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Perrier A, Guiglielmoni N, Naquin D, Gorrichon K, Thermes C, Lameiras S, Dammermann A, Schiffer PH, Brunstein M, Canman JC, Dumont J. Maternal inheritance of functional centrioles in two parthenogenetic nematodes. Nat Commun 2024; 15:6042. [PMID: 39025889 PMCID: PMC11258339 DOI: 10.1038/s41467-024-50427-5] [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: 08/14/2023] [Accepted: 07/09/2024] [Indexed: 07/20/2024] Open
Abstract
Centrioles are the core constituent of centrosomes, microtubule-organizing centers involved in directing mitotic spindle assembly and chromosome segregation in animal cells. In sexually reproducing species, centrioles degenerate during oogenesis and female meiosis is usually acentrosomal. Centrioles are retained during male meiosis and, in most species, are reintroduced with the sperm during fertilization, restoring centriole numbers in embryos. In contrast, the presence, origin, and function of centrioles in parthenogenetic species is unknown. We found that centrioles are maternally inherited in two species of asexual parthenogenetic nematodes and identified two different strategies for maternal inheritance evolved in the two species. In Rhabditophanes diutinus, centrioles organize the poles of the meiotic spindle and are inherited by both the polar body and embryo. In Disploscapter pachys, the two pairs of centrioles remain close together and are inherited by the embryo only. Our results suggest that maternally-inherited centrioles organize the embryonic spindle poles and act as a symmetry-breaking cue to induce embryo polarization. Thus, in these parthenogenetic nematodes, centrioles are maternally-inherited and functionally replace their sperm-inherited counterparts in sexually reproducing species.
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Affiliation(s)
- Aurélien Perrier
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Nadège Guiglielmoni
- Worm∼lab, Institute for Zoology, University of Cologne, Cologne, NRW, Germany
| | - Delphine Naquin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Kevin Gorrichon
- Centre de Référence, d'Innovation, d'eXpertise et de transfert (CRefIX), US 039 CEA/INRIA/INSERM, Evry, France
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Claude Thermes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Sonia Lameiras
- Institut Curie, PSL University, ICGex Next-Generation Sequencing Platform, 75005, Paris, France
| | - Alexander Dammermann
- Max Perutz Labs, Vienna Biocenter Campus (VBC), 1030, Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, 1030, Vienna, Austria
| | - Philipp H Schiffer
- Worm∼lab, Institute for Zoology, University of Cologne, Cologne, NRW, Germany
| | - Maia Brunstein
- Institut Pasteur, Université Paris Cité, INSERM, Institut de l'Audition, F-75012, Paris, France
| | - Julie C Canman
- Columbia University Irving Medical Center; Department of Pathology and Cell Biology, New York, NY, 10032, USA
| | - Julien Dumont
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France.
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Xu S, Neupane S, Wang H, Pham TP, Snyman M, Huynh TV, Wang L. Efficient CRISPR genome editing and integrative genomic analyses reveal the mosaicism of Cas-induced mutations and pleiotropic effects of scarlet gene in an emerging model system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577787. [PMID: 38352317 PMCID: PMC10862705 DOI: 10.1101/2024.01.29.577787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Despite the revolutionary impacts of CRISPR-Cas gene editing systems, the effective and widespread use of CRISPR technologies in emerging model organisms still faces significant challenges. These include the inefficiency in generating heritable mutations at the organismal level, limited knowledge about the genomic consequences of gene editing, and an inadequate understanding of the inheritance patterns of CRISPR-Cas-induced mutations. This study addresses these issues by 1) developing an efficient microinjection delivery method for CRISPR editing in the microcrustacean Daphnia pulex; 2) assessing the editing efficiency of Cas9 and Cas12a nucleases, examining mutation inheritance patterns, and analyzing the local and global mutation spectrum in the scarlet mutants; and 3) investigating the transcriptomes of scarlet mutants to understand the pleiotropic effects of scarlet underlying their swimming behavior changes. Our reengineered CRISPR microinjection method results in efficient biallelic editing with both nucleases. While indels are dominant in Cas-induced mutations, a few on-site large deletions (>1kb) are observed, most likely caused by microhomology-mediated end joining repair. Knock-in of a stop codon cassette to the scarlet locus was successful, despite complex induced mutations surrounding the target site. Moreover, extensive germline mosaicism exists in some mutants, which unexpectedly produce different phenotypes/genotypes in their asexual progenies. Lastly, our transcriptomic analyses unveil significant gene expression changes associated with scarlet knock-out and altered swimming behavior in mutants, including several genes (e.g., NMDA1, ABAT, CNTNAP2) involved in human neurodegenerative diseases. This study expands our understanding of the dynamics of gene editing in the tractable model organism Daphnia and highlights its promising potential as a neurological disease model.
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Affiliation(s)
- Sen Xu
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
| | - Swatantra Neupane
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
| | - Hongjun Wang
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019, USA
| | - Thinh Phu Pham
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019, USA
| | - Marelize Snyman
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019, USA
| | - Trung V. Huynh
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
| | - Li Wang
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
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3
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Molinier C, Lenormand T, Haag CR. No recombination suppression in asexually produced males of Daphnia pulex. Evolution 2023; 77:1987-1999. [PMID: 37345677 DOI: 10.1093/evolut/qpad114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/26/2023] [Accepted: 06/20/2023] [Indexed: 06/23/2023]
Abstract
Obligate parthenogenesis (OP) is often thought to evolve by disruption of reductional meiosis and suppression of crossover recombination. In the crustacean Daphnia pulex, OP lineages, which have evolved from cyclical parthenogenetic (CP) ancestors, occasionally produce males that are capable of reductional meiosis. Here, by constructing high-density linkage maps, we find that these males show only slightly and nonsignificantly reduced recombination rates compared to CP males and females. Both meiosis disruption and recombination suppression are therefore sex-limited (or partly so), which speaks against the evolution of OP by disruption of a gene that is essential for meiosis or recombination in both sexes. The findings may be explained by female-limited action of genes that suppress recombination, but previously identified candidate genes are known to be expressed in both sexes. Alternatively, and equally consistent with the data, OP might have evolved through a reuse of the parthenogenesis pathways already present in CP and through their extension to all events of oogenesis. The causal mutations for the CP to OP transition may therefore include mutations in genes involved in oogenesis regulation and may not necessarily be restricted to genes of the "meiosis toolkit." More generally, our study emphasizes that there are many ways to achieve asexuality, and elucidating the possible mechanisms is key to ultimately identify the genes and traits involved.
