide range of chemicals such as endocrine disruptors (EDs). This study investigated the gene expression variation in E. affinis after exposure to ED pesticides-chosen as model EDs-in order to (i) improve the knowledge on their effects in crustaceans, and (ii) highlight relevant transcripts for further development of potential biomarkers of ED exposure/effect. The study focused on the reproduction function in response to ED. Copepods were exposed to sublethal concentrations of pyriproxyfen (PXF) and chlordecone (CLD) separately. After 48h, males and females (400 individuals each) were sorted for RNA extraction. Their transcriptome was pyrosequenced using the Illumina(®) technology. Contigs were blasted and functionally annotated using Blast2GO(®). The differential expression analysis between ED- and acetone-exposed organisms was performed according to sexes and contaminants. Half of the 19,721 contigs provided by pyrosequencing were annotated, mostly (80%) from arthropod sequences. Overall, 2,566 different genes were differentially expressed after ED exposures in comparison with controls. As many genes were differentially expressed after PXF exposure as after CLD exposure. In contrast, more genes were differentially expressed in males than in females after both exposures. Ninety-seven genes overlapped in all conditions. Finally, 31 transcripts involved in reproduction, growth and development, and changed in both chemical exposures were selected as potential candidates for future development of biomarkers.
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Affiliation(s)
- Eléna Legrand
- Normandy University, ULH, UMR-I 02 INERIS, Environmental Stresses and Biomonitoring of Aquatic Ecosystems (SEBIO)-SFR SCALE 4116, F-76600 Le Havre, France.
| | - Joëlle Forget-Leray
- Normandy University, ULH, UMR-I 02 INERIS, Environmental Stresses and Biomonitoring of Aquatic Ecosystems (SEBIO)-SFR SCALE 4116, F-76600 Le Havre, France.
| | - Aurélie Duflot
- Normandy University, ULH, UMR-I 02 INERIS, Environmental Stresses and Biomonitoring of Aquatic Ecosystems (SEBIO)-SFR SCALE 4116, F-76600 Le Havre, France.
| | - Stéphanie Olivier
- Normandy University, ULH, UMR-I 02 INERIS, Environmental Stresses and Biomonitoring of Aquatic Ecosystems (SEBIO)-SFR SCALE 4116, F-76600 Le Havre, France.
| | - Jean-Pierre Thomé
- University of Liège, Laboratory of Animal Ecology and Ecotoxicology (LEAE), Centre for Analytical Research and Technology (CART), 4000 SART-Tilman, Belgium.
| | - Jean-Michel Danger
- Normandy University, ULH, UMR-I 02 INERIS, Environmental Stresses and Biomonitoring of Aquatic Ecosystems (SEBIO)-SFR SCALE 4116, F-76600 Le Havre, France.
| | - Céline Boulangé-Lecomte
- Normandy University, ULH, UMR-I 02 INERIS, Environmental Stresses and Biomonitoring of Aquatic Ecosystems (SEBIO)-SFR SCALE 4116, F-76600 Le Havre, France.
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Sun M, Ting Li Y, Liu Y, Chin Lee S, Wang L. Transcriptome assembly and expression profiling of molecular responses to cadmium toxicity in hepatopancreas of the freshwater crab Sinopotamon henanense. Sci Rep 2016; 6:19405. [PMID: 26786678 PMCID: PMC4726346 DOI: 10.1038/srep19405] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 12/10/2015] [Indexed: 11/25/2022] Open
Abstract
Cadmium (Cd) pollution is a serious global problem, which causes irreversible toxic effects on animals. Freshwater crab, Sinopotamon henanense, is a useful environmental indicator since it is widely distributed in benthic habitats whereby it tends to accumulate Cd and other toxicants. However, its molecular responses to Cd toxicity remain unclear. In this study, we performed transcriptome sequencing and gene expression analyses of its hepatopancreas with and without Cd treatments. A total of 7.78 G clean reads were obtained from the pooled samples, and 68,648 unigenes with an average size of 622 bp were assembled, in which 5,436 were metabolism-associated and 2,728 were stimulus response-associated that include 380 immunity-related unigenes. Expression profile analysis demonstrated that most genes involved in macromolecular metabolism, oxidative phosphorylation, detoxification and anti-oxidant defense were up-regulated by Cd exposure, whereas immunity-related genes were down-regulated, except the genes involved in phagocytosis were up-regulated. The current data indicate that Cd exposure alters gene expressions in a concentration-dependent manner. Therefore, our results provide the first comprehensive S.henanense transcriptome dataset, which is useful for biological and ecotoxicological studies on this crab and its related species at molecular level, and some key Cd-responsive genes may provide candidate biomarkers for monitoring aquatic pollution by heavy metals.
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Affiliation(s)
- Min Sun
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Yi Ting Li
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Yang Liu
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Shao Chin Lee
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Lan Wang
- School of Life Science, Shanxi University, Taiyuan 030006, China
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Brinke A, Buchinger S. Toxicogenomics in Environmental Science. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 157:159-186. [DOI: 10.1007/10_2016_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Hook SE, Osborn HL, Spadaro DA, Simpson SL. Challenges for using quantitative PCR test batteries as a TIE-type approach to identify metal exposure in benthic invertebrates. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:17280-17289. [PMID: 24994105 DOI: 10.1007/s11356-014-3234-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 06/18/2014] [Indexed: 06/03/2023]
Abstract
The epibenthic amphipod Melita plumulosa shows unique gene expression profiles when exposed to different contaminants. We hypothesized that specific changes in transcript abundance could be used in a battery of quantitative polymerase chain reaction (qPCR) assays as a toxicity identification evaluation (TIE)-like approach to identify the most relevant stressor in field-contaminated sediments. To test this hypothesis, seven candidate transcriptomic markers were selected, and their specificity following metal exposure was confirmed. The performance of these markers across different levels of added metals was verified. The ability of these transcripts to act as markers was tested by exposing amphipods to metal-contaminated field-collected sediments and measuring changes in transcript abundance via qPCR. For two of the three sediments tested, at least some of the transcriptomic patterns matched our predictions, suggesting that they would be effective in helping to identify metal exposure in field sediments. However, following exposure to the third sediment, transcriptomic patterns were unlike our predictions. These results suggest that the seven transcripts may be insufficient to discern individual contaminants from complex mixtures and that microarray or RNA-Seq global gene expression profiles may be more effective for TIE. Changes in transcriptomics based on laboratory exposures to single compounds should be carefully validated before the results are used to analyze mixtures.
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Affiliation(s)
- Sharon E Hook
- CSIRO Land and Water, Locked Bag 2007, Kirrawee, NSW, 2232, Australia.
| | - Hannah L Osborn
- CSIRO Land and Water, Locked Bag 2007, Kirrawee, NSW, 2232, Australia
| | - David A Spadaro
- CSIRO Land and Water, Locked Bag 2007, Kirrawee, NSW, 2232, Australia
| | - Stuart L Simpson
- CSIRO Land and Water, Locked Bag 2007, Kirrawee, NSW, 2232, Australia
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Impacts of a newly identified behaviour-altering trematode on its host amphipod: from the level of gene expression to population. Parasitology 2015; 142:1469-80. [PMID: 26282621 DOI: 10.1017/s0031182015000918] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Changes to host behaviour induced by some trematode species, as a means of increased trophic transmission, represents one of the seminal examples of host manipulation by a parasite. The amphipod Echinogammarus marinus (Leach, 1815) is infected with a previously undescribed parasite, with infected individuals displaying positive phototaxic and negative geotaxic behaviour. This study reveals that the unknown parasite encysts in the brain, nerve cord and the body cavity of E. marinus, and belongs to the Microphallidae family. An 18 month population study revealed that host abundance significantly and negatively correlated with parasite prevalence. Investigation of the trematode's influence at the transcriptomic level revealed genes with putative neurological functions, such as serotonin receptor 1A, an inebriated-like neurotransmitter, tryptophan hydroxylase and amino acid decarboxylase, present consistent altered expression in infected animals. Therefore, this study provides one of the first transcriptomic insights into the neuronal gene pathways altered in amphipods infected with a trematode parasite associated with changes to its host's behaviour and population structure.
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28
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Trapp J, Almunia C, Gaillard JC, Pible O, Chaumot A, Geffard O, Armengaud J. Proteogenomic insights into the core-proteome of female reproductive tissues from crustacean amphipods. J Proteomics 2015; 135:51-61. [PMID: 26170043 DOI: 10.1016/j.jprot.2015.06.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/11/2015] [Accepted: 06/29/2015] [Indexed: 11/27/2022]
Abstract
As a result of the poor genome sequence coverage of crustacean amphipods, characterization of their evolutionary biology relies mostly on phenotypic traits. Here, we analyzed the proteome of ovaries from five amphipods, all from the Senticaudata suborder, with the objective to obtain insights into the core-proteome of female reproductive systems. These amphipods were from either the Gammarida infraorder: Gammarus fossarum, Gammarus pulex, Gammarus roeseli, or the Talitrida infraorder: Parhyale hawaiensis and Hyalella azteca. Ovaries from animals sampled at the end of their reproductive cycle were dissected. Their whole protein contents were extracted and their proteomes were recorded by high-throughput nanoLC-MS/MS with a high-resolution mass spectrometer. We interpreted tandem mass spectrometry data with the protein sequence resource from G. fossarum and P. hawaiensis, both recently established by RNA sequencing. The large molecular biodiversity within amphipods was assessed by the ratio of MS/MS spectra assigned for each sample, which tends to diverge rapidly along the taxonomic level considered. The core-proteome was defined as the proteins conserved along all samples, thus detectable by the homology-based proteomic assignment procedure. This specific subproteome may be further enriched in the future with the analysis of new species and update of the protein sequence resource.
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Affiliation(s)
- Judith Trapp
- Irstea, Unité de Recherche MALY, Laboratoire d'écotoxicologie, CS70077, F-69626 Villeurbanne, France; CEA-Marcoule, DSV/IBICTEC-S/SPI/Li2D, Laboratory "Innovative Technologies for Detection and Diagnostic", BP 17171, F-30200 Bagnols-sur-Cèze, France
| | - Christine Almunia
- CEA-Marcoule, DSV/IBICTEC-S/SPI/Li2D, Laboratory "Innovative Technologies for Detection and Diagnostic", BP 17171, F-30200 Bagnols-sur-Cèze, France
| | - Jean-Charles Gaillard
- CEA-Marcoule, DSV/IBICTEC-S/SPI/Li2D, Laboratory "Innovative Technologies for Detection and Diagnostic", BP 17171, F-30200 Bagnols-sur-Cèze, France
| | - Olivier Pible
- CEA-Marcoule, DSV/IBICTEC-S/SPI/Li2D, Laboratory "Innovative Technologies for Detection and Diagnostic", BP 17171, F-30200 Bagnols-sur-Cèze, France
| | - Arnaud Chaumot
- Irstea, Unité de Recherche MALY, Laboratoire d'écotoxicologie, CS70077, F-69626 Villeurbanne, France
| | - Olivier Geffard
- Irstea, Unité de Recherche MALY, Laboratoire d'écotoxicologie, CS70077, F-69626 Villeurbanne, France.
| | - Jean Armengaud
- CEA-Marcoule, DSV/IBICTEC-S/SPI/Li2D, Laboratory "Innovative Technologies for Detection and Diagnostic", BP 17171, F-30200 Bagnols-sur-Cèze, France.
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29
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Holtman IR, Noback M, Bijlsma M, Duong KN, van der Geest MA, Ketelaars PT, Brouwer N, Vainchtein ID, Eggen BJL, Boddeke HWGM. Glia Open Access Database (GOAD): A comprehensive gene expression encyclopedia of glia cells in health and disease. Glia 2015; 63:1495-506. [PMID: 25808223 DOI: 10.1002/glia.22810] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 02/13/2015] [Indexed: 12/20/2022]
Abstract
Recently, the number of genome-wide transcriptome profiles of pure populations of glia cells has drastically increased, resulting in an unprecedented amount of data that offer opportunities to study glia phenotypes and functions in health and disease. To make genome-wide transcriptome data easily accessible, we developed the Glia Open Access Database (GOAD), available via www.goad.education. GOAD contains a collection of previously published and unpublished transcriptome data, including datasets from isolated microglia, astrocytes and oligodendrocytes both at homeostatic and pathological conditions. It contains an intuitive web-based interface that consists of three features that enable searching, browsing, analyzing, and downloading of the data. The first feature is differential gene expression (DE) analysis that provides genes that are significantly up and down-regulated with the associated fold changes and p-values between two conditions of interest. In addition, an interactive Venn diagram is generated to illustrate the overlap and differences between several DE gene lists. The second feature is quantitative gene expression (QE) analysis, to investigate which genes are expressed in a particular glial cell type and to what degree. The third feature is a search utility, which can be used to find a gene of interest and depict its expression in all available expression data sets by generating a gene card. In addition, quality guidelines and relevant concepts for transcriptome analysis are discussed. Finally, GOAD is discussed in relation to several online transcriptome tools developed in neuroscience and immunology. In conclusion, GOAD is a unique platform to facilitate integration of bioinformatics in glia biology.
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Affiliation(s)
- Inge R Holtman
- Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Michiel Noback
- School for Life Science and Technology, Hanze University of Applied Sciences, Groningen, The Netherlands
| | - Marieke Bijlsma
- School for Life Science and Technology, Hanze University of Applied Sciences, Groningen, The Netherlands
| | - Kim N Duong
- School for Life Science and Technology, Hanze University of Applied Sciences, Groningen, The Netherlands
| | - Marije A van der Geest
- School for Life Science and Technology, Hanze University of Applied Sciences, Groningen, The Netherlands
| | - Peer T Ketelaars
- School for Life Science and Technology, Hanze University of Applied Sciences, Groningen, The Netherlands
| | - Nieske Brouwer
- Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ilia D Vainchtein
- Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Bart J L Eggen
- Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hendrikus W G M Boddeke
- Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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Trapp J, Armengaud J, Salvador A, Chaumot A, Geffard O. Next-generation proteomics: toward customized biomarkers for environmental biomonitoring. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:13560-13572. [PMID: 25345346 DOI: 10.1021/es501673s] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Because of their ecological representativeness, invertebrates are commonly employed as test organisms in ecotoxicological assessment; however, to date, biomarkers employed for these species were the result of a direct transposition from vertebrates, despite deep evolutionary divergence. To gain efficiency in the diagnostics of ecosystem health, specific biomarkers must be developed. In this sense, next-generation proteomics enables the specific identification of proteins involved in key physiological functions or defense mechanisms, which are responsive to ecotoxicological challenges. However, the analytical investment required restricts use in biomarker discovery. Routine biomarker validation and assays rely on more conventional mass spectrometers. Here, we describe how proteomics remains a challenge for ecotoxicological test organisms because of the lack of appropriate protein sequences databases, thus restricting the analysis on conserved and ubiquitous proteins. These limits and some strategies used to overcome them are discussed. These new tools, such as proteogenomics and targeted proteomics, should result in new biomarkers specific to relevant environmental organisms and applicable to routine ecotoxicological assessment.
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Affiliation(s)
- Judith Trapp
- Irstea, Unité de Recherche MALY, Laboratoire d'écotoxicologie, CS70077, F-69626 Villeurbanne, France
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31
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Hook SE, Johnston EL, Nair S, Roach AC, Moncuquet P, Twine NA, Raftos DA. Next generation sequence analysis of the transcriptome of Sydney rock oysters (Saccostrea glomerata) exposed to a range of environmental stressors. Mar Genomics 2014; 18 Pt B:109-11. [PMID: 25151890 DOI: 10.1016/j.margen.2014.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 08/13/2014] [Indexed: 11/15/2022]
Abstract
Sydney rock oysters (Saccostrea glomerata) were exposed to environmental stressors at contaminated field sites or in a controlled laboratory setting. RNA seq transcriptome data were generated for the gill and digestive gland using Roche's 454 pyrosequencing technology. 28,685 contigs were de novo assembled which encoded 11,671 different protein products. The data will act as a reference for future studies in ecology, immunology and environmental toxicology.
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Affiliation(s)
- Sharon E Hook
- CSIRO Centre for Environmental Contaminants Research, Land and Water, Locked Bag 2007, Kirrawee, NSW 2232, Australia.
| | - Emma L Johnston
- Evolution and Ecology Research Centre School of Biological, Earth and Environmental Sciences, UNSW Australia, Sydney, NSW 2052, Australia
| | - Sham Nair
- Department of Biological Sciences, Macquarie University, Sydney, 2109 NSW, Australia
| | - Anthony C Roach
- NSW Dept of Environment, Climate Change & Water (DECCW), Australia
| | | | - Natalie A Twine
- NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - David A Raftos
- Department of Biological Sciences, Macquarie University, Sydney, 2109 NSW, Australia
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32
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Amin S, Prentis PJ, Gilding EK, Pavasovic A. Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of de novo assemblers. BMC Res Notes 2014; 7:488. [PMID: 25084827 PMCID: PMC4124492 DOI: 10.1186/1756-0500-7-488] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 07/25/2014] [Indexed: 01/22/2023] Open
Abstract
Background The sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, is a critically important step for transcriptome assemblies generated from short read sequences. Typical benchmarks for assembly and annotation reliability have been performed with model species. To address the reliability and accuracy of de novo transcriptome assembly in non-model species, we generated an RNAseq dataset for an intertidal gastropod mollusc species, Nerita melanotragus, and compared the assembly produced by four different de novo transcriptome assemblers; Velvet, Oases, Geneious and Trinity, for a number of quality metrics and redundancy. Results Transcriptome sequencing on the Ion Torrent PGM™ produced 1,883,624 raw reads with a mean length of 133 base pairs (bp). Both the Trinity and Oases de novo assemblers produced the best assemblies based on all quality metrics including fewer contigs, increased N50 and average contig length and contigs of greater length. Overall the BLAST and annotation success of our assemblies was not high with only 15-19% of contigs assigned a putative function. Conclusions We believe that any improvement in annotation success of gastropod species will require more gastropod genome sequences, but in particular an increase in mollusc protein sequences in public databases. Overall, this paper demonstrates that reliable and accurate de novo transcriptome assemblies can be generated from short read sequencers with the right assembly algorithms.
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Affiliation(s)
| | | | | | - Ana Pavasovic
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, GPO Box 2434, Brisbane, Qld 4001, Australia.
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