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Wright A, Wilkinson MD, Mungall C, Cain S, Richards S, Sternberg P, Provin E, Jacobs JL, Geib S, Raciti D, Yook K, Stein L, Molik DC. FAIR Header Reference genome: a TRUSTworthy standard. Brief Bioinform 2024; 25:bbae122. [PMID: 38555475 PMCID: PMC10981671 DOI: 10.1093/bib/bbae122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 04/02/2024] Open
Abstract
The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR bioHeaders Reference genome (FHR), a metadata standard guided by the principles of Findability, Accessibility, Interoperability and Reuse (FAIR) in addition to the principles of Transparency, Responsibility, User focus, Sustainability and Technology. The objective of FHR is to provide an extensive set of data serialisation methods and minimum data field requirements while still maintaining extensibility, flexibility and expressivity in an increasingly decentralised genomic data ecosystem. The effort needed to implement FHR is low; FHR's design philosophy ensures easy implementation while retaining the benefits gained from recording both machine and human-readable provenance.
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Affiliation(s)
- Adam Wright
- Adaptive Oncology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 500, Toronto, ON M5G 0A3, Canada
| | - Mark D Wilkinson
- Departamento de Biotecnolog’ıa-Biolog’ıa Vegetal, Escuela T’ecnica Superior de Ingenier’ıa Agron’omica, Alimentaria y de Biosistemas,Centro de Biotecnolog’ıa y Gen’omica de Plantas (CBGP, UPM-INIA/CSIC), Universidad Polit’ecnica de Madrid (UPM) - Instituto Nacional de Investigaci’on y Tecnolog’ıa Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarc’on, Madrid, ES, Spain
| | - Christopher Mungall
- Biosystems Data Science, Lawrence Berkeley National Laboratory, Building: 977, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Scott Cain
- Adaptive Oncology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 500, Toronto, ON M5G 0A3, Canada
| | - Stephen Richards
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS: BCM226, Houston, TX 77030, USA
| | - Paul Sternberg
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ellen Provin
- Department of Horticultural Studies, Texas A&M University, HFSB 204, TAMU 2133, College Station, TX 77848, USA
| | - Jonathan L Jacobs
- American Type Culture Collection, 10801 University Blvd, Manassas, VA 20110, USA
| | - Scott Geib
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo HI 96720, USA
| | - Daniela Raciti
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Karen Yook
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lincoln Stein
- Adaptive Oncology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 500, Toronto, ON M5G 0A3, Canada
| | - David C Molik
- Arthropod-borne Animal Diseases Research Unit, Center for Grain and Animal Health Research United States Department of Agriculture, Agricultural Research Service, 1515 College Ave, Manhattan, KS 66502 USA
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Wright A, Wilkinson MD, Mungall C, Cain S, Richards S, Sternberg P, Provin E, Jacobs JL, Geib S, Raciti D, Yook K, Stein L, Molik DC. DATA RESOURCES AND ANALYSES FAIR Header Reference genome: A TRUSTworthy standard. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569306. [PMID: 38076838 PMCID: PMC10705436 DOI: 10.1101/2023.11.29.569306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR-bioHeaders Reference genome (FHR), a metadata standard guided by the principles of Findability, Accessibility, Interoperability, and Reuse (FAIR) in addition to the principles of Transparency, Responsibility, User focus, Sustainability, and Technology (TRUST). The objective of FHR is to provide an extensive set of data serialisation methods and minimum data field requirements while still maintaining extensibility, flexibility, and expressivity in an increasingly decentralised genomic data ecosystem. The effort needed to implement FHR is low; FHR's design philosophy ensures easy implementation while retaining the benefits gained from recording both machine and human-readable provenance.
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Affiliation(s)
- Adam Wright
- Adaptive Oncology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 500, Toronto, ON M5G 0A3, Canada
| | - Mark D Wilkinson
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas,Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Madrid, ES, Spain
| | - Chris Mungall
- Biosystems Data Science, Lawrence Berkeley National Laboratory, Building: 977, 1 Cyclotron Rd, Berkeley, CA 94720 USA
| | - Scott Cain
- Adaptive Oncology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 500, Toronto, ON M5G 0A3, Canada
| | - Stephen Richards
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS: BCM226, Houston, TX 77030, USA
| | - Paul Sternberg
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ellen Provin
- Department of Horticultural Studies, Texas A&M University, HFSB 204, TAMU 2133, College Station, TX 77848, USA
| | - Jonathan L Jacobs
- American Type Culture Collection, 10801 University Blvd, Manassas, VA 20110, USA
| | - Scott Geib
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo HI 96720 USA
| | - Daniela Raciti
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Karen Yook
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lincoln Stein
- Adaptive Oncology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 500, Toronto, ON M5G 0A3, Canada
| | - David C Molik
- Arthropod-borne Animal Diseases Research Unit, Center for Grain and Animal Health Research United States Department of Agriculture, Agricultural Research Service, 1515 College Ave, Manhattan, KS 66502 USA
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Davidović P, Blagojević D, Meriluoto J, Simeunović J, Svirčev Z. Biotests in Cyanobacterial Toxicity Assessment-Efficient Enough or Not? BIOLOGY 2023; 12:biology12050711. [PMID: 37237524 DOI: 10.3390/biology12050711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/27/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023]
Abstract
Cyanobacteria are a diverse group of organisms known for producing highly potent cyanotoxins that pose a threat to human, animal, and environmental health. These toxins have varying chemical structures and toxicity mechanisms and several toxin classes can be present simultaneously, making it difficult to assess their toxic effects using physico-chemical methods, even when the producing organism and its abundance are identified. To address these challenges, alternative organisms among aquatic vertebrates and invertebrates are being explored as more assays evolve and diverge from the initially established and routinely used mouse bioassay. However, detecting cyanotoxins in complex environmental samples and characterizing their toxic modes of action remain major challenges. This review provides a systematic overview of the use of some of these alternative models and their responses to harmful cyanobacterial metabolites. It also assesses the general usefulness, sensitivity, and efficiency of these models in investigating the mechanisms of cyanotoxicity expressed at different levels of biological organization. From the reported findings, it is clear that cyanotoxin testing requires a multi-level approach. While studying changes at the whole-organism level is essential, as the complexities of whole organisms are still beyond the reach of in vitro methodologies, understanding cyanotoxicity at the molecular and biochemical levels is necessary for meaningful toxicity evaluations. Further research is needed to refine and optimize bioassays for cyanotoxicity testing, which includes developing standardized protocols and identifying novel model organisms for improved understanding of the mechanisms with fewer ethical concerns. In vitro models and computational modeling can complement vertebrate bioassays and reduce animal use, leading to better risk assessment and characterization of cyanotoxins.
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Affiliation(s)
- Petar Davidović
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
| | - Dajana Blagojević
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
| | - Jussi Meriluoto
- Faculty of Science and Engineering, Biochemistry, Åbo Akademi, Tykistökatu 6 A, 20520 Turku, Finland
| | - Jelica Simeunović
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
| | - Zorica Svirčev
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
- Faculty of Science and Engineering, Biochemistry, Åbo Akademi, Tykistökatu 6 A, 20520 Turku, Finland
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Oliver A, Cavalheri HB, Lima TG, Jones NT, Podell S, Zarate D, Allen E, Burton RS, Shurin JB. Phenotypic and transcriptional response of Daphnia pulicaria to the combined effects of temperature and predation. PLoS One 2022; 17:e0265103. [PMID: 35834446 PMCID: PMC9282536 DOI: 10.1371/journal.pone.0265103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/09/2022] [Indexed: 11/18/2022] Open
Abstract
Daphnia, an ecologically important zooplankton species in lakes, shows both genetic adaptation and phenotypic plasticity in response to temperature and fish predation, but little is known about the molecular basis of these responses and their potential interactions. We performed a factorial experiment exposing laboratory-propagated Daphnia pulicaria clones from two lakes in the Sierra Nevada mountains of California to normal or high temperature (15°C or 25°C) in the presence or absence of fish kairomones, then measured changes in life history and gene expression. Exposure to kairomones increased upper thermal tolerance limits for physiological activity in both clones. Cloned individuals matured at a younger age in response to higher temperature and kairomones, while size at maturity, fecundity and population intrinsic growth were only affected by temperature. At the molecular level, both clones expressed more genes differently in response to temperature than predation, but specific genes involved in metabolic, cellular, and genetic processes responded differently between the two clones. Although gene expression differed more between clones from different lakes than experimental treatments, similar phenotypic responses to predation risk and warming arose from these clone-specific patterns. Our results suggest that phenotypic plasticity responses to temperature and kairomones interact synergistically, with exposure to fish predators increasing the tolerance of Daphnia pulicaria to stressful temperatures, and that similar phenotypic responses to temperature and predator cues can be produced by divergent patterns of gene regulation.
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Affiliation(s)
- Aaron Oliver
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Hamanda B. Cavalheri
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
| | - Thiago G. Lima
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
| | - Natalie T. Jones
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
| | - Sheila Podell
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Daniela Zarate
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
| | - Eric Allen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Ronald S. Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Jonathan B. Shurin
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
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5
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Jia J, Dong C, Han M, Ma S, Chen W, Dou J, Feng C, Liu X. Multi-omics perspective on studying reproductive biology in Daphnia sinensis. Genomics 2022; 114:110309. [DOI: 10.1016/j.ygeno.2022.110309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/28/2021] [Accepted: 02/01/2022] [Indexed: 11/30/2022]
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O’Connor M, Sadler DE, Brunner FS, Reynolds A, White N, Price S, Plaistow SJ. Measuring Daphnia life history in the wild: The efficacy of individual field cages. Ecol Evol 2021; 11:16927-16935. [PMID: 34938482 PMCID: PMC8668787 DOI: 10.1002/ece3.8326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 10/14/2021] [Indexed: 11/30/2022] Open
Abstract
Life-history studies are often conducted in a laboratory environment where it is easy to assay individual animals. However, factors such as temperature, photoperiod, and nutrition vary greatly between laboratory and field environments, making it difficult to compare results. Consequently, there is a need to study individual life histories in the field, but this is currently difficult in systems such as Daphnia where it is not possible to mark and track individual animals. Here, we present a proof of principle study showing that field cages are a reliable method for collecting individual-level life-history data in Daphnia magna. As a first step, we compared the life history of paired animals reared outside and inside cages to test the hypothesis that cages allow free flow of algal food resources. We then used a seminatural mesocosm setting to compare the performance of individual field cages versus glass jars refilled with mesocosm water each day. We found that cages did not inhibit food flow and that differences in life histories between three clones detected in the jar assays were also detectable using the much less labor-intensive field cages. We conclude that field cages are a feasible approach for collecting individual-level life-history data in systems such as Daphnia where individual animals cannot be marked and tracked.
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Affiliation(s)
- Michael O’Connor
- Institute of InfectionVeterinary & Ecological SciencesThe University of LiverpoolLiverpoolUK
| | - Daniel E. Sadler
- Institute of InfectionVeterinary & Ecological SciencesThe University of LiverpoolLiverpoolUK
| | - Franziska S. Brunner
- Institute of InfectionVeterinary & Ecological SciencesThe University of LiverpoolLiverpoolUK
| | - Alan Reynolds
- Institute of InfectionVeterinary & Ecological SciencesThe University of LiverpoolLiverpoolUK
| | - Nicola White
- Institute of InfectionVeterinary & Ecological SciencesThe University of LiverpoolLiverpoolUK
| | - Stephen Price
- Institute of InfectionVeterinary & Ecological SciencesThe University of LiverpoolLiverpoolUK
| | - Stewart J. Plaistow
- Institute of InfectionVeterinary & Ecological SciencesThe University of LiverpoolLiverpoolUK
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7
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Clark AD, Howell BK, Wilson AE, Schwartz TS. Draft genomes for one Microcystis-resistant and one Microcystis-sensitive strain of the water flea, Daphnia pulicaria. G3 (BETHESDA, MD.) 2021; 11:jkab266. [PMID: 34849790 PMCID: PMC8527513 DOI: 10.1093/g3journal/jkab266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/23/2021] [Indexed: 11/17/2022]
Abstract
Daphnia species are well-suited for studying local adaptation and evolutionary responses to stress(ors) including those caused by algal blooms. Algal blooms, characterized by an overgrowth (bloom) of cyanobacteria, are detrimental to the health of aquatic and terrestrial members of freshwater ecosystems. Some strains of Daphnia pulicaria have demonstrated resistance to toxic algae and the ability to mitigate toxic algal blooms. Understanding the genetic mechanism associated with this toxin resistance requires adequate genomic resources. Using whole-genome sequence data mapped to the Daphnia pulex reference genome (PA42), we present reference-guided draft assemblies from one tolerant and one sensitive strain of D. pulicaria, Wintergreen-6 (WI-6), and Bassett-411 (BA-411), respectively. Assessment of the draft assemblies reveal low contamination levels, and high levels (95%) of genic content. Reference scaffolds had coverage breadths of 98.9-99.4%, and average depths of 33X and 29X for BA-411 and WI-6, respectively. Within, we discuss caveats and suggestions for improving these draft assemblies. These genomic resources are presented with a goal of contributing to the resources necessary to understand the genetic mechanisms and associations of toxic prey resistance observed in this species.
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Affiliation(s)
- Amanda D Clark
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Bailey K Howell
- Bioinformatics REU Program, Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Alan E Wilson
- Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Tonia S Schwartz
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
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Poulsen R, De Fine Licht HH, Hansen M, Cedergreen N. Grandmother's pesticide exposure revealed bi-generational effects in Daphnia magna. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 236:105861. [PMID: 34049113 DOI: 10.1016/j.aquatox.2021.105861] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 05/02/2021] [Accepted: 05/04/2021] [Indexed: 06/12/2023]
Abstract
Man-made chemicals are a significant contributor to the ongoing deterioration of numerous ecosystems. Currently, risk assessment of these chemicals is based on observations in a single generation of animals, despite potential adverse intergenerational effects. Here, we investigate the effect of the fungicide prochloraz across three generations of Daphnia magna. We studied both the effects of continuous exposure over all generations and the effects of first-generation (F0) exposure on two subsequent generations. Effects at different levels of biological organization from genome-wide gene expression, whole organism metabolite levels, CYP enzyme activity and key phenotypic effects, such as reproduction, were monitored. Acclimation to prochloraz was found after continuous exposure. Following F0-exposure, embryonically exposed F1-offspring showed no significant effects. However, in the potentially germline exposed F2 animals, several parameters differed significantly from controls. A direct association between these F2 effects and the toxic mode of action of prochloraz was found, showing that chemicals can be harmful not only to the directly exposed generation, but also to prenatally exposed generations and in that way effects may even appear to skip a generation. This implies that current risk assessment practices are neglecting an important aspect of toxicity, such as delayed effects across generations due to a time gap between chemical exposure and emergence of effects.
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Affiliation(s)
- Rikke Poulsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark; Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark.
| | - Henrik H De Fine Licht
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Martin Hansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Nina Cedergreen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
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9
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DNMT3.1 controls trade-offs between growth, reproduction, and life span under starved conditions in Daphnia magna. Sci Rep 2021; 11:7326. [PMID: 33795753 PMCID: PMC8016896 DOI: 10.1038/s41598-021-86578-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/25/2021] [Indexed: 02/01/2023] Open
Abstract
The cladoceran crustacean Daphnia has long been a model of energy allocation studies due to its important position in the trophic cascade of freshwater ecosystems. However, the loci for controlling energy allocation between life history traits still remain unknown. Here, we report CRISPR/Cas-mediated target mutagenesis of DNA methyltransferase 3.1 (DNMT3.1) that is upregulated in response to caloric restriction in Daphnia magna. The resulting biallelic mutant is viable and did not show any change in growth rate, reproduction, and longevity under nutrient rich conditions. In contrast, under starved conditions, the growth rate of this DNMT3.1 mutant was increased but its reproduction was reciprocally reduced compared to the wild type when the growth and reproduction activities competed during a period from instar 4 to 8. The life span of this mutant was significantly shorter than that of the wild type. We also compared transcriptomes between DNMT3.1 mutant and wild type under nutrient-rich and starved conditions. Consistent with the DNMT3.1 mutant phenotypes, the starved condition led to changes in the transcriptomes of the mutant including differential expression of vitellogenin genes. In addition, we found upregulation of the I am not dead yet (INDY) ortholog, which has been known to shorten the life span in Drosophila, explaining the shorter life span of the DNMT3.1 mutant. These results establish DNMT3.1 as a key regulator for life span and energy allocation between growth and reproduction during caloric restriction. Our findings reveal how energy allocation is implemented by selective expression of a DNMT3 ortholog that is widely distributed among animals. We also infer a previously unidentified adaptation of Daphnia that invests more energy for reproduction than growth under starved conditions.
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10
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Jones CLC, Shafer ABA, Kim WD, Prater C, Wagner ND, Frost PC. The complexity of co-limitation: nutrigenomics reveal non-additive interactions of calcium and phosphorus on gene expression in Daphnia pulex. Proc Biol Sci 2020; 287:20202302. [PMID: 33352081 DOI: 10.1098/rspb.2020.2302] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Many lakes across Canada and northern Europe have experienced declines in ambient phosphorus (P) and calcium (Ca) supply for over 20 years. While these declines might create or exacerbate nutrient limitation in aquatic food webs, our ability to detect and quantify different types of nutrient stress on zooplankton remains rudimentary. Here, we used growth bioassay experiments and whole transcriptome RNAseq, collectively nutrigenomics, to examine the nutritional phenotypes produced by low supplies of P and Ca separately and together in the freshwater zooplankter Daphnia pulex. We found that daphniids in all three nutrient-deficient categories grew slower and differed in their elemental composition. Our RNAseq results show distinct responses in singly limited treatments (Ca or P) and largely a mix of these responses in animals under low Ca and P conditions. Deeper investigation of effect magnitude and gene functional annotations reveals this patchwork of responses to cumulatively represent a co-limited nutritional phenotype. Linear discriminant analysis identified a significant separation between nutritional treatments based upon gene expression patterns with the expression patterns of just five genes needed to predict animal nutritional status with 99% accuracy. These data reveal how nutritional phenotypes are altered by individual and co-limitation of two highly important nutritional elements (Ca and P) and provide evidence that aquatic consumers can respond to limitation by more than one nutrient at a time by differentially altering their metabolism. This use of nutrigenomics demonstrates its potential to address many of the inherent complexities in studying interactions between multiple nutritional stressors in ecology and beyond.
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Affiliation(s)
- Catriona L C Jones
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Canada K9K 0A7
| | - Aaron B A Shafer
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Canada K9K 0A7.,Department of Forensic Science, Trent University, Peterborough, Ontario, Canada
| | - William D Kim
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Canada K9K 0A7
| | - Clay Prater
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA
| | - Nicole D Wagner
- Center for Reservoir and Aquatic Systems Research, Baylor University, Waco, TX, USA
| | - Paul C Frost
- Department of Biology, Trent University, Peterborough, Ontario, Canada
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11
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Shaked SA, Abehsera S, Levy T, Chalifa-Caspi V, Sagi A. From sporadic single genes to a broader transcriptomic approach: Insights into the formation of the biomineralized exoskeleton in decapod crustaceans. J Struct Biol 2020; 212:107612. [PMID: 32896659 DOI: 10.1016/j.jsb.2020.107612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 08/27/2020] [Accepted: 08/29/2020] [Indexed: 01/01/2023]
Abstract
One fundamental character common to pancrustaceans (Crustacea and Hexapoda) is a mineralized rigid exoskeleton whose principal organic components are chitin and proteins. In contrast to traditional research in the field that has been devoted to the structural and physicochemical aspects of biomineralization, the present study explores transcriptomic aspects of biomineralization as a first step towards adding a complementary molecular layer to this field. The rigidity of the exoskeleton in pancrustaceans dictates essential molt cycles enabling morphological changes and growth. Thus, formation and mineralization of the exoskeleton are concomitant to the timeline of the molt cycle. Skeletal proteinaceous toolkit elements have been discovered in previous studies using innovative molt-related binary gene expression patterns derived from transcriptomic libraries representing the major stages comprising the molt cycle of the decapod crustacean Cherax quadricarinatus. Here, we revisited some prominent exoskeleton-related structural proteins encoding and, using the above molt-related binary pattern methodology, enlarged the transcriptomic database of C. quadricarinatus. The latter was done by establishing a new transcriptomic library of the cuticle forming epithelium and molar tooth at four different molt stages (i.e., inter-molt, early pre-molt, late pre-molt and post-molt) and incorporating it to a previous transcriptome derived from the gastroliths and mandible. The wider multigenic approach facilitated by the newly expanded transcriptomic database not only revisited single genes of the molecular toolkit, but also provided both scattered and specific information that broaden the overview of proteins and gene clusters which are involved in the construction and biomineralization of the exoskeleton in decapod crustaceans.
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Affiliation(s)
- Shai A Shaked
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Shai Abehsera
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tom Levy
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Vered Chalifa-Caspi
- Bioinformatics Core Facility, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Amir Sagi
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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12
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Yan N, Tsim SMJ, He X, Tang BZ, Wang WX. Direct Visualization and Quantification of Maternal Transfer of Silver Nanoparticles in Zooplankton. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:10763-10771. [PMID: 32786596 DOI: 10.1021/acs.est.0c03228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The immense application of silver nanoparticles (AgNPs) in biomedical fields is likely to increase the exposure of humans. However, little is known about whether these nanoparticles can be maternally transferred, especially regarding their biodistribution in the younger generation, maternal transfer efficiency, and toxic effects. In the present study, maternal transfer of AgNPs in model zooplankton (Daphnia magna) was for the first time visualized and quantified. We found that AgNPs were transferred from mother to offspring and mainly accumulated in the lipids due to the strong colocalization with lipid droplets, which were the major energy sources of Daphnia embryos. In contrast, Ag+ was irregularly distributed in different sites, probably due to the mobility and reactivity of Ag+. The maternal transfer efficiency quantified by the radiolabeling methodology was 2.37 ± 0.25 and 6.05 ± 0.89% for 110mAgNPs and 110mAg, respectively. Furthermore, AgNPs and Ag+ significantly inhibited the reproduction capability of F0 and F1 generations, but such maternal toxic effect inhibition was only found within the first two broods of F0 and F1 generations. Our bioimaging findings demonstrated that AgNPs could be maternally transferred to the next generation; thus, it is critical to produce AgNPs with lower toxic effects, higher delivery efficacy, and more precise targeting.
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Affiliation(s)
- Neng Yan
- School of Energy and Environment, State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Hong Kong, China
| | - Synn Man Jennifer Tsim
- School of Energy and Environment, State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Hong Kong, China
| | - Xuewen He
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, HKUST, Clear Water Bay, Kowloon LG5313, Hong Kong, China
| | - Ben Zhong Tang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, HKUST, Clear Water Bay, Kowloon LG5313, Hong Kong, China
| | - Wen-Xiong Wang
- School of Energy and Environment, State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Hong Kong, China
- Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
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Windisch HS, Fink P. Transcriptome sequencing of a keystone aquatic herbivore yields insights on the temperature-dependent metabolism of essential lipids. BMC Genomics 2019; 20:894. [PMID: 31752680 PMCID: PMC6873670 DOI: 10.1186/s12864-019-6268-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 11/06/2019] [Indexed: 11/10/2022] Open
Abstract
Background Nutritional quality of phytoplankton is a major determinant of the trophic transfer efficiency at the plant-herbivore interface in freshwater food webs. In particular, the phytoplankton’s content of the essential polyunsaturated omega-3 fatty acid eicosapentaenoic acid (EPA) has been repeatedly shown to limit secondary production in the major zooplankton herbivore genus Daphnia. Despite extensive research efforts on the biological model organism Daphnia, and the availability of several Daphnia genomes, little is known regarding the molecular mechanisms underlying the limitations in Daphnia related to dietary EPA availability. Results We used RNA-seq to analyse the transcriptomic response of Daphnia magna which were fed with two different diets — each with or without supplementation of EPA — at two different temperature levels (15 and 20 °C). The transcripts were mapped to the D. magna genome assembly version 2.4, containing 26,646 translations. When D. magna fed on green alga, changing the temperature provoked a differential expression of 2001 transcripts, and in cyanobacteria-fed daphnia, 3385 transcripts were affected. The supplementation of EPA affected 1635 (on the green algal diet), or 175 transcripts (on the cyanobacterial diet), respectively. Combined effects for diet and temperature were also observed (669 for the green algal and 128 transcripts for the cyanobacterial diet). Searching for orthologous genes (COG-analysis) yielded a functional overview of the altered transcriptomes. Cross-matched transcript sets from both feed types were compiled to illuminate core responses to the factors temperature and EPA-supplementation. Conclusions Our highly controlled eco-physiological experiments revealed an orchestrated response of genes involved in the transformation and signalling of essential fatty acids, including eicosanoid-signalling pathways with potential immune functions. We provide an overview of downstream-regulated genes, which contribute to enhance growth and reproductive output. We also identified numerous EPA-responsive candidate genes of yet unknown function, which constitute new targets for future studies on the molecular basis of EPA-dependent effects at the freshwater plant-herbivore interface.
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Affiliation(s)
- Heidrun S Windisch
- Heinrich-Heine-University, Institute for Cell Biology and Zoology, Universitätsstrasse 1, 40225, Düsseldorf, Germany. .,Fraunhofer IME, Institute for Molecular Ecology, Am Aberg 1, 57392, Schmallenberg, Germany.
| | - Patrick Fink
- Institute for Zoology, University of Cologne, Zülpicher Strasse 47b, 50674, Köln, Germany.,Department River Ecology, Helmholtz Centre for Environmental Science, Brückstrasse 3a, 39114, Magdeburg, Germany.,Department Aquatic Ecosystem Analysis and Management, Helmholtz Centre for Environmental Science, Brückstrasse 3a, 39114, Magdeburg, Germany
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MicroRNAs in Daphnia magna identified and characterized by deep sequencing, genome mapping and manual curation. Sci Rep 2019; 9:15945. [PMID: 31685896 PMCID: PMC6828783 DOI: 10.1038/s41598-019-52387-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 10/11/2019] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that function in RNA silencing and post-transcriptional regulation of gene expression in most organisms. The water flea, Daphnia magna is a key model to study phenotypic, physiological and genomic responses to environmental cues and miRNAs can potentially mediate these responses. By using deep sequencing, genome mapping and manual curations, we have characterised the miRNAome of D. magna. We identified 66 conserved miRNAs and 13 novel miRNAs; all of these were found in the three studied life stages of D. magna (juveniles, subadults, adults), but with variation in expression levels between stages. Forty-one of the miRNAs were clustered into 13 genome clusters also present in the D. pulex genome. Most miRNAs contained sequence variants (isomiRs). The highest expressed isomiRs were 3′ template variants with one nucleotide deletion or 3′ non-template variants with addition of A or U at the 3′ end. We also identified offset RNAs (moRs) and loop RNAs (loRs). Our work extends the base for further work on all species (miRNA, isomiRs, moRNAs, loRNAs) of the miRNAome of Daphnia as biomarkers in response to chemical substances and environment cues, and underline age dependency.
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Gómez-Canela C, Rovira García X, Martínez-Jerónimo F, Marcé RM, Barata C. Analysis of neurotransmitters in Daphnia magna affected by neuroactive pharmaceuticals using liquid chromatography-high resolution mass spectrometry. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 254:113029. [PMID: 31454584 DOI: 10.1016/j.envpol.2019.113029] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 06/10/2023]
Abstract
Neurotransmission plays an essential role during the central nervous system (CNS) development. During the last years, several studies based on the changes produced in neurotransmitters of aquatic organisms caused by pharmaceuticals have been reported. Daphnia magna, the aquatic ecotoxicological model organism, shares several of the neurotransmitters targeted by antidepressant and other neuro-active drugs with vertebrates. Therefore, a method based on liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS) has been applied for the first time to study the levels of 41 neurotransmitters in Daphnia magna under the effect of four different neuro-active pharmaceuticals (sertraline, venlafaxine, duloxetine and fluoxetine). In addition, the performance of LC-HRMS was studied in terms of linearity, sensitivity, intra- and inter-day precision, and overall robustness. The developed analytical method using LC-HRMS is a new tool for neurotoxicology research using the Daphnia magna model. As a result, general differences on the concentrations of those neurotransmitters exposed to the mentioned pharmaceuticals were observed.
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Affiliation(s)
- Cristian Gómez-Canela
- Department of Analytical Chemistry and Organic Chemistry, Campus Sescelades, Faculty of Chemistry, Universitat Rovira i Virgili, Marcel∙lí Domingo s/n, Tarragona, Catalonia, Spain.
| | - Xavier Rovira García
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034, Barcelona, Catalonia, Spain
| | | | - Rosa María Marcé
- Department of Analytical Chemistry and Organic Chemistry, Campus Sescelades, Faculty of Chemistry, Universitat Rovira i Virgili, Marcel∙lí Domingo s/n, Tarragona, Catalonia, Spain
| | - Carlos Barata
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034, Barcelona, Catalonia, Spain
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Ravindran SP, Lüneburg J, Gottschlich L, Tams V, Cordellier M. Daphnia stressor database: Taking advantage of a decade of Daphnia '-omics' data for gene annotation. Sci Rep 2019; 9:11135. [PMID: 31366898 PMCID: PMC6668405 DOI: 10.1038/s41598-019-47226-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 07/09/2019] [Indexed: 11/09/2022] Open
Abstract
Gene expression patterns help to measure and characterize the effect of environmental perturbations at the cellular and organism-level. Complicating interpretation is the presence of uncharacterized or "hypothetical" gene functions for a large percentage of genomes. This is particularly evident in Daphnia genomes, which contains many regions coding for "hypothetical proteins" and are significantly divergent from many of the available arthropod model species, but might be ecologically important. In the present study, we developed a gene expression database, the Daphnia stressor database (http://www.daphnia-stressordb.uni-hamburg.de/dsdbstart.php), built from 90 published studies on Daphnia gene expression. Using a comparative genomics approach, we used the database to annotate D. galeata transcripts. The extensive body of literature available for Daphnia species allowed to associate stressors with gene expression patterns. We believe that our stressor based annotation strategy allows for better understanding and interpretation of the functional role of the understudied hypothetical or uncharacterized Daphnia genes, thereby increasing our understanding of Daphnia's genetic and phenotypic variability.
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Affiliation(s)
- Suda Parimala Ravindran
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, 452 96, Strömstad, Sweden
| | - Jennifer Lüneburg
- Universität Hamburg, Institute of Zoology, Martin-Luther-King Platz 3, 20146, Hamburg, Germany
| | - Lisa Gottschlich
- Universität Hamburg, Institute of Zoology, Martin-Luther-King Platz 3, 20146, Hamburg, Germany
| | - Verena Tams
- Universität Hamburg, Institut für marine Ökosystem- und Fischereiwissenschaften, Große Elbstraße 133, 22767, Hamburg, Germany
| | - Mathilde Cordellier
- Universität Hamburg, Institute of Zoology, Martin-Luther-King Platz 3, 20146, Hamburg, Germany.
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Baldwin-Brown JG, Weeks SC, Long AD. A New Standard for Crustacean Genomes: The Highly Contiguous, Annotated Genome Assembly of the Clam Shrimp Eulimnadia texana Reveals HOX Gene Order and Identifies the Sex Chromosome. Genome Biol Evol 2018; 10:143-156. [PMID: 29294012 PMCID: PMC5765565 DOI: 10.1093/gbe/evx280] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2017] [Indexed: 02/06/2023] Open
Abstract
Vernal pool clam shrimp (Eulimnadia texana) are a promising model system due to their ease of lab culture, short generation time, modest sized genome, a somewhat rare stable androdioecious sex determination system, and a requirement to reproduce via desiccated diapaused eggs. We generated a highly contiguous genome assembly using 46× of PacBio long read data and 216× of Illumina short reads, and annotated using Illumina RNAseq obtained from adult males or hermaphrodites. Of the 120 Mb genome 85% is contained in the largest eight contigs, the smallest of which is 4.6 Mb. The assembly contains 98% of transcripts predicted via RNAseq. This assembly is qualitatively different from scaffolded Illumina assemblies: It is produced from long reads that contain sequence data along their entire length, and is thus gap free. The contiguity of the assembly allows us to order the HOX genes within the genome, identifying two loci that contain HOX gene orthologs, and which approximately maintain the order observed in other arthropods. We identified a partial duplication of the Antennapedia complex adjacent to the few genes homologous to the Bithorax locus. Because the sex chromosome of an androdioecious species is of special interest, we used existing allozyme and microsatellite markers to identify the E. texana sex chromosome, and find that it comprises nearly half of the genome of this species. Linkage patterns indicate that recombination is extremely rare and perhaps absent in hermaphrodites, and as a result the location of the sex determining locus will be difficult to refine using recombination mapping.
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Affiliation(s)
| | | | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California Irvine
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18
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Russo C, Isidori M, Deaver JA, Poynton HC. Toxicogenomic responses of low level anticancer drug exposures in Daphnia magna. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 203:40-50. [PMID: 30075441 DOI: 10.1016/j.aquatox.2018.07.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/11/2018] [Accepted: 07/11/2018] [Indexed: 06/08/2023]
Abstract
The use of anticancer drugs in chemotherapy is increasing, leading to growing environmental concentrations of imatinib mesylate (IMA), cisplatinum (CDDP), and etoposide (ETP) in aquatic systems. Previous studies have shown that these anticancer drugs cause DNA damage in the crustacean Daphnia magna at low, environmentally relevant concentrations. To explore the mechanism of action of these compounds and the downstream effects of DNA damage on D. magna growth and development at a sensitive life stage, we exposed neonates to low level concentrations equivalent to those that elicit DNA damage (IMA: 2000 ng/L, ETP: 300 ng/L, CDDP: 10 ng/L) and performed transcriptomic analysis using an RNA-seq approach. RNA sequencing generated 14 million reads per sample, which were aligned to the D. magna genome and assembled, producing approximately 23,000 transcripts per sample. Over 90% of the transcripts showed homology to proteins in GenBank, revealing a high quality transcriptome assembly, although functional annotation was much lower. RT-qPCR was used to identify robust biomarkers and confirmed the downregulation of an angiotensin converting enzyme-like gene (ance) involved in neuropeptide regulation across all three anticancer drugs and the down-regulation of DNA topoisomerase II by ETP. RNA-seq analysis also allowed for an in depth exploration of the differential splicing of transcripts revealing that regulation of different gene isoforms predicts potential impacts on translation and protein expression, providing a more meaningful assessment of transcriptomic data. Enrichment analysis and investigation of affected biological processes suggested that the DNA damage caused by ETP and IMA influences cell cycle regulation and GPCR signaling. This dysregulation is likely responsible for effects to neurological system processes and development, and overall growth and development. Our transcriptomic approach provided insight into the mechanisms that respond to DNA damage caused by anticancer drug exposure and generated novel hypotheses on how these chemicals may impact the growth and survival of this ecologically important zooplankton species.
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Affiliation(s)
- Chiara Russo
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università della Campania L. Vanvitelli, Via Vivaldi 43, I-81100, Caserta, Italy
| | - Marina Isidori
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università della Campania L. Vanvitelli, Via Vivaldi 43, I-81100, Caserta, Italy
| | - Jessica A Deaver
- School for the Environment, University of Massachusetts, 100 Morrissey Blvd., Boston, MA, 02125-3393, United States
| | - Helen C Poynton
- School for the Environment, University of Massachusetts, 100 Morrissey Blvd., Boston, MA, 02125-3393, United States.
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19
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Gottardi M, Tyzack JD, Bender A, Cedergreen N. Can the inhibition of cytochrome P450 in aquatic invertebrates due to azole fungicides be estimated with in silico and in vitro models and extrapolated between species? AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 201:11-20. [PMID: 29859403 DOI: 10.1016/j.aquatox.2018.05.017] [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: 03/12/2018] [Revised: 05/23/2018] [Accepted: 05/24/2018] [Indexed: 06/08/2023]
Abstract
Azole fungicides, designed to halt fungal growth by specific inhibition of fungal cytochrome P450 (CYP51), inhibit cytochrome P450s involved in the metabolism of xenobiotics in several non-target organisms thus raising environmental concern. The present study investigates the degree by which inhibition strengths of azoles toward cytochrome P450 in rat liver, the insect Chironomus riparius larvae and the snail Lymnaea stagnalis can be extrapolated from estimated in silico affinities. Azoles' affinities toward human cytochrome P450 isoforms involved in xenobiotic metabolism (CYP3A4, CYP2C9 and CYP2D6) as well as fungal CYP51 were estimated with a ligand-protein docking model based on the ChemScore scoring function. Estimated affinities toward the selected enzymatic structures correlated strongly with measured inhibition strengths in rat liver (ChemScore vs. logIC50 among cytochrome P450 isoforms: -0.662 < r < -0.891, n = 17 azoles), while weaker correlations were found for C. riparius larvae (-0.167 < r < -0.733, n = 9) and L. stagnalis (-0.084 < r < -0.648, n = 8). Inhibition strengths toward C. riparius and rat liver activities were found to be highly correlated to each other (r: 0.857) while no significant relationship was found between either of the species and L. stagnalis. The inhibition of cytochrome P450 due to azole fungicides could be estimated in vitro and to a lesser extent in silico for C. riparius but not for L. stagnalis, possibly due to different enzymatic susceptibility toward azole inhibition among the species.
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Affiliation(s)
- Michele Gottardi
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Jonathan D Tyzack
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Nina Cedergreen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark.
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Comparative Transcriptome Analysis for Understanding Predator-Induced Polyphenism in the Water Flea Daphnia pulex. Int J Mol Sci 2018; 19:ijms19072110. [PMID: 30036973 PMCID: PMC6073494 DOI: 10.3390/ijms19072110] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/13/2018] [Accepted: 07/18/2018] [Indexed: 11/17/2022] Open
Abstract
The crustacean Daphnia pulex is one of the best model organisms for studying inducible defense mechanisms due to their inducible morphology in response to the predator Chaoborus larvae. In this study, multiple developmental stages of D. pulex were exposed to C. flavicans larvae and transcriptome profiles of samples from late embryo to fifth instar were sequenced by the RNA-seq technique to investigate the genetic background underlying inducible defenses. In comparison, differentially expressed genes between defensive and normal morphs were identified, including 908 genes in late embryo, 1383 genes in the first-third (1–3) instar, and 1042 genes in fourth-fifth (4–5) instar. Gene ontology enrichment analysis showed that structural constituents of the cuticle and structural molecule activity genes were prominent up-regulated genes in late embryos. Down-regulated genes in late embryos and 1–3 instar comprised metabolic process, hydrolase activity, and peptidase activity gene classes. Pathway analysis indicated that small molecule neurotransmitter pathways were potentially involved in the development of inducible defenses. The characterization of genes and pathways in multiple developmental stages can improve our understanding of inducible defense responses of D. pulex to predation at the molecular level.
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21
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Campos B, Fletcher D, Piña B, Tauler R, Barata C. Differential gene transcription across the life cycle in Daphnia magna using a new all genome custom-made microarray. BMC Genomics 2018; 19:370. [PMID: 29776339 PMCID: PMC5960145 DOI: 10.1186/s12864-018-4725-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/25/2018] [Indexed: 11/23/2022] Open
Abstract
Background Unravelling the link between genes and environment across the life cycle is a challenging goal that requires model organisms with well-characterized life-cycles, ecological interactions in nature, tractability in the laboratory, and available genomic tools. Very few well-studied invertebrate model species meet these requirements, being the waterflea Daphnia magna one of them. Here we report a full genome transcription profiling of D. magna during its life-cycle. The study was performed using a new microarray platform designed from the complete set of gene models representing the whole transcribed genome of D. magna. Results Up to 93% of the existing 41,317 D. magna gene models showed differential transcription patterns across the developmental stages of D. magna, 59% of which were functionally annotated. Embryos showed the highest number of unique transcribed genes, mainly related to DNA, RNA, and ribosome biogenesis, likely related to cellular proliferation and morphogenesis of the several body organs. Adult females showed an enrichment of transcripts for genes involved in reproductive processes. These female-specific transcripts were essentially absent in males, whose transcriptome was enriched in specific genes of male sexual differentiation genes, like doublesex. Conclusion Our results define major characteristics of transcriptional programs involved in the life-cycle, differentiate males and females, and show that large scale gene-transcription data collected in whole animals can be used to identify genes involved in specific biological and biochemical processes. Electronic supplementary material The online version of this article (10.1186/s12864-018-4725-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bruno Campos
- IDAEA-CSIC: Institute of Environmental Diagnosis and Water Research, CSIC, Barcelona, Spain.
| | | | - Benjamín Piña
- IDAEA-CSIC: Institute of Environmental Diagnosis and Water Research, CSIC, Barcelona, Spain
| | - Romà Tauler
- IDAEA-CSIC: Institute of Environmental Diagnosis and Water Research, CSIC, Barcelona, Spain
| | - Carlos Barata
- IDAEA-CSIC: Institute of Environmental Diagnosis and Water Research, CSIC, Barcelona, Spain
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Xu L, Lin Q, Xu S, Gu Y, Hou J, Liu Y, Dumont HJ, Han B. Daphnia diversity on the Tibetan Plateau measured by DNA taxonomy. Ecol Evol 2018; 8:5069-5078. [PMID: 29876082 PMCID: PMC5980554 DOI: 10.1002/ece3.4071] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 03/25/2018] [Accepted: 03/26/2018] [Indexed: 02/04/2023] Open
Abstract
Daphnia on the Tibetan Plateau has been little studied, and information on species diversity and biogeography is lacking. Here, we conducted a 4-year survey using the barcoding fragment of the mitochondrial COI gene to determine the distribution and diversity of Daphnia species found across the Plateau. Our results show that species richness is higher than previously thought, with total described and provisional species number doubling from 5 to 10. Six of the taxonomic units recovered by DNA taxonomy agreed well with morphology, but DNA barcoding distinguished three clades each for the D. longispina (D. galeata, D. dentifera, and D. longispina) and D. pulex (D. pulex, D. cf. tenebrosa, and D. pulicaria) complexes. The sequence divergence between congeneric species varied within a large range, from 9.25% to 30.71%. The endemic D. tibetana was the most common and widespread species, occurring in 12 hyposaline to mesosaline lakes. The lineage of D. longispina is the first confirmed occurrence in west Tibet.
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Affiliation(s)
- Lei Xu
- South China Sea Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Institute of HydrobiologyJinan UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Fishery Ecology and EnvironmentGuangzhouChina
- Key Laboratory of South China Sea Fishery ResourcesDevelopment and UtilizationMinistry of AgricultureGuangzhouChina
| | - Qiuqi Lin
- Institute of HydrobiologyJinan UniversityGuangzhouChina
| | - Shaolin Xu
- Institute of HydrobiologyJinan UniversityGuangzhouChina
| | - Yangliang Gu
- Institute of HydrobiologyJinan UniversityGuangzhouChina
| | - Juzhi Hou
- Institute of Tibetan Plateau ResearchChinese Academy of SciencesBeijingChina
| | - Yongqin Liu
- Institute of Tibetan Plateau ResearchChinese Academy of SciencesBeijingChina
| | | | - Bo‐Ping Han
- Institute of HydrobiologyJinan UniversityGuangzhouChina
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Kim RO, Jo MA, Song J, Kim IC, Yoon S, Kim WK. Novel approach for evaluating pharmaceuticals toxicity using Daphnia model: analysis of the mode of cytochrome P450-generated metabolite action after acetaminophen exposure. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 196:35-42. [PMID: 29328974 DOI: 10.1016/j.aquatox.2017.12.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 12/22/2017] [Accepted: 12/30/2017] [Indexed: 06/07/2023]
Abstract
Because of its widespread use, the pharmaceutical acetaminophen (APAP) is frequently detected in aquatic environments. APAP can have serious physiological effects, such as reduced reproduction, low growth rates, and abnormal behavior, in aquatic organisms. However, the methods available for evaluation of the aquatic toxicity of APAP are of limited usefulness. The present study aimed to develop reliable and sensitive markers for evaluation of APAP toxicity using Daphnia as a model organism. We focused on N-acetyl-p-benzoquinoneimine (NAPQI) production from APAP via cytochrome P450 metabolism because NAPQI causes APAP toxicity. Daphnia magna were exposed to APAP (0, 50, or 100 mg/L for 12 h or 24 h), and the total metabolites were extracted and analyzed for NAPQI. Direct detection of NAPQI was difficult because of its high reactivity, and its peak was close to that for APAP. Therefore, we tried to identify molecular and biochemical indicators associated with NAPQI generation, elimination, and its interactions with macromolecules. We identified changes in CYP370A13 gene expression, glutathione depletion, inhibition of thioredoxin reductase activity, and production of reactive oxygen species as indicators of D. magna exposure to APAP. These indicators could be used to develop sensitive and accurate techniques to evaluate the environmental toxicity of APAP.
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Affiliation(s)
- Ryeo-Ok Kim
- System Toxicology Research Center, Korea Institute of Toxicology, Daejeon 34114, South Korea
| | - Min-A Jo
- System Toxicology Research Center, Korea Institute of Toxicology, Daejeon 34114, South Korea
| | - Jinhaeng Song
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, South Korea
| | - Il-Chan Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, South Korea
| | - Seokjoo Yoon
- System Toxicology Research Center, Korea Institute of Toxicology, Daejeon 34114, South Korea
| | - Woo-Keun Kim
- System Toxicology Research Center, Korea Institute of Toxicology, Daejeon 34114, South Korea.
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Abehsera S, Zaccai S, Mittelman B, Glazer L, Weil S, Khalaila I, Davidov G, Bitton R, Zarivach R, Li S, Li F, Xiang J, Manor R, Aflalo ED, Sagi A. CPAP3 proteins in the mineralized cuticle of a decapod crustacean. Sci Rep 2018; 8:2430. [PMID: 29403068 PMCID: PMC5799365 DOI: 10.1038/s41598-018-20835-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/24/2018] [Indexed: 12/29/2022] Open
Abstract
The pancrustacean theory groups crustaceans and hexapods (once thought to comprise separate clades within the Arthropoda) into a single clade. A key feature common to all pancrustaceans is their chitinous exoskeleton, with a major contribution by cuticular proteins. Among these, are the CPAP3’s, a family of cuticular proteins, first identified in the hexapod Drosophila melanogaster and characterized by an N-terminal signaling peptide and three chitin-binding domains. In this study, CPAP3 proteins were mined from a transcriptomic library of a decapod crustacean, the crayfish Cherax quadricarinatus. Phylogenetic analysis of other CPAP3 proteins from hexapods and other crustaceans showed a high degree of conservation. Characterization of the crayfish proteins, designated CqCPAP3’s, suggested a major role for CPAP3’sin cuticle formation. Loss-of-function experiments using RNAi supported such a notion by demonstrating crucial roles for several CqCPAP3 proteins during molting. A putative mode of action for the CqCPAP3 proteins –theoretically binding three chitin strands– was suggested by the structural data obtained from a representative recombinant CqCPAP3. The similarities between the CqCPAP3 proteins and their hexapod homologues further demonstrated common genetic and proteinaceous features of cuticle formation in pancrustaceans, thereby reinforcing the linkage between these two highly important phylogenetic groups.
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Affiliation(s)
- Shai Abehsera
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Shir Zaccai
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Binyamin Mittelman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Lilah Glazer
- Department of Psychiatry and Behavioral Science, Duke University Medical Center, Durham, USA
| | - Simy Weil
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Isam Khalaila
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Geula Davidov
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ronit Bitton
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Shihao Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Rivka Manor
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Eliahu D Aflalo
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Amir Sagi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel. .,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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25
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Orsini L, Brown JB, Shams Solari O, Li D, He S, Podicheti R, Stoiber MH, Spanier KI, Gilbert D, Jansen M, Rusch DB, Pfrender ME, Colbourne JK, Frilander MJ, Kvist J, Decaestecker E, De Schamphelaere KAC, De Meester L. Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes. Mol Ecol 2017; 27:886-897. [PMID: 28746735 DOI: 10.1111/mec.14261] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/12/2017] [Accepted: 07/05/2017] [Indexed: 01/08/2023]
Abstract
Natural habitats are exposed to an increasing number of environmental stressors that cause important ecological consequences. However, the multifarious nature of environmental change, the strength and the relative timing of each stressor largely limit our understanding of biological responses to environmental change. In particular, early response to unpredictable environmental change, critical to survival and fitness in later life stages, is largely uncharacterized. Here, we characterize the early transcriptional response of the keystone species Daphnia magna to twelve environmental perturbations, including biotic and abiotic stressors. We first perform a differential expression analysis aimed at identifying differential regulation of individual genes in response to stress. This preliminary analysis revealed that a few individual genes were responsive to environmental perturbations and they were modulated in a stressor and genotype-specific manner. Given the limited number of differentially regulated genes, we were unable to identify pathways involved in stress response. Hence, to gain a better understanding of the genetic and functional foundation of tolerance to multiple environmental stressors, we leveraged the correlative nature of networks and performed a weighted gene co-expression network analysis. We discovered that approximately one-third of the Daphnia genes, enriched for metabolism, cell signalling and general stress response, drives transcriptional early response to environmental stress and it is shared among genetic backgrounds. This initial response is followed by a genotype- and/or condition-specific transcriptional response with a strong genotype-by-environment interaction. Intriguingly, genotype- and condition-specific transcriptional response is found in genes not conserved beyond crustaceans, suggesting niche-specific adaptation.
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Affiliation(s)
- Luisa Orsini
- Environmental Genomics Group, School of Biosciences, University of Birmingham Edgbaston, Birmingham, UK
| | - James B Brown
- Environmental Bioinformatics, Centre for Computational Biology, School of Biosciences, University of Birmingham Edgbaston, Birmingham, UK.,Department of Molecular Ecosystems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Statistics Department, University of California, Berkeley, CA, USA.,Preminon LLC, Rodeo, CA, USA
| | | | - Dong Li
- School of Computer Science, University of Birmingham Edgbaston, Birmingham, UK
| | - Shan He
- School of Computer Science, University of Birmingham Edgbaston, Birmingham, UK
| | - Ram Podicheti
- School of Informatics and Computing, Indiana University, Bloomington, IN, USA.,Center for Genomics and Bioinformatics, Indiana University and School of Informatics and Computing, Indiana University, Bloomington, IN, USA
| | - Marcus H Stoiber
- Department of Molecular Ecosystems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Katina I Spanier
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Donald Gilbert
- Biology Department, Indiana University, Bloomington, IN, USA
| | - Mieke Jansen
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, School of Informatics and Computing, Indiana University, Bloomington, IN, USA
| | - Michael E Pfrender
- Department of Biological Sciences, Eck Institute for Global Health & Environmental Change Initiative, Galvin Life Science Center, Notre Dame, IN, USA
| | - John K Colbourne
- Environmental Genomics Group, School of Biosciences, University of Birmingham Edgbaston, Birmingham, UK
| | - Mikko J Frilander
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jouni Kvist
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ellen Decaestecker
- Aquatic Biology, Interdisciplinary Research Facility Life Sciences KU Leuven Campus Kortrijk, Kortrijk, Belgium
| | - Karel A C De Schamphelaere
- Laboratory of Environmental Toxicology and Aquatic Ecology, GhEnToxLab, Ghent University, Ghent, Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
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26
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Abehsera S, Peles S, Tynyakov J, Bentov S, Aflalo ED, Li S, Li F, Xiang J, Sagi A. MARS: A protein family involved in the formation of vertical skeletal elements. J Struct Biol 2017; 198:92-102. [DOI: 10.1016/j.jsb.2017.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 04/04/2017] [Accepted: 04/05/2017] [Indexed: 01/06/2023]
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27
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Koussoroplis AM, Schwarzenberger A, Wacker A. Diet quality determines lipase gene expression and lipase/esterase activity in Daphnia pulex. Biol Open 2017; 6:210-216. [PMID: 28069588 PMCID: PMC5312099 DOI: 10.1242/bio.022046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We studied the short- (12 h) and long-term (144 h) response of Daphnia pulex lipases to quality shifts in diets consisting of different mixtures of the green alga Scenedesmus with the cyanobacterium Synechococcus, two species with contrasting lipid compositions. The lipase/esterase activity in both the gut and the body tissues had fast responses to the diet shift and increased with higher dietary contributions of Synechococcus When screening the Daphnia genome for TAG lipases, we discovered a large gene-family expansion of these enzymes. We used a subset of eight genes for mRNA expression analyses and distinguished between influences of time and diet on the observed gene expression patterns. We identified five diet-responsive lipases of which three showed a sophisticated short- and long-term pattern of expression in response to small changes in food-quality. Furthermore, the gene expression of one of the lipases was strongly correlated to lipase/esterase activity in the gut suggesting its potentially major role in digestion. These findings demonstrate that the lipid-related enzymatic machinery of D. pulex is finely tuned to diet and might constitute an important mechanism of physiological adaptation in nutritionally complex environments.
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Affiliation(s)
- Apostolos-Manuel Koussoroplis
- Theoretical Aquatic Ecology an Ecophysiology Group, Institute for Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
| | - Anke Schwarzenberger
- Theoretical Aquatic Ecology an Ecophysiology Group, Institute for Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
| | - Alexander Wacker
- Theoretical Aquatic Ecology an Ecophysiology Group, Institute for Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
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28
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Giraudo M, Douville M, Cottin G, Houde M. Transcriptomic, cellular and life-history responses of Daphnia magna chronically exposed to benzotriazoles: Endocrine-disrupting potential and molting effects. PLoS One 2017; 12:e0171763. [PMID: 28196088 PMCID: PMC5308779 DOI: 10.1371/journal.pone.0171763] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 01/25/2017] [Indexed: 11/19/2022] Open
Abstract
Benzotriazoles (BZTs) are ubiquitous aquatic contaminants used in a wide range of industrial and domestic applications from aircraft deicers to dishwasher tablets. Acute toxicity has been reported in aquatic organisms for some of the BZTs but their mode of action remains unknown. The objectives of this study were to evaluate the transcriptomic response of D. magna exposed to sublethal doses of 1H-benzotriazole (BTR), 5-methyl-1H-benzotriazole (5MeBTR) and 5-chloro-1H-benzotriazole (5ClBTR) using RNA-sequencing and quantitative real-time PCR. Cellular and life-history endpoints (survival, number of neonates, growth) were also investigated. Significant effects on the molting frequency were observed after 21-d exposure to 5MeBTR and 5ClBTR. No effects on molting frequency were observed for BTR but RNA-seq results indicated that this BZT induced the up-regulation of genes coding for cuticular proteins, which could have compensated the molting disruption. Molting in cladocerans is actively controlled by ecdysteroid hormones. Complementary short-term temporal analysis (4- and 8-d exposure) of the transcription of genes related to molting and hormone-mediated processes indicated that the three compounds had specific modes of action. BTR induced the transcription of genes involved in 20-hydroxyecdysone synthesis, which suggests pro-ecdysteroid properties. 5ClBTR exposure induced protein activity and transcriptional levels of chitinase enzymes, associated with an impact on ecdysteroid signaling pathways, which could explain the decrease in molt frequency. Finally, 5MeBTR seemed to increase molt frequency through epigenetic processes. Overall, results suggested that molting effects observed at the physiological level could be linked to endocrine regulation impacts of BZTs at the molecular level.
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Affiliation(s)
- Maeva Giraudo
- Environment and Climate Change Canada, Aquatic Contaminants Research Division, Water Science and Technology Directorate, Montreal, Québec, Canada
| | - Mélanie Douville
- Environment and Climate Change Canada, Aquatic Contaminants Research Division, Water Science and Technology Directorate, Montreal, Québec, Canada
| | - Guillaume Cottin
- Environment and Climate Change Canada, Aquatic Contaminants Research Division, Water Science and Technology Directorate, Montreal, Québec, Canada
- Université Paris Descartes, Paris, France
| | - Magali Houde
- Environment and Climate Change Canada, Aquatic Contaminants Research Division, Water Science and Technology Directorate, Montreal, Québec, Canada
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29
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Zdobnov EM, Tegenfeldt F, Kuznetsov D, Waterhouse RM, Simão FA, Ioannidis P, Seppey M, Loetscher A, Kriventseva EV. OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs. Nucleic Acids Res 2016; 45:D744-D749. [PMID: 27899580 PMCID: PMC5210582 DOI: 10.1093/nar/gkw1119] [Citation(s) in RCA: 302] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 10/26/2016] [Accepted: 11/08/2016] [Indexed: 11/25/2022] Open
Abstract
OrthoDB is a comprehensive catalog of orthologs, genes inherited by extant species from a single gene in their last common ancestor. In 2016 OrthoDB reached its 9th release, growing to over 22 million genes from over 5000 species, now adding plants, archaea and viruses. In this update we focused on usability of this fast-growing wealth of data: updating the user and programmatic interfaces to browse and query the data, and further enhancing the already extensive integration of available gene functional annotations. Collating functional annotations from over 100 resources, and enabled us to propose descriptive titles for 87% of ortholog groups. Additionally, OrthoDB continues to provide computed evolutionary annotations and to allow user queries by sequence homology. The OrthoDB resource now enables users to generate publication-quality comparative genomics charts, as well as to upload, analyze and interactively explore their own private data. OrthoDB is available from http://orthodb.org.
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Affiliation(s)
- Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Fredrik Tegenfeldt
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Dmitry Kuznetsov
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Robert M Waterhouse
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Felipe A Simão
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Mathieu Seppey
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Alexis Loetscher
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Evgenia V Kriventseva
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
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30
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Suwansa-Ard S, Kankuan W, Thongbuakaew T, Saetan J, Kornthong N, Kruangkum T, Khornchatri K, Cummins SF, Isidoro C, Sobhon P. Transcriptomic analysis of the autophagy machinery in crustaceans. BMC Genomics 2016; 17:587. [PMID: 27506197 PMCID: PMC4979118 DOI: 10.1186/s12864-016-2996-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 08/04/2016] [Indexed: 01/31/2023] Open
Abstract
Background The giant freshwater prawn, Macrobrachium rosenbergii, is a decapod crustacean that is commercially important as a food source. Farming of commercial crustaceans requires an efficient management strategy because the animals are easily subjected to stress and diseases during the culture. Autophagy, a stress response process, is well-documented and conserved in most animals, yet it is poorly studied in crustaceans. Results In this study, we have performed an in silico search for transcripts encoding autophagy-related (Atg) proteins within various tissue transcriptomes of M. rosenbergii. Basic Local Alignment Search Tool (BLAST) search using previously known Atg proteins as queries revealed 41 transcripts encoding homologous M. rosenbergii Atg proteins. Among these Atg proteins, we selected commonly used autophagy markers, including Beclin 1, vacuolar protein sorting (Vps) 34, microtubule-associated proteins 1A/1B light chain 3B (MAP1LC3B), p62/sequestosome 1 (SQSTM1), and lysosomal-associated membrane protein 1 (Lamp-1) for further sequence analyses using comparative alignment and protein structural prediction. We found that crustacean autophagy marker proteins contain conserved motifs typical of other animal Atg proteins. Western blotting using commercial antibodies raised against human Atg marker proteins indicated their presence in various M. rosenbergii tissues, while immunohistochemistry localized Atg marker proteins within ovarian tissue, specifically late stage oocytes. Conclusions This study demonstrates that the molecular components of autophagic process are conserved in crustaceans, which is comparable to autophagic process in mammals. Furthermore, it provides a foundation for further studies of autophagy in crustaceans that may lead to more understanding of the reproduction- and stress-related autophagy, which will enable the efficient aquaculture practices. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2996-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Saowaros Suwansa-Ard
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand.,Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, QLD, Australia
| | - Wilairat Kankuan
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand.,Laboratory of Molecular Pathology, Department of Health Sciences, Amedeo Avogadro University, Novara, Italy
| | - Tipsuda Thongbuakaew
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand.,School of Medicine, Walailak University, Nakhon Si Thammarat, Thailand
| | - Jirawat Saetan
- Department of Anatomy, Faculty of Science, Prince of Songkla University, Hatyai, Songkhla, Thailand
| | - Napamanee Kornthong
- Chulabhorn International College of Medicine, Thammsat University, Klongluang, Phathumthani, Thailand
| | - Thanapong Kruangkum
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kanjana Khornchatri
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Scott F Cummins
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, QLD, Australia
| | - Ciro Isidoro
- Laboratory of Molecular Pathology, Department of Health Sciences, Amedeo Avogadro University, Novara, Italy.
| | - Prasert Sobhon
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand. .,Faculty of Allied Health Sciences, Burapha University, Chonburi, Thailand.
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31
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Bernatowicz PP, Kotwica-Rolinska J, Joachimiak E, Sikora A, Polanska MA, Pijanowska J, Bębas P. Temporal Expression of the Clock Genes in the Water FleaDaphnia pulex(Crustacea: Cladocera). ACTA ACUST UNITED AC 2016; 325:233-54. [DOI: 10.1002/jez.2015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 04/14/2016] [Accepted: 04/18/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Piotr P. Bernatowicz
- Department of Paleobiology and Evolution, Institute of Zoology, Faculty of Biology; University of Warsaw; Biological and Chemical Research Centre; Warsaw Poland
| | - Joanna Kotwica-Rolinska
- Department of Animal Physiology, Institute of Zoology, Faculty of Biology; University of Warsaw; Warsaw Poland
| | - Ewa Joachimiak
- Department of Cell Biology; Nencki Institute of Experimental Biology PAS; Warsaw Poland
| | - Anna Sikora
- Department of Hydrobiology, Institute of Zoology, Faculty of Biology; University of Warsaw; Biological and Chemical Research Centre; Warsaw Poland
| | - Marta A. Polanska
- Department of Animal Physiology, Institute of Zoology, Faculty of Biology; University of Warsaw; Warsaw Poland
| | - Joanna Pijanowska
- Department of Hydrobiology, Institute of Zoology, Faculty of Biology; University of Warsaw; Biological and Chemical Research Centre; Warsaw Poland
| | - Piotr Bębas
- Department of Animal Physiology, Institute of Zoology, Faculty of Biology; University of Warsaw; Warsaw Poland
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32
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Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors. Sci Data 2016; 3:160030. [PMID: 27164179 PMCID: PMC4862326 DOI: 10.1038/sdata.2016.30] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/19/2016] [Indexed: 11/08/2022] Open
Abstract
The full exploration of gene-environment interactions requires model organisms with well-characterized ecological interactions in their natural environment, manipulability in the laboratory and genomic tools. The waterflea Daphnia magna is an established ecological and toxicological model species, central to the food webs of freshwater lentic habitats and sentinel for water quality. Its tractability and cyclic parthenogenetic life-cycle are ideal to investigate links between genes and the environment. Capitalizing on this unique model system, the STRESSFLEA consortium generated a comprehensive RNA-Seq data set by exposing two inbred genotypes of D. magna and a recombinant cross of these genotypes to a range of environmental perturbations. Gene models were constructed from the transcriptome data and mapped onto the draft genome of D. magna using EvidentialGene. The transcriptome data generated here, together with the available draft genome sequence of D. magna and a high-density genetic map will be a key asset for future investigations in environmental genomics.
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33
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Dölling R, Becker D, Hawat S, Koch M, Schwarzenberger A, Zeis B. Adjustments of serine proteases of Daphnia pulex in response to temperature changes. Comp Biochem Physiol B Biochem Mol Biol 2016; 194-195:1-10. [DOI: 10.1016/j.cbpb.2016.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 12/17/2015] [Accepted: 01/02/2016] [Indexed: 10/22/2022]
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34
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Takahashi T, Ohnuma M. Identification and Expression Analysis of Upregulated Genes in the Resting Egg-Producing Water Flea (Daphnia pulex). Zoolog Sci 2016; 33:106-15. [PMID: 26853876 DOI: 10.2108/zs150068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Water fleas (Daphnia pulex) normally produce subitaneous eggs that initiate development immediately after oviposition. However, in response to habitat degradation, resting eggs are produced, which are enclosed in a sturdy outer envelope (ephippium) and can survive in harsh environments for an extended time. To understand the molecular mechanism underlying resting egg production in D. pulex, we investigated the genes whose expression patterns played a role in the production and identified the following six candidate genes: Dpfa-1, Dpfa-2, Dpep-1, Dpep-2, Dpep-3, and Dpep-4. These six genes displayed > 40-fold higher expression levels in resting egg-producing animals compared with those in subitaneous egg-producing animals at the period when the ovaries were mature. Dpfa-1 and Dpfa-2 were expressed in the fat cells, and their expression patterns were synchronized with the development of resting egg oocytes in the ovary. In contrast, Dpep-1-4 were expressed in the morphologically altered epidermal cells of the brood chamber with the formation of the ephippium, and their expression patterns were also related to ephippium formation. Our results suggest that the former two genes encode the resting egg-specific components produced by fat cells and that the latter four genes encode the components related to the ephippium formation synthesized by epidermal cells.
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Affiliation(s)
- Tomoko Takahashi
- Department of Biology, School of Medicine, Kurume University, Fukuoka 830-0011, Japan
| | - Masaaki Ohnuma
- Department of Biology, School of Medicine, Kurume University, Fukuoka 830-0011, Japan
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35
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Chen S, McKinney GJ, Nichols KM, Colbourne JK, Sepúlveda MS. Novel Cadmium Responsive MicroRNAs in Daphnia pulex. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:14605-13. [PMID: 26550707 DOI: 10.1021/acs.est.5b03988] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Daphnia pulex is a widely used toxicological model and is known for its sensitivity to cadmium (Cd). Recent research suggests that microRNAs (miRNAs) play a critical role in animal responses to heavy metals. To investigate the functions of D. pulex miRNAs under Cd exposure, we analyzed the miRNA profiles of D. pulex after 48 h using miRNA microarrays and validated our findings by q-PCR. miRNA dpu-let-7 was identified as a stably expressed gene and used as a reference. We identified 22 and 21 differentially expressed miRNAs under low (20 μg/L CdCl2) and high-exposure (40 μg/L CdCl2) concentrations compared to controls, respectively. Cellular functions of predicted miRNA target Cd-responsive genes included oxidative stress, ion transport, mitochondrial damage, and DNA repair. An insulin-related network was also identified in relation to several Cd-responsive miRNAs. The expression of three predicted target genes for miR-71 and miR-210 were evaluated, and expression of two of them (SCN2A and SLC31A1) was negatively correlated with the expression of their regulator miRNAs. We show miR-210 is hypoxia-responsive in D. pulex and propose Cd and hypoxia induce miR-210 via a same HIF1α modulated pathway. Collectively, this research advances our understanding on the role of miRNAs in response to heavy-metal exposure.
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Affiliation(s)
- Shuai Chen
- Department of Forestry and Natural Resources, Purdue University , West Lafayette, Indiana, 47907 United States
| | - Garrett J McKinney
- School of Aquatic and Fishery Sciences, University of Washington , Seattle, Washington, 98195 United States
| | - Krista M Nichols
- Department of Forestry and Natural Resources, Purdue University , West Lafayette, Indiana, 47907 United States
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Ocean and Atmospheric Administration , Seattle, Washington, 98112 United States
| | - John K Colbourne
- Environmental Genomics Group, School of Biosciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, U.K
| | - Maria S Sepúlveda
- Department of Forestry and Natural Resources, Purdue University , West Lafayette, Indiana, 47907 United States
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The evolutionary landscape of intergenic trans-splicing events in insects. Nat Commun 2015; 6:8734. [PMID: 26521696 PMCID: PMC4667647 DOI: 10.1038/ncomms9734] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 09/24/2015] [Indexed: 01/29/2023] Open
Abstract
To explore the landscape of intergenic trans-splicing events and characterize their functions and evolutionary dynamics, we conduct a mega-data study of a phylogeny containing eight species across five orders of class Insecta, a model system spanning 400 million years of evolution. A total of 1,627 trans-splicing events involving 2,199 genes are identified, accounting for 1.58% of the total genes. Homology analysis reveals that mod(mdg4)-like trans-splicing is the only conserved event that is consistently observed in multiple species across two orders, which represents a unique case of functional diversification involving trans-splicing. Thus, evolutionarily its potential for generating proteins with novel function is not broadly utilized by insects. Furthermore, 146 non-mod trans-spliced transcripts are found to resemble canonical genes from different species. Trans-splicing preserving the function of 'breakup' genes may serve as a general mechanism for relaxing the constraints on gene structure, with profound implications for the evolution of genes and genomes.
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Asselman J, Pfrender ME, Lopez JA, De Coninck DIM, Janssen CR, Shaw JR, De Schamphelaere KAC. Conserved transcriptional responses to cyanobacterial stressors are mediated by alternate regulation of paralogous genes in Daphnia. Mol Ecol 2015; 24:1844-55. [PMID: 25754071 DOI: 10.1111/mec.13148] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 03/04/2015] [Accepted: 03/05/2015] [Indexed: 11/28/2022]
Abstract
Despite a significant increase in genomic data, our knowledge of gene functions and their transcriptional responses to environmental stimuli remains limited. Here, we use the model keystone species Daphnia pulex to study environmental responses of genes in the context of their gene family history to better understand the relationship between genome structure and gene function in response to environmental stimuli. Daphnia were exposed to five different treatments, each consisting of a diet supplemented with one of five cyanobacterial species, and a control treatment consisting of a diet of only green algae. Differential gene expression profiles of Daphnia exposed to each of these five cyanobacterial species showed that genes with known functions are more likely to be shared by different expression profiles, whereas genes specific to the lineage of Daphnia are more likely to be unique to a given expression profile. Furthermore, while only a small number of nonlineage-specific genes were conserved across treatment type, there was a high degree of overlap in expression profiles at the functional level. The conservation of functional responses across the different cyanobacterial treatments can be attributed to the treatment-specific expression of different paralogous genes within the same gene family. Comparison with available gene expression data in the literature suggests differences in nutritional composition in diets with cyanobacterial species compared to diets of green algae as a primary driver for cyanobacterial effects on Daphnia. We conclude that conserved functional responses in Daphnia across different cyanobacterial treatments are mediated through alternate regulation of paralogous gene families.
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Affiliation(s)
- Jana Asselman
- Laboratory of Environmental Toxicology and Aquatic Ecology, GhEnToxLab unit, Ghent University, J. Plateaustraat 22, 9000, Gent, Belgium; Department of Biological Sciences, University of Notre Dame, Notre Dame, 46556, IN, USA
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Harney E, Plaistow SJ, Paterson S. Transcriptional changes during Daphnia pulex development indicate that the maturation decision resembles a rate more than a threshold. J Evol Biol 2015; 28:944-58. [PMID: 25786891 DOI: 10.1111/jeb.12624] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/04/2015] [Accepted: 03/12/2015] [Indexed: 01/05/2023]
Abstract
Maturation is a critical developmental process, and the age and size at which it occurs have important fitness consequences. Although maturation is remarkably variable, certain mechanisms, including a minimum size or state threshold, are proposed to underlie the process across a broad diversity of taxa. Recent evidence suggests that thresholds may themselves be developmentally plastic, and in the crustacean Daphnia pulex it is unclear whether maturation follows a threshold or is a gradual process more akin to a rate. Changes in gene expression across four instars before and during maturation were compared in a cDNA microarray experiment. Developmental stage was treated statistically both as a discontinuous and as a continuous variable, to determine whether genes showed gradual or discrete changes in expression. The continuous analysis identified a greater number of genes with significant differential expression (45) than the discontinuous analysis (11). The majority of genes, including those coding for histones, factors relating to transcription and cell cycle processes, and a putative developmental hormone showed continuous increases or decreases in expression from the first to the fourth instars that were studied, suggestive of a prolonged and gradual maturation process. Three genes coding for a fused vitellogenin/superoxide dismutase showed increases in expression following the second instar and coincided with the posited maturation threshold, but even their expression increased in a continuous fashion.
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Affiliation(s)
- E Harney
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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Tang S, Wu Y, Ryan CN, Yu S, Qin G, Edwards DS, Mayer GD. Distinct expression profiles of stress defense and DNA repair genes in Daphnia pulex exposed to cadmium, zinc, and quantum dots. CHEMOSPHERE 2015; 120:92-9. [PMID: 25014899 DOI: 10.1016/j.chemosphere.2014.06.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/31/2014] [Accepted: 06/04/2014] [Indexed: 05/27/2023]
Abstract
The ever-increasing production and use of nanocrystaline semiconductors (Quantum dots; QDs) will inevitably result in increased appearance of these nanomaterials in the aquatic environment. However, the behavior and potential toxicity of heavy metal constituted nanoparticulates in aquatic invertebrates is largely unknown, especially with regard to molecular responses. The freshwater crustacean Daphnia pulex is a well-suited toxicological and ecological model to study molecular responses to environmental stressors. In this study, D. pulex were exposed for 48 h to sublethal doses of QDs (25% and 50% of LC50) with differing spectral properties (CdTe and CdSe/ZnS QDs) and Cd and Zn salts. Our data suggest that acute exposure to both CdSO4 and Cd-based QDs leads to Cd uptake in vivo, which was biologically supported by the observation of increased expression of metallothionein (MT-1). Furthermore, Cd, Zn, and CdSe/ZnS QDs induced different patterns of gene expression regarding stress defense and DNA repair, which furthers our knowledge regarding which response pathways are affected by nanoparticulate forms of metals versus ionic forms in aquatic crustaceans.
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Affiliation(s)
- Song Tang
- The Institute of Environmental and Human Health, Texas Tech University, Lubbock, TX 79416, USA; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada
| | - Yonggan Wu
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Caitlin N Ryan
- The Institute of Environmental and Human Health, Texas Tech University, Lubbock, TX 79416, USA
| | - Shuangying Yu
- The Institute of Environmental and Human Health, Texas Tech University, Lubbock, TX 79416, USA
| | - Guangqiu Qin
- Institute of Toxicology, Guangxi Center for Disease Prevention and Control, Nanning, Guangxi 530028, China
| | - Donn S Edwards
- The Institute of Environmental and Human Health, Texas Tech University, Lubbock, TX 79416, USA
| | - Gregory D Mayer
- The Institute of Environmental and Human Health, Texas Tech University, Lubbock, TX 79416, USA; Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA.
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Extensive error in the number of genes inferred from draft genome assemblies. PLoS Comput Biol 2014; 10:e1003998. [PMID: 25474019 PMCID: PMC4256071 DOI: 10.1371/journal.pcbi.1003998] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 10/22/2014] [Indexed: 11/19/2022] Open
Abstract
Current sequencing methods produce large amounts of data, but genome assemblies based on these data are often woefully incomplete. These incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. In this paper we investigate the magnitude of the problem, both in terms of total gene number and the number of copies of genes in specific families. To do this, we compare multiple draft assemblies against higher-quality versions of the same genomes, using several new assemblies of the chicken genome based on both traditional and next-generation sequencing technologies, as well as published draft assemblies of chimpanzee. We find that upwards of 40% of all gene families are inferred to have the wrong number of genes in draft assemblies, and that these incorrect assemblies both add and subtract genes. Using simulated genome assemblies of Drosophila melanogaster, we find that the major cause of increased gene numbers in draft genomes is the fragmentation of genes onto multiple individual contigs. Finally, we demonstrate the usefulness of RNA-Seq in improving the gene annotation of draft assemblies, largely by connecting genes that have been fragmented in the assembly process. The initial publication of the genome sequence of many plants, animals, and microbes is often accompanied with great fanfare. However, these genomes are almost always first-drafts, with a lot of missing data, many gaps, and many errors in the published sequences. Compounding this problem, the genes identified in draft genome sequences are also affected by incomplete genome assemblies: the number and exact structure of predicted genes may be incorrect. Here we quantify the extent of such errors, by comparing several draft genomes against completed versions of the same sequences. Surprisingly, we find huge numbers of errors in the number of genes predicted from draft assemblies, with more than half of all genes having the wrong number of copies in the draft genomes examined. Our investigation also reveals the major causes of these errors, and further analyses using additional functional data demonstrate that many of the gene predictions can be corrected. The results presented here suggest that many inferences based on published draft genomes may be erroneous, but offer a way forward for future analyses.
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Kriventseva EV, Tegenfeldt F, Petty TJ, Waterhouse RM, Simão FA, Pozdnyakov IA, Ioannidis P, Zdobnov EM. OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software. Nucleic Acids Res 2014; 43:D250-6. [PMID: 25428351 PMCID: PMC4383991 DOI: 10.1093/nar/gku1220] [Citation(s) in RCA: 241] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Orthology, refining the concept of homology, is the cornerstone of evolutionary comparative studies. With the ever-increasing availability of genomic data, inference of orthology has become instrumental for generating hypotheses about gene functions crucial to many studies. This update of the OrthoDB hierarchical catalog of orthologs (http://www.orthodb.org) covers 3027 complete genomes, including the most comprehensive set of 87 arthropods, 61 vertebrates, 227 fungi and 2627 bacteria (sampling the most complete and representative genomes from over 11,000 available). In addition to the most extensive integration of functional annotations from UniProt, InterPro, GO, OMIM, model organism phenotypes and COG functional categories, OrthoDB uniquely provides evolutionary annotations including rates of ortholog sequence divergence, copy-number profiles, sibling groups and gene architectures. We re-designed the entirety of the OrthoDB website from the underlying technology to the user interface, enabling the user to specify species of interest and to select the relevant orthology level by the NCBI taxonomy. The text searches allow use of complex logic with various identifiers of genes, proteins, domains, ontologies or annotation keywords and phrases. Gene copy-number profiles can also be queried. This release comes with the freely available underlying ortholog clustering pipeline (http://www.orthodb.org/software).
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Affiliation(s)
- Evgenia V Kriventseva
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Fredrik Tegenfeldt
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Tom J Petty
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Robert M Waterhouse
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Felipe A Simão
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Igor A Pozdnyakov
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
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Schwarzenberger A, Sadler T, Motameny S, Ben-Khalifa K, Frommolt P, Altmüller J, Konrad K, von Elert E. Deciphering the genetic basis of microcystin tolerance. BMC Genomics 2014; 15:776. [PMID: 25199885 PMCID: PMC4168211 DOI: 10.1186/1471-2164-15-776] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 08/29/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cyanobacteria constitute a serious threat to freshwater ecosystems by producing toxic secondary metabolites, e.g. microcystins. These microcystins have been shown to harm livestock, pets and humans and to affect ecosystem service and functioning. Cyanobacterial blooms are increasing worldwide in intensity and frequency due to eutrophication and global warming. However, Daphnia, the main grazer of planktonic algae and cyanobacteria, has been shown to be able to suppress bloom-forming cyanobacteria and to adapt to cyanobacteria that produce microcystins. Since Daphnia's genome was published only recently, it is now possible to elucidate the underlying molecular mechanisms of microcystin tolerance of Daphnia. RESULTS Daphnia magna was fed with either a cyanobacterial strain that produces microcystins or its genetically engineered microcystin knock-out mutant. Thus, it was possible to distinguish between effects due to the ingestion of cyanobacteria and effects caused specifically by microcystins. By using RNAseq the differentially expressed genes between the different treatments were analyzed and affected KOG-categories were calculated. Here we show that the expression of transporter genes in Daphnia was regulated as a specific response to microcystins. Subsequent qPCR and dietary supplementation with pure microcystin confirmed that the regulation of transporter gene expression was correlated with the tolerance of several Daphnia clones. CONCLUSIONS Here, we were able to identify new candidate genes that specifically respond to microcystins by separating cyanobacterial effects from microcystin effects. The involvement of these candidate genes in tolerance to microcystins was validated by correlating the difference in transporter gene expression with clonal tolerance. Thus, the prevention of microcystin uptake most probably constitutes a key mechanism in the development of tolerance and adaptation of Daphnia. With the availability of clear candidate genes, future investigations examining the process of local adaptation of Daphnia populations to microcystins are now possible.
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Affiliation(s)
- Anke Schwarzenberger
- University of Cologne, Cologne Biocenter, Aquatic Chemical Ecology, Zuelpicher Str, 47b, 50674 Cologne, Germany.
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Bellati A, Tiberti R, Cocca W, Galimberti A, Casiraghi M, Bogliani G, Galeotti P. A dark shell hiding great variability: a molecular insight into the evolution and conservation of melanicDaphniapopulations in the Alps. Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12151] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Adriana Bellati
- Department of Earth and Environmental Sciences; University of Pavia; Via Ferrata 9 27100 Pavia Italy
| | - Rocco Tiberti
- Department of Earth and Environmental Sciences; University of Pavia; Via Ferrata 9 27100 Pavia Italy
- Alpine Wildlife Research Centre; Gran Paradiso National Park; Degioz 11 11010 Valsavarenche Aosta Italy
| | - Walter Cocca
- Department of Earth and Environmental Sciences; University of Pavia; Via Ferrata 9 27100 Pavia Italy
| | - Andrea Galimberti
- ZooPlantLab; Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milano Italy
| | - Maurizio Casiraghi
- ZooPlantLab; Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milano Italy
| | - Giuseppe Bogliani
- Department of Earth and Environmental Sciences; University of Pavia; Via Ferrata 9 27100 Pavia Italy
| | - Paolo Galeotti
- Department of Earth and Environmental Sciences; University of Pavia; Via Ferrata 9 27100 Pavia Italy
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Asselman J, Shaw JR, Glaholt SP, Colbourne JK, De Schamphelaere KAC. Transcription patterns of genes encoding four metallothionein homologs in Daphnia pulex exposed to copper and cadmium are time- and homolog-dependent. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2013; 142-143:422-30. [PMID: 24113165 PMCID: PMC3891374 DOI: 10.1016/j.aquatox.2013.09.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 09/03/2013] [Accepted: 09/08/2013] [Indexed: 05/21/2023]
Abstract
Metallothioneins are proteins that play an essential role in metal homeostasis and detoxification in nearly all organisms studied to date. Yet discrepancies between outcomes of chronic and acute exposure experiments hamper the understanding of the regulatory mechanisms of their isoforms following metal exposure. Here, we investigated transcriptional differences among four identified homologs (mt1-mt4) in Daphnia pulex exposed across time to copper and cadmium relative to a control. Transcriptional upregulation of mt1 and mt3 was detected on day four following exposure to cadmium, whereas that of mt2 and mt4 was detected on day two and day eight following exposure to copper. These results confirm temporal and metal-specific differences in the transcriptional induction of genes encoding metallothionein homologs upon metal exposure which should be considered in ecotoxicological monitoring programs of metal-contaminated water bodies. Indeed, the mRNA expression patterns observed here illustrate the complex regulatory system associated with metallothioneins, as these patterns are not only dependent on the metal, but also on exposure time and the homolog studied. Further phylogenetic analysis and analysis of regulatory elements in upstream promoter regions revealed a high degree of similarity between metallothionein genes of Daphnia pulex and Daphnia magna, a species belonging to the same genus. These findings, combined with a limited amount of available expression data for D. magna metallothionein genes, tentatively suggest a potential generalization of the metallothionein response system between these Daphnia species.
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Affiliation(s)
- Jana Asselman
- Laboratory of Environmental Toxicology and Aquatic Ecology, Ghent University, Ghent, Belgium.
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Christie AE, Roncalli V, Wu LS, Ganote CL, Doak T, Lenz PH. Peptidergic signaling in Calanus finmarchicus (Crustacea, Copepoda): in silico identification of putative peptide hormones and their receptors using a de novo assembled transcriptome. Gen Comp Endocrinol 2013; 187:117-35. [PMID: 23578900 DOI: 10.1016/j.ygcen.2013.03.018] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/15/2013] [Accepted: 03/19/2013] [Indexed: 02/05/2023]
Abstract
The copepod Calanus finmarchicus is the most abundant zooplankton species in the North Atlantic. While the life history of this crustacean is well studied, little is known about its peptidergic signaling systems despite the fact that these pathways are undoubtedly important components of its physiological/behavioral control systems. Here we have generated and used a de novo assembled transcriptome for C. finmarchicus (206,041 sequences in total) to identify peptide precursor proteins and receptors. Using known protein queries, 34 transcripts encoding peptide preprohormones and 18 encoding peptide receptors were identified. Using a combination of online software programs and homology to known arthropod isoforms, 148 mature peptides were predicted from the deduced precursors, including members of the allatostatin-A, allatostatin-B, allatostatin-C, bursicon, crustacean cardioactive peptide (CCAP), crustacean hyperglycemic hormone, diuretic hormone 31 (DH31), diuretic hormone 44 (DH44), FMRFamide-like peptide (myosuppressin, neuropeptide F [NPF] and extended FL/IRFamide subfamilies), leucokinin, neuroparsin, orcokinin, orcomyotropin, periviscerokinin, RYamide and tachykinin-related peptide (TRP) families. The identified receptors included ones for allatostatin-A, allatostatin-C, bursicon, CCAP, DH31, DH44, ecdysis-triggering hormone, NPF, short NPF, FMRFamide, insulin-like peptide, leucokinin, periviscerokinin, pigment dispersing hormone, and TRP. Developmental profiling of the identified transcripts in embryos, early nauplii, late nauplii, early copepodites, late copepodites, and adult females was also undertaken, with all showing the highest expression levels in the naupliar and copepodite stages. Collectively, these data radically expand the catalog of known C. finmarchicus peptidergic signaling proteins and provide a foundation for experiments directed at understanding the physiological roles served by them in this species.
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Affiliation(s)
- Andrew E Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA.
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Wang Y, Huang J, Hu H, Li J, Liu B, Zhang G. Field and laboratory studies on the impact of two Bt rice lines expressing a fusion protein Cry1Ab/1Ac on aquatic organisms. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2013; 92:87-93. [PMID: 23523003 DOI: 10.1016/j.ecoenv.2013.02.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 01/30/2013] [Accepted: 02/27/2013] [Indexed: 06/02/2023]
Abstract
Genetically modified (GM) rice expressing Bt toxins is at the edge of commercial release in China. However, little information is available concerning the impact of Bt rice on aquatic organisms which are abundant in paddy field. A two-year study was conducted to assess the effects of two GM rice lines expressing a fusion protein Cry1Ab/1Ac (Bt rice) on three groups of zooplankton, rotifers, cladocerans and copepods in field conditions. Multi-factor ANOVA revealed that the population densities of rotifers, cladocerans and copepods in paddy field varied significantly between years and rice developmental stages, but did not differ significantly between Bt and non-Bt rice treatments. In all the field investigations, only one significant difference was found on copepods in the tillering stage of 2009, but the difference was not related to the presence of the Cry toxin. Under open-air conditions, we simulated the farming practice of straw mulch, using Bt rice straw as a food source for the water flea Daphnia hyalina. After one and two months of culture, the density of D. hyalina did not differ between Bt rice treatments and non-Bt rice treatments. A laboratory experiment found that purified Bt toxins Cry1Ab and Cry1Ac had no toxic effect on D. hyalina even in the treatment in which the Bt toxin concentration was as high as 2500ng/ml. Those above results indicate that the two Bt rice lines have no negative effect on the three groups of zooplankton. However, further studies are needed to compare the effects of Bt rice and non-Bt rice on the paddy zooplankton community in the context of integrated pest management which includes the use of pesticides.
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Affiliation(s)
- Yongmo Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, Wuhan 430070, Hubei, PR China
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Toyota K, Kato Y, Sato M, Sugiura N, Miyagawa S, Miyakawa H, Watanabe H, Oda S, Ogino Y, Hiruta C, Mizutani T, Tatarazako N, Paland S, Jackson C, Colbourne JK, Iguchi T. Molecular cloning of doublesex genes of four cladocera (water flea) species. BMC Genomics 2013; 14:239. [PMID: 23575357 PMCID: PMC3637828 DOI: 10.1186/1471-2164-14-239] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Accepted: 03/26/2013] [Indexed: 11/10/2022] Open
Abstract
Background The gene doublesex (dsx) is known as a key factor regulating genetic sex determination in many organisms. We previously identified two dsx genes (DapmaDsx1 and DapmaDsx2) from a freshwater branchiopod crustacean, Daphnia magna, which are expressed in males but not in females. D. magna produces males by parthenogenesis in response to environmental cues (environmental sex determination) and we showed that DapmaDsx1 expression during embryonic stages is responsible for the male trait development. The D. magna dsx genes are thought to have arisen by a cladoceran-specific duplication; therefore, to investigate evolutionary conservation of sex specific expression of dsx genes and to further assess their functions in the environmental sex determination, we searched for dsx homologs in four closely related cladoceran species. Results We identified homologs of both dsx genes from, D. pulex, D. galeata, and Ceriodaphnia dubia, yet only a single dsx gene was found from Moina macrocopa. The deduced amino acid sequences of all 9 dsx homologs contained the DM and oligomerization domains, which are characteristic for all arthropod DSX family members. Molecular phylogenetic analysis suggested that the dsx gene duplication likely occurred prior to the divergence of these cladoceran species, because that of the giant tiger prawn Penaeus monodon is rooted ancestrally to both DSX1 and DSX2 of cladocerans. Therefore, this result also suggested that M. macrocopa lost dsx2 gene secondarily. Furthermore, all dsx genes identified in this study showed male-biased expression levels, yet only half of the putative 5’ upstream regulatory elements are preserved in D. magna and D. pulex. Conclusions The all dsx genes of five cladoceran species examined had similar amino acid structure containing highly conserved DM and oligomerization domains, and exhibited sexually dimorphic expression patterns, suggesting that these genes may have similar functions for environmental sex determination in cladocerans.
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Affiliation(s)
- Kenji Toyota
- Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, and Department of Basic Biology, Faculty of Life Science, Graduate University for Advanced Studies (SOKENDAI), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, Japan
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Abstract
The nature of the olfactory receptor in crustaceans, a major group of arthropods, has remained elusive. We report that spiny lobsters, Panulirus argus, express ionotropic receptors (IRs), the insect chemosensory variants of ionotropic glutamate receptors. Unlike insects IRs, which are expressed in a specific subset of olfactory cells, two lobster IR subunits are expressed in most, if not all, lobster olfactory receptor neurons (ORNs), as confirmed by antibody labeling and in situ hybridization. Ligand-specific ORN responses visualized by calcium imaging are consistent with a restricted expression pattern found for other potential subunits, suggesting that cell-specific expression of uncommon IR subunits determines the ligand sensitivity of individual cells. IRs are the only type of olfactory receptor that we have detected in spiny lobster olfactory tissue, suggesting that they likely mediate olfactory signaling. Given long-standing evidence for G protein-mediated signaling in activation of lobster ORNs, this finding raises the interesting specter that IRs act in concert with second messenger-mediated signaling.
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Gibson AK, Smith Z, Fuqua C, Clay K, Colbourne JK. Why so many unknown genes? Partitioning orphans from a representative transcriptome of the lone star tick Amblyomma americanum. BMC Genomics 2013; 14:135. [PMID: 23445305 PMCID: PMC3616916 DOI: 10.1186/1471-2164-14-135] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 02/21/2013] [Indexed: 11/10/2022] Open
Abstract
Background Genomic resources within the phylum Arthropoda are largely limited to the true insects but are beginning to include unexplored subphyla, such as the Crustacea and Chelicerata. Investigations of these understudied taxa uncover high frequencies of orphan genes, which lack detectable sequence homology to genes in pre-existing databases. The ticks (Acari: Chelicerata) are one such understudied taxon for which genomic resources are urgently needed. Ticks are obligate blood-feeders that vector major diseases of humans, domesticated animals, and wildlife. In analyzing a transcriptome of the lone star tick Amblyomma americanum, one of the most abundant disease vectors in the United States, we find a high representation of unannotated sequences. We apply a general framework for quantifying the origin and true representation of unannotated sequences in a dataset and for evaluating the biological significance of orphan genes. Results Expressed sequence tags (ESTs) were derived from different life stages and populations of A. americanum and combined with ESTs available from GenBank to produce 14,310 ESTs, over twice the number previously available. The vast majority (71%) has no sequence homology to proteins archived in UniProtKB. We show that poor sequence or assembly quality is not a major contributor to this high representation by orphan genes. Moreover, most unannotated sequences are functional: a microarray experiment demonstrates that 59% of functional ESTs are unannotated. Lastly, we attempt to further annotate our EST dataset using genomic datasets from other members of the Acari, including Ixodes scapularis, four other tick species and the mite Tetranychus urticae. We find low homology with these species, consistent with significant divergence within this subclass. Conclusions We conclude that the abundance of orphan genes in A. americanum likely results from 1) taxonomic isolation stemming from divergence within the tick lineage and limited genomic resources for ticks and 2) lineage-specific genes needing functional genomic studies to evaluate their association with the unique biology of ticks. The EST sequences described here will contribute substantially to the development of tick genomics. Moreover, the framework provided for the evaluation of orphan genes can guide analyses of future transcriptome sequencing projects.
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Affiliation(s)
- Amanda K Gibson
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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Waterhouse RM, Tegenfeldt F, Li J, Zdobnov EM, Kriventseva EV. OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. Nucleic Acids Res 2012. [PMID: 23180791 PMCID: PMC3531149 DOI: 10.1093/nar/gks1116] [Citation(s) in RCA: 265] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The concept of orthology provides a foundation for formulating hypotheses on gene and genome evolution, and thus forms the cornerstone of comparative genomics, phylogenomics and metagenomics. We present the update of OrthoDB—the hierarchical catalog of orthologs (http://www.orthodb.org). From its conception, OrthoDB promoted delineation of orthologs at varying resolution by explicitly referring to the hierarchy of species radiations, now also adopted by other resources. The current release provides comprehensive coverage of animals and fungi representing 252 eukaryotic species, and is now extended to prokaryotes with the inclusion of 1115 bacteria. Functional annotations of orthologous groups are provided through mapping to InterPro, GO, OMIM and model organism phenotypes, with cross-references to major resources including UniProt, NCBI and FlyBase. Uniquely, OrthoDB provides computed evolutionary traits of orthologs, such as gene duplicability and loss profiles, divergence rates, sibling groups, and now extended with exon–intron architectures, syntenic orthologs and parent–child trees. The interactive web interface allows navigation along the species phylogenies, complex queries with various identifiers, annotation keywords and phrases, as well as with gene copy-number profiles and sequence homology searches. With the explosive growth of available data, OrthoDB also provides mapping of newly sequenced genomes and transcriptomes to the current orthologous groups.
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Affiliation(s)
- Robert M Waterhouse
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
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