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Affiliation(s)
- Cécile Molinier
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Tuebingen, Germany
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4
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Snyman M, Xu S. Transcriptomics and the origin of obligate parthenogenesis. Heredity (Edinb) 2023; 131:119-129. [PMID: 37280308 PMCID: PMC10382572 DOI: 10.1038/s41437-023-00628-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 05/18/2023] [Accepted: 05/18/2023] [Indexed: 06/08/2023] Open
Abstract
Despite the presence of obligately parthenogenetic (OP) lineages derived from sexual ancestors in diverse phylogenetic groups, the genetic mechanisms giving rise to the OP lineages remain poorly understood. The freshwater microcrustacean Daphnia pulex typically reproduces via cyclical parthenogenesis. However, some populations of OP D. pulex have emerged due to ancestral hybridization and introgression events between two cyclically parthenogenetic (CP) species D. pulex and D. pulicaria. These OP hybrids produce both subitaneous and resting eggs parthenogenetically, deviating from CP isolates where resting eggs are produced via conventional meiosis and mating. This study examines the genome-wide expression and alternative splicing patterns of early subitaneous versus early resting egg production in OP D. pulex isolates to gain insight into the genes and mechanisms underlying this transition to obligate parthenogenesis. Our differential expression and functional enrichment analyses revealed a downregulation of meiosis and cell cycle genes during early resting egg production, as well as divergent expression patterns of metabolism, biosynthesis, and signaling pathways between the two reproductive modes. These results provide important gene candidates for future experimental verification, including the CDC20 gene that activates the anaphase-promoting complex in meiosis.
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Affiliation(s)
- Marelize Snyman
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, TX, 75235, USA
| | - Sen Xu
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA.
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA.
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5
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Huynh TV, Hall AS, Xu S. The Transcriptomic Signature of Cyclical Parthenogenesis. Genome Biol Evol 2023; 15:evad122. [PMID: 37392457 PMCID: PMC10340444 DOI: 10.1093/gbe/evad122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 06/13/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023] Open
Abstract
Cyclical parthenogenesis, where females can engage in sexual or asexual reproduction depending on environmental conditions, represents a novel reproductive phenotype that emerged during eukaryotic evolution. The fact that environmental conditions can trigger cyclical parthenogens to engage in distinct reproductive modes strongly suggests that gene expression plays a key role in the origin of cyclical parthenogenesis. However, the genetic basis underlying cyclical parthenogenesis remains understudied. In this study, we characterize the female transcriptomic signature of sexual versus asexual reproduction in the cyclically parthenogenetic microcrustacean Daphnia pulex and Daphnia pulicaria. Our analyses of differentially expressed genes (DEGs), pathway enrichment, and gene ontology (GO) term enrichment clearly show that compared with sexual reproduction, the asexual reproductive stage is characterized by both the underregulation of meiosis and cell cycle genes and the upregulation of metabolic genes. The consensus set of DEGs that this study identifies within the meiotic, cell cycle, and metabolic pathways serves as candidate genes for future studies investigating how the two reproductive cycles in cyclical parthenogenesis are mediated at a molecular level. Furthermore, our analyses identify some cases of divergent expression among gene family members (e.g., doublesex and NOTCH2) associated with asexual or sexual reproductive stage, suggesting potential functional divergence among gene family members.
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Affiliation(s)
- Trung Viet Huynh
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - Alexander S Hall
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - Sen Xu
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
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6
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Xu LY, Wu WT, Bi N, Yan ZJ, Yang F, Yang WJ, Yang JS. A cytological revisit on parthenogenetic Artemia and the deficiency of a meiosis-specific recombinase DMC1 in the possible transition from bisexuality to parthenogenesis. Chromosoma 2023:10.1007/s00412-023-00790-x. [PMID: 36939898 DOI: 10.1007/s00412-023-00790-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 03/21/2023]
Abstract
Although parthenogenesis is widespread in nature and known to have close relationships with bisexuality, the transitional mechanism is poorly understood. Artemia is an ideal model to address this issue because bisexuality and "contagious" obligate parthenogenesis independently exist in its congeneric members. In the present study, we first performed chromosome spreading and immunofluorescence to compare meiotic processes of Artemia adopting two distinct reproductive ways. The results showed that, unlike conventional meiosis in bisexual Artemia, meiosis II in parthenogenic Artemia is entirely absent and anaphase I is followed by a single mitosis-like equational division. Interspecific comparative transcriptomics showed that two central molecules in homologous recombination (HR), Dmc1 and Rad51, exhibited significantly higher expression in bisexual versus parthenogenetic Artemia. qRT-PCR indicated that the expression of both genes peaked at the early oogenesis and gradually decreased afterward. Knocking-down by RNAi of Dmc1 in unfertilized females of bisexual Artemia resulted in a severe deficiency of homologous chromosome pairing and produced univalents at the middle oogenesis stage, which was similar to that of parthenogenic Artemia, while in contrast, silencing Rad51 led to no significant chromosome morphological change. Our results indicated that Dmc1 is vital for HR in bisexual Artemia, and the deficiency of Dmc1 may be correlated with or even possibly one of core factors in the transition from bisexuality to parthenogenesis.
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Affiliation(s)
- Lian-Ying Xu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wen-Tao Wu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ning Bi
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhi-Jun Yan
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fan Yang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wei-Jun Yang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jin-Shu Yang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
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7
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Agrelius TC, Altman J, Dudycha JL. The maternal effects of dietary restriction on Dnmt expression and reproduction in two clones of Daphnia pulex. Heredity (Edinb) 2023; 130:73-81. [PMID: 36477021 PMCID: PMC9905607 DOI: 10.1038/s41437-022-00581-7] [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: 07/13/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022] Open
Abstract
The inheritance of epigenetic marks induced by environmental variation in a previous generation is broadly accepted as a mediator of phenotypic plasticity. Transgenerational effects linking maternal experiences to changes in morphology, gene expression, and life history of successive generations are known across many taxa. While the number of studies linking epigenetic variation to ecological maternal effects is increasing rapidly, few if any attempts have been made to investigate molecular mechanisms governing epigenetic functions in the context of ecologically relevant maternal effects. Daphnia make an ideal model for investigating molecular epigenetic mechanisms and ecological maternal effects because they will reproduce asexually in the lab. Daphnia are also known to have strong maternal effects, involving a variety of traits and environmental variables. Using two clones of Daphnia pulex, we investigated the plasticity of life history and DNA methyltransferase (Dnmt) gene expression with respect to food limitation within and across generations. We found strong evidence of genotypic variation of responses of life history and Dnmt expression to low food diets, both within and across generations. In general, effects of offspring diet were larger than either the direct maternal effect or offspring-maternal environment interactions, but the direction of the maternal effect was usually in the opposite direction of the within-generation effect. For both life history and Dnmt expression, we also found that when offspring had low food, effects of the maternal environment were stronger than when offspring had high food.
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Affiliation(s)
- Trenton C Agrelius
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA.
- Department of Biological Sciences, University of Notre Dame, Notre Dame, USA.
| | - Julia Altman
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Jeffry L Dudycha
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
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8
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Terwagne M, Nicolas E, Hespeels B, Herter L, Virgo J, Demazy C, Heuskin AC, Hallet B, Van Doninck K. DNA repair during nonreductional meiosis in the asexual rotifer Adineta vaga. SCIENCE ADVANCES 2022; 8:eadc8829. [PMID: 36449626 PMCID: PMC9710870 DOI: 10.1126/sciadv.adc8829] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
Rotifers of the class Bdelloidea are microscopic animals notorious for their long-term persistence in the apparent absence of sexual reproduction and meiotic recombination. This evolutionary paradox is often counterbalanced by invoking their ability to repair environmentally induced genome breakage. By studying the dynamics of DNA damage response in the bdelloid species Adineta vaga, we found that it occurs rapidly in the soma, producing a partially reassembled genome. By contrast, germline DNA repair is delayed to a specific time window of oogenesis during which homologous chromosomes adopt a meiotic-like juxtaposed configuration, resulting in accurate reconstitution of the genome in the offspring. Our finding that a noncanonical meiosis is the mechanism of germline DNA repair in bdelloid rotifers gives previously unidentified insights on their enigmatic long-term evolution.
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Affiliation(s)
- Matthieu Terwagne
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
- Institute of Biomolecular Science and Technology (LIBST), Université Catholique de Louvain (UCLouvain), Louvain-la-Neuve 1348, Belgium
| | - Emilien Nicolas
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
- Institute of Biomolecular Science and Technology (LIBST), Université Catholique de Louvain (UCLouvain), Louvain-la-Neuve 1348, Belgium
- Research Unit of Molecular Biology and Evolution (MBE), Université Libre de Bruxelles (ULB), Brussels, 1050, Belgium
| | - Boris Hespeels
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth and Environment (ILEE), University of Namur (UNamur), Namur 5000, Belgium
| | - Ludovic Herter
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
| | - Julie Virgo
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
| | - Catherine Demazy
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
- Cellular Biology Research Unit (URBC), University of Namur (UNamur), Namur 5000, Belgium
| | - Anne-Catherine Heuskin
- Laboratory of Analysis by Nuclear Reaction (LARN), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
| | - Bernard Hallet
- Institute of Biomolecular Science and Technology (LIBST), Université Catholique de Louvain (UCLouvain), Louvain-la-Neuve 1348, Belgium
| | - Karine Van Doninck
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur 5000, Belgium
- Research Unit of Molecular Biology and Evolution (MBE), Université Libre de Bruxelles (ULB), Brussels, 1050, Belgium
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth and Environment (ILEE), University of Namur (UNamur), Namur 5000, Belgium
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Lari E, Jeong TY, Labine LM, Simpson MJ. Metabolomic analysis predicted changes in growth rate in Daphnia magna exposed to acetaminophen. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 249:106233. [PMID: 35779485 DOI: 10.1016/j.aquatox.2022.106233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/08/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
As urbanization and the global population increases, pollutants associated with municipal wastewater such as pharmaceuticals are becoming more prevalent in aquatic environments. Acetaminophen (paracetamol) is a widely used drug worldwide and one of the most frequently detected pharmaceuticals in freshwater ecosystems. This study investigated the impact of acetaminophen on the metabolite profile of Daphnia magna at two life stages; and used these metabolomic findings to hypothesize a potential impact at a higher organismal level which was subsequently tested experimentally. Targeted polar metabolite analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to measure changes in the concentration of 51 metabolites in the neonate (> 24 h old) and adult (8 day-old) daphnids following a 48-h exposure to sub-lethal concentrations of acetaminophen. The impact of acetaminophen on the metabolic profile of neonates was widely different from adults. Also, acetaminophen exposure perturbed the abundance of nucleotides more extensively than other metabolites. The acute metabolomic experimental results led to the hypotheses that exposure to sub-lethal concentrations of acetaminophen upregulates protein synthesis in D. magna and subsequently increases growth during early life stages and has an opposite impact on adults. Accordingly, a 10 day growth rate experiment indicated that exposure to acetaminophen elevated biomass production in neonates but not in adults. These novel findings demonstrate that a targeted analysis and interpretation of the changes in the polar metabolic profile of organisms in response to environmental stressors could be used as a tool to predict changes at higher biological levels. As such, this study further emphasizes the incorporation of molecular-level platforms as critical and robust tools in environmental assessment frameworks and biomonitoring of aquatic ecosystems.
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Affiliation(s)
- Ebrahim Lari
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada; Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Tae-Yong Jeong
- Department of Physical and Environmental Sciences and Environmental NMR Centre, University of Toronto Scarborough, Ontario, Canada; Department of Environmental Science, College of Natural Sciences, Hankuk University of Foreign Studies, 81, Oedae-ro, Mohyeon-eup, Cheoin-gu, Yongin-si, Gyeonggi-do 17035, Republic of Korea
| | - Lisa M Labine
- Department of Physical and Environmental Sciences and Environmental NMR Centre, University of Toronto Scarborough, Ontario, Canada
| | - Myrna J Simpson
- Department of Physical and Environmental Sciences and Environmental NMR Centre, University of Toronto Scarborough, Ontario, Canada.
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10
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Foe VE. Does the Pachytene Checkpoint, a Feature of Meiosis, Filter Out Mistakes in Double-Strand DNA Break Repair and as a side-Effect Strongly Promote Adaptive Speciation? Integr Org Biol 2022; 4:obac008. [PMID: 36827645 PMCID: PMC8998493 DOI: 10.1093/iob/obac008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
This essay aims to explain two biological puzzles: why eukaryotic transcription units are composed of short segments of coding DNA interspersed with long stretches of non-coding (intron) DNA, and the near ubiquity of sexual reproduction. As is well known, alternative splicing of its coding sequences enables one transcription unit to produce multiple variants of each encoded protein. Additionally, padding transcription units with non-coding DNA (often many thousands of base pairs long) provides a readily evolvable way to set how soon in a cell cycle the various mRNAs will begin being expressed and the total amount of mRNA that each transcription unit can make during a cell cycle. This regulation complements control via the transcriptional promoter and facilitates the creation of complex eukaryotic cell types, tissues, and organisms. However, it also makes eukaryotes exceedingly vulnerable to double-strand DNA breaks, which end-joining break repair pathways can repair incorrectly. Transcription units cover such a large fraction of the genome that any mis-repair producing a reorganized chromosome has a high probability of destroying a gene. During meiosis, the synaptonemal complex aligns homologous chromosome pairs and the pachytene checkpoint detects, selectively arrests, and in many organisms actively destroys gamete-producing cells with chromosomes that cannot adequately synapse; this creates a filter favoring transmission to the next generation of chromosomes that retain the parental organization, while selectively culling those with interrupted transcription units. This same meiotic checkpoint, reacting to accidental chromosomal reorganizations inflicted by error-prone break repair, can, as a side effect, provide a mechanism for the formation of new species in sympatry. It has been a long-standing puzzle how something as seemingly maladaptive as hybrid sterility between such new species can arise. I suggest that this paradox is resolved by understanding the adaptive importance of the pachytene checkpoint, as outlined above.
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11
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Xu S, Huynh TV, Snyman M. The transcriptomic signature of obligate parthenogenesis. Heredity (Edinb) 2022; 128:132-138. [PMID: 35039663 PMCID: PMC8814003 DOI: 10.1038/s41437-022-00498-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 02/03/2023] Open
Abstract
Investigating the origin of parthenogenesis through interspecific hybridization can provide insight into how meiosis may be altered by genetic incompatibilities, which is fundamental for our understanding of the formation of reproductive barriers. Yet the genetic mechanisms giving rise to obligate parthenogenesis in eukaryotes remain understudied. In the microcrustacean Daphnia pulex species complex, obligately parthenogenetic (OP) isolates emerged as backcrosses of two cyclically parthenogenetic (CP) parental species, D. pulex and D. pulicaria, two closely related but ecologically distinct species. We examine the genome-wide expression in OP females at the early resting egg production stage, a life-history stage distinguishing OP and CP reproductive strategies, in comparison to CP females of the same stage from the two parental species. Our analyses of the expression data reveal that underdominant and overdominant genes are abundant in OP isolates, suggesting widespread regulatory incompatibilities between the parental species. More importantly, underdominant genes (i.e., genes with expression lower than both parentals) in the OP isolates are enriched in meiosis and cell-cycle pathways, indicating an important role of underdominance in the origin of obligate parthenogenesis. Furthermore, metabolic and biosynthesis pathways enriched with overdominant genes (i.e., expression higher than both parentals) are another genomic signature of OP isolates.
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Affiliation(s)
- Sen Xu
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA.
| | - Trung V Huynh
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Marelize Snyman
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
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12
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Ye Z, Jiang X, Pfrender ME, Lynch M. Genome-Wide Allele-Specific Expression in Obligately Asexual Daphnia pulex and the Implications for the Genetic Basis of Asexuality. Genome Biol Evol 2021; 13:6415829. [PMID: 34726699 PMCID: PMC8598174 DOI: 10.1093/gbe/evab243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2021] [Indexed: 01/17/2023] Open
Abstract
Although obligately asexual lineages are thought to experience selective disadvantages associated with reduced efficiency of fixing beneficial mutations and purging deleterious mutations, such lineages are phylogenetically and geographically widespread. However, despite several genome-wide association studies, little is known about the genetic elements underlying the origin of obligate asexuality and how they spread. Because many obligately asexual lineages have hybrid origins, it has been suggested that asexuality is caused by the unbalanced expression of alleles from the hybridizing species. Here, we investigate this idea by identifying genes with allele-specific expression (ASE) in a Daphnia pulex population, in which obligate parthenogens (OP) and cyclical parthenogens (CP) coexist, with the OP clones having been originally derived from hybridization between CP D. pulex and its sister species, Daphnia pulicaria. OP D. pulex have significantly more ASE genes (ASEGs) than do CP D. pulex. Whole-genomic comparison of OP and CP clones revealed ∼15,000 OP-specific markers and 42 consistent ASEGs enriched in marker-defined regions. Ten of the 42 ASEGs have alleles coding for different protein sequences, suggesting functional differences between the products of the two parental alleles. At least three of these ten genes appear to be directly involved in meiosis-related processes, for example, RanBP2 can cause abnormal chromosome segregation in anaphase I, and the presence of Wee1 in immature oocytes leads to failure to enter meiosis II. These results provide a guide for future molecular resolution of the genetic basis of the transition to ameiotic parthenogenesis.
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Affiliation(s)
- Zhiqiang Ye
- Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona
| | | | - Michael E Pfrender
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana
| | - Michael Lynch
- Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona
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13
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Simion P, Narayan J, Houtain A, Derzelle A, Baudry L, Nicolas E, Arora R, Cariou M, Cruaud C, Gaudray FR, Gilbert C, Guiglielmoni N, Hespeels B, Kozlowski DKL, Labadie K, Limasset A, Llirós M, Marbouty M, Terwagne M, Virgo J, Cordaux R, Danchin EGJ, Hallet B, Koszul R, Lenormand T, Flot JF, Van Doninck K. Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga. SCIENCE ADVANCES 2021; 7:eabg4216. [PMID: 34613768 PMCID: PMC8494291 DOI: 10.1126/sciadv.abg4216] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Bdelloid rotifers are notorious as a speciose ancient clade comprising only asexual lineages. Thanks to their ability to repair highly fragmented DNA, most bdelloid species also withstand complete desiccation and ionizing radiation. Producing a well-assembled reference genome is a critical step to developing an understanding of the effects of long-term asexuality and DNA breakage on genome evolution. To this end, we present the first high-quality chromosome-level genome assemblies for the bdelloid Adineta vaga, composed of six pairs of homologous (diploid) chromosomes with a footprint of paleotetraploidy. The observed large-scale losses of heterozygosity are signatures of recombination between homologous chromosomes, either during mitotic DNA double-strand break repair or when resolving programmed DNA breaks during a modified meiosis. Dynamic subtelomeric regions harbor more structural diversity (e.g., chromosome rearrangements, transposable elements, and haplotypic divergence). Our results trigger the reappraisal of potential meiotic processes in bdelloid rotifers and help unravel the factors underlying their long-term asexual evolutionary success.
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Affiliation(s)
- Paul Simion
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Corresponding author. (K.V.D.); (J.-F.F.); (P.S.)
| | - Jitendra Narayan
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Antoine Houtain
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Alessandro Derzelle
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Lyam Baudry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris F-75015, France
- Collège Doctoral, Sorbonne Université, F-75005 Paris, France
| | - Emilien Nicolas
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Molecular Biology and Evolution, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
| | - Rohan Arora
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Molecular Biology and Evolution, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
| | - Marie Cariou
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | | | - Clément Gilbert
- Évolution, Génomes, Comportement et Écologie, Université Paris-Saclay, CNRS, IRD, UMR, 91198 Gif-sur-Yvette, France
| | - Nadège Guiglielmoni
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
| | - Boris Hespeels
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Djampa K. L. Kozlowski
- INRAE, Université Côte-d’Azur, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis 06903, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Antoine Limasset
- Université de Lille, CNRS, UMR 9189 - CRIStAL, 59655 Villeneuve-d’Ascq, France
| | - Marc Llirós
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Institut d’Investigació Biomédica de Girona, Malalties Digestives i Microbiota, 17190 Salt, Spain
| | - Martial Marbouty
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris F-75015, France
| | - Matthieu Terwagne
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Julie Virgo
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Richard Cordaux
- Ecologie et Biologie des interactions, Université de Poitiers, UMR CNRS 7267, 5 rue Albert Turpain, 86073 Poitiers, France
| | - Etienne G. J. Danchin
- INRAE, Université Côte-d’Azur, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis 06903, France
| | - Bernard Hallet
- LIBST, Université Catholique de Louvain (UCLouvain), Croix du Sud 4/5, Louvain-la-Neuve 1348, Belgium
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris F-75015, France
| | - Thomas Lenormand
- CEFE, Univ Montpellier, CNRS, Univ Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
| | - Jean-Francois Flot
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
- Interuniversity Institute of Bioinformatics in Brussels - (IB), Brussels 1050, Belgium
- Corresponding author. (K.V.D.); (J.-F.F.); (P.S.)
| | - Karine Van Doninck
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Molecular Biology and Evolution, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
- Corresponding author. (K.V.D.); (J.-F.F.); (P.S.)
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14
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Huylmans AK, Macon A, Hontoria F, Vicoso B. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. Proc Biol Sci 2021; 288:20211720. [PMID: 34547909 PMCID: PMC8456138 DOI: 10.1098/rspb.2021.1720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/31/2021] [Indexed: 11/12/2022] Open
Abstract
While sexual reproduction is widespread among many taxa, asexual lineages have repeatedly evolved from sexual ancestors. Despite extensive research on the evolution of sex, it is still unclear whether this switch represents a major transition requiring major molecular reorganization, and how convergent the changes involved are. In this study, we investigated the phylogenetic relationship and patterns of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp, to assess how gene expression patterns are affected by the transition to asexuality. We find only a few genes that are consistently associated with the evolution of asexuality, suggesting that this shift may not require an extensive overhauling of the meiotic machinery. While genes with sex-biased expression have high rates of expression divergence within Eurasian Artemia, neither female- nor male-biased genes appear to show unusual evolutionary patterns after sexuality is lost, contrary to theoretical expectations.
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Affiliation(s)
- Ann Kathrin Huylmans
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Ariana Macon
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Francisco Hontoria
- Instituto de Acuicultura de Torre de la Sal (IATS-CSIC), 12595 Ribera de Cabanes, Castellón, Spain
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
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15
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Boyer L, Jabbour-Zahab R, Mosna M, Haag CR, Lenormand T. Not so clonal asexuals: Unraveling the secret sex life of Artemia parthenogenetica. Evol Lett 2021; 5:164-174. [PMID: 33868712 PMCID: PMC8045904 DOI: 10.1002/evl3.216] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 01/08/2021] [Accepted: 01/15/2021] [Indexed: 12/11/2022] Open
Abstract
The maintenance of sex is paradoxical as sexual species pay the “twofold cost of males” and should thus quickly be replaced by asexual mutants reproducing clonally. However, asexuals may not be strictly clonal and engage in “cryptic sex,” challenging this simple scenario. We study the cryptic sex life of the brine shrimp Artemia parthenogenetica, which has once been termed an “ancient asexual” and where no genetic differences have ever been observed between parents and offspring. This asexual species rarely produces males, which can hybridize with sexual females of closely related species and transmit asexuality to their offspring. Using such hybrids, we show that recombination occurs in asexual lineages, causing loss‐of‐heterozygosity and parent‐offspring differences. These differences cannot generally be observed in field‐sampled asexuals because once heterozygosity is lost, subsequent recombination leaves no footprint. Furthermore, using extensive paternity tests, we show that hybrid females can reproduce both sexually and asexually, and transmit asexuality to both sexually and asexually produced offspring in a dominant fashion. Finally, we show that, contrary to previous reports, field‐sampled asexual females also rarely reproduce sexually (rate ∼2‰). Overall, most previously known facts about Artemia asexuality turned out to be erroneous. More generally, our findings suggest that the evidence for strictly clonal reproduction of asexual species needs to be reconsidered, and that rare sex and consequences of nonclonal asexuality, such as gene flow within asexuals, need to be more widely taken into account in more realistic models for the maintenance of sex and the persistence of asexual lineages.
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Affiliation(s)
- Loreleï Boyer
- CEFE Univ Montpellier, CNRS, Univ Paul Valéry Montpellier 3, EPHE, IRD Montpellier France
| | - Roula Jabbour-Zahab
- CEFE Univ Montpellier, CNRS, Univ Paul Valéry Montpellier 3, EPHE, IRD Montpellier France
| | - Marta Mosna
- CEFE Univ Montpellier, CNRS, Univ Paul Valéry Montpellier 3, EPHE, IRD Montpellier France
| | - Christoph R Haag
- CEFE Univ Montpellier, CNRS, Univ Paul Valéry Montpellier 3, EPHE, IRD Montpellier France
| | - Thomas Lenormand
- CEFE Univ Montpellier, CNRS, Univ Paul Valéry Montpellier 3, EPHE, IRD Montpellier France
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16
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Jeong TY, Simpson MJ. Reproduction stage specific dysregulation of Daphnia magna metabolites as an early indicator of reproductive endocrine disruption. WATER RESEARCH 2020; 184:116107. [PMID: 32717493 DOI: 10.1016/j.watres.2020.116107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/17/2020] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
Rapid biomolecular observation in model indicator organisms has been considered as a potential predictor of water pollution from chronic and trace toxicants. This study evaluated the use of Daphnia magna metabolomic measurements as indicators for exposure to reproductive endocrine disruptors by using the model juvenile hormone analogue fenoxycarb. Because D. magna reproduction controls metabolic regulation, the reproduction stage was also carefully considered in metabolic observations and data analysis to examine differences. Comparisons of metabolite abundance regulation between 1 and 12 days of fenoxycarb exposure were performed to investigate the predictability of the sub-chronic (12 days) adverse impacts on reproduction and metabolic regulation based on acute (1 day) metabolic observations. ANOVA-simultaneous component analysis (ASCA) detected reversed patterns in direction of time-course metabolite abundance regulation with fenoxycarb exposure. For example, decreases in the abundances of leucine, asparagine, methionine, and isoleucine which then changed to increases were observed with time during fenoxycarb exposures. The reversed regulation pattern was observed at the last reproduction stage (stage 3), exclusively. Pearson correlation analysis showed that correlations of pairwise metabolites were disrupted with fenoxycarb exposure. Similar to ASCA, data normalization based on the reproduction stage improved the detectability of significant correlations. The disruption on ambient metabolite regulation patterns and pairwise metabolite correlations was consistently observed with both 1 and 12 days of fenoxycarb exposures for sets of select metabolites. The observed regulatory disruptions to these specific metabolites suggest altered oogenesis as the affected metabolites and the specific reproduction stage are related to successful oogenesis. This study demonstrates that D. magna metabolic dysregulation is a predictor of water contamination by endocrine disrupting compounds. The high predictability of sub-chronic (12 days) endocrine disruption was confirmed based on acute (1 day) metabolic observations. Furthermore, integration of the reproduction cycle information in D. magna metabolomics was validated by observing a reproduction stage specific dysregulation in metabolite abundance regulation, which was not observable from the broader data analysis. Consequently, this study confirms the potential for establishing a quantitative relationship between water quality and indicator species metabolic observations. Additionally, it was found that constraining variables relevant to toxicity mechanisms of interest, such as the reproduction stage, is a key consideration for extraction of ecologically meaningful information in environmental metabolomics.
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Affiliation(s)
- Tae-Yong Jeong
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C1A4, Canada.
| | - Myrna J Simpson
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C1A4, Canada.
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17
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Toyota K, Sato T, Iguchi T, Ohira T. Methyl farnesoate regulatory mechanisms underlying photoperiod-dependent sex determination in the freshwater crustacean Daphnia magna. J Appl Toxicol 2020; 41:216-223. [PMID: 32662114 DOI: 10.1002/jat.4035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/06/2020] [Accepted: 06/22/2020] [Indexed: 11/08/2022]
Abstract
Freshwater zooplankton Daphnia magna has been widely used in ecotoxicology studies. During the last 20 years, it has been demonstrated that the topical application of juvenile hormone (JH) or JH analogs to mother daphnids induce male offspring production. Based on this finding, an in vivo screening validation method for chemicals with JH agonistic effect has developed. Although this screening system successfully identified a number of JH-like chemicals, molecular mechanisms underlying the male sex-determining process remain largely unknown. To address this issue, we established a reliable male- or female-producing system using Daphnia pulex WTN6 strain by changing the rearing photoperiod. Taking advantage of this rearing system, we successfully found several factors involving male sex determination such as ionotropic glutamate receptors, protein kinase C and pantothenate. Here, we used two D. magna strains that can also control the production of female or male offspring by photoperiod differences as model species for ecotoxicology studies. We demonstrated that either treatment of antagonist of ionotropic glutamate receptors or inhibitor of protein kinase C strongly suppressed male offspring production even under male-producing conditions. Moreover, we revealed that male sex-determining processes are likely diverged between D. magna and D. pulex based on the current experiment. This study provides a fine experimental method for in vivo screening not only JH agonists but also JH antagonists. Moreover, using daphnids with photoperiod-dependent sex determination manner will hugely contribute to understanding the mode-of-action of JH in daphnids.
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Affiliation(s)
- Kenji Toyota
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Hiratsuka, Kanagawa, Japan.,Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Katsushika-ku, Tokyo, Japan
| | - Tomomi Sato
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Taisen Iguchi
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Tsuyoshi Ohira
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Hiratsuka, Kanagawa, Japan
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18
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Sellinger TPP, Abu Awad D, Moest M, Tellier A. Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data. PLoS Genet 2020; 16:e1008698. [PMID: 32251472 PMCID: PMC7173940 DOI: 10.1371/journal.pgen.1008698] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 04/21/2020] [Accepted: 02/24/2020] [Indexed: 02/04/2023] Open
Abstract
Several methods based on the Sequential Markovian coalescence (SMC) have been developed that make use of genome sequence data to uncover population demographic history, which is of interest in its own right and is a key requirement to generate a null model for selection tests. While these methods can be applied to all possible kind of species, the underlying assumptions are sexual reproduction in each generation and non-overlapping generations. However, in many plants, invertebrates, fungi and other taxa, those assumptions are often violated due to different ecological and life history traits, such as self-fertilization or long term dormant structures (seed or egg-banking). We develop a novel SMC-based method to infer 1) the rates/parameters of dormancy and of self-fertilization, and 2) the populations' past demographic history. Using simulated data sets, we demonstrate the accuracy of our method for a wide range of demographic scenarios and for sequence lengths from one to 30 Mb using four sampled genomes. Finally, we apply our method to a Swedish and a German population of Arabidopsis thaliana demonstrating a selfing rate of ca. 0.87 and the absence of any detectable seed-bank. In contrast, we show that the water flea Daphnia pulex exhibits a long lived egg-bank of three to 18 generations. In conclusion, we here present a novel method to infer accurate demographies and life-history traits for species with selfing and/or seed/egg-banks. Finally, we provide recommendations for the use of SMC-based methods for non-model organisms, highlighting the importance of the per site and the effective ratios of recombination over mutation.
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Affiliation(s)
| | - Diala Abu Awad
- Department of Population Genetics, Technische Universitaet Muenchen, Freising, Germany
| | - Markus Moest
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Aurélien Tellier
- Department of Population Genetics, Technische Universitaet Muenchen, Freising, Germany
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19
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Lamelza P, Young JM, Noble LM, Caro L, Isakharov A, Palanisamy M, Rockman MV, Malik HS, Ailion M. Hybridization promotes asexual reproduction in Caenorhabditis nematodes. PLoS Genet 2019; 15:e1008520. [PMID: 31841515 PMCID: PMC6946170 DOI: 10.1371/journal.pgen.1008520] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 01/07/2020] [Accepted: 11/15/2019] [Indexed: 02/04/2023] Open
Abstract
Although most unicellular organisms reproduce asexually, most multicellular eukaryotes are obligately sexual. This implies that there are strong barriers that prevent the origin or maintenance of asexuality arising from an obligately sexual ancestor. By studying rare asexual animal species we can gain a better understanding of the circumstances that facilitate their evolution from a sexual ancestor. Of the known asexual animal species, many originated by hybridization between two ancestral sexual species. The balance hypothesis predicts that genetic incompatibilities between the divergent genomes in hybrids can modify meiosis and facilitate asexual reproduction, but there are few instances where this has been shown. Here we report that hybridizing two sexual Caenorhabditis nematode species (C. nouraguensis females and C. becei males) alters the normal inheritance of the maternal and paternal genomes during the formation of hybrid zygotes. Most offspring of this interspecies cross die during embryogenesis, exhibiting inheritance of a diploid C. nouraguensis maternal genome and incomplete inheritance of C. becei paternal DNA. However, a small fraction of offspring develop into viable adults that can be either fertile or sterile. Fertile offspring are produced asexually by sperm-dependent parthenogenesis (also called gynogenesis or pseudogamy); these progeny inherit a diploid maternal genome but fail to inherit a paternal genome. Sterile offspring are hybrids that inherit both a diploid maternal genome and a haploid paternal genome. Whole-genome sequencing of individual viable worms shows that diploid maternal inheritance in both fertile and sterile offspring results from an altered meiosis in C. nouraguensis oocytes and the inheritance of two randomly selected homologous chromatids. We hypothesize that hybrid incompatibility between C. nouraguensis and C. becei modifies maternal and paternal genome inheritance and indirectly induces gynogenetic reproduction. This system can be used to dissect the molecular mechanisms by which hybrid incompatibilities can facilitate the emergence of asexual reproduction.
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Affiliation(s)
- Piero Lamelza
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, United States of America
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Janet M. Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Luke M. Noble
- Department of Biology and Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
| | - Lews Caro
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, United States of America
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Arielle Isakharov
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Meenakshi Palanisamy
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Matthew V. Rockman
- Department of Biology and Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
| | - Harmit S. Malik
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, United States of America
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Michael Ailion
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, United States of America
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
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20
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Lee D, Nah JS, Yoon J, Kim W, Rhee K. Live observation of the oviposition process in Daphnia magna. PLoS One 2019; 14:e0224388. [PMID: 31682612 PMCID: PMC6827901 DOI: 10.1371/journal.pone.0224388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 10/13/2019] [Indexed: 11/19/2022] Open
Abstract
In favorable conditions, Daphnia magna undergoes parthenogenesis to increase progeny production in a short time. However, in unfavorable conditions, Daphnia undergoes sexual reproduction instead and produces resting eggs. Here, we report live observations of the oviposition process in Daphnia magna. We observed that the cellular contents flowed irregularly through the narrow egg canal during oviposition. Amorphous ovarian eggs developed an oval shape immediately after oviposition and, eventually, a round shape. Oviposition of resting eggs occurred in a similar way. Based on the observations, we propose that, unlike Drosophila eggs, Daphnia eggs cannot maintain cytoplasmic integrity during oviposition. We also determined that the parthenogenetic eggs were activated within 20 min, as demonstrated by vitelline envelope formation. Therefore, it is plausible that the eggs of Daphnia magna may be activated by squeezing pressure during oviposition.
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Affiliation(s)
- Dohyong Lee
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Ji Soo Nah
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Jungbin Yoon
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Won Kim
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Kunsoo Rhee
- Department of Biological Sciences, Seoul National University, Seoul, Korea
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21
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Abstract
The absence of a paternal contribution in an unfertilized ovum presents two developmental constraints against the evolution of parthenogenesis. We discuss the constraint caused by the absence of a centrosome and the one caused by the missing set of chromosomes and how they have been broken in specific taxa. They are examples of only a few well-underpinned examples of developmental constraints acting at macro-evolutionary scales in animals. Breaking of the constraint of the missing chromosomes is the best understood and generally involves rare occasions of drastic changes of meiosis. These drastic changes can be best explained by having been induced, or at least facilitated, by sudden cytological events (e.g., repeated rounds of hybridization, endosymbiont infections, and contagious infections). Once the genetic and developmental machinery is in place for regular or obligate parthenogenesis, shifts to other types of parthenogenesis can apparently rather easily evolve, for example, from facultative to obligate parthenogenesis, or from pseudoarrhenotoky to haplodiploidy. We argue that the combination of the two developmental constraints forms a near-absolute barrier against the gradual evolution from sporadic to obligate or regular facultative parthenogenesis, which can probably explain why the occurrence of the highly advantageous mode of regular facultative parthenogenesis is so rare and entirely absent in vertebrates.
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22
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Molinier C, Reisser CMO, Fields PD, Ségard A, Galimov Y, Haag CR. Evolution of Gene Expression during a Transition from Environmental to Genetic Sex Determination. Mol Biol Evol 2019; 36:1551-1564. [PMID: 31173134 DOI: 10.1093/molbev/msz123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Genetic sex determination (GSD) can evolve from environmental sex determination (ESD) via an intermediate state in which both coexist in the same population. Such mixed populations are found in the crustacean Daphnia magna, where non-male producers (NMP, genetically determined females) coexist with male producers (MP), in which male production is environmentally inducible and can also artificially be triggered by exposure to juvenile hormone. This makes Daphnia magna a rare model species for the study of evolutionary transitions from ESD to GSD. Although the chromosomal location of the NMP-determining mutation has been mapped, the actual genes and pathways involved in the evolution of GSD from ESD remain unknown. Here, we present a transcriptomic analysis of MP and NMP females under control (female producing) and under hormone exposure conditions. We found ∼100 differentially expressed genes between MP and NMP under control conditions. Genes in the NMP-determining chromosome region were especially likely to show such constitutive expression differences. Hormone exposure led to expression changes of an additional ∼100 (MP) to ∼600 (NMP) genes, with an almost systematic upregulation of those genes in NMP. These observations suggest that the NMP phenotype is not determined by a simple "loss-of-function" mutation. Rather, homeostasis of female offspring production under hormone exposure appears to be an active state, tightly regulated by complex mechanisms involving many genes. In a broader view, this illustrates that the evolution of GSD, while potentially initiated by a single mutation, likely leads to secondary integration involving many genes and pathways.
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Affiliation(s)
- Cécile Molinier
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
| | - Céline M O Reisser
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France.,Université de Fribourg, Ecology and Evolution, Fribourg, Switzerland.,IFREMER Centre du Pacifique, UMR 241 EIO, Labex CORAIL, Taravao, Tahiti, Polynésie Française
| | - Peter D Fields
- Universität Basel, Zoology Institute, Evolutionary Biology, Basel, Switzerland
| | - Adeline Ségard
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
| | - Yan Galimov
- Koltsov Institute of Developmental Biology, RAS, Moscow, Russia
| | - Christoph R Haag
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France.,Université de Fribourg, Ecology and Evolution, Fribourg, Switzerland
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23
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Dukić M, Berner D, Haag CR, Ebert D. How clonal are clones? A quest for loss of heterozygosity during asexual reproduction in Daphnia magna. J Evol Biol 2019; 32:619-628. [PMID: 30888725 PMCID: PMC6850383 DOI: 10.1111/jeb.13443] [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: 06/07/2018] [Accepted: 03/04/2019] [Indexed: 12/25/2022]
Abstract
Due to the lack of recombination, asexual organisms are predicted to accumulate mutations and show high levels of within‐individual allelic divergence (heterozygosity); however, empirical evidence for this prediction is largely missing. Instead, evidence of genome homogenization during asexual reproduction is accumulating. Ameiotic crossover recombination is a mechanism that could lead to long genomic stretches of loss of heterozygosity (LOH) and unmasking of mutations that have little or no effect in heterozygous state. Therefore, LOH might be an important force for inducing variation among asexual offspring and may contribute to the limited longevity of asexual lineages. To investigate the genetic consequences of asexuality, here we used high‐throughput sequencing of Daphnia magna for assessing the rate of LOH over a single generation of asexual reproduction. Comparing parthenogenetic daughters with their mothers at several thousand genetic markers generated by restriction site‐associated DNA (RAD) sequencing resulted in high LOH rate estimation that largely overlapped with our estimates for the error rate. To distinguish these two, we Sanger re‐sequenced the top 17 candidate RAD‐loci for LOH, and all of them proved to be false positives. Hence, even though we cannot exclude the possibility that short stretches of LOH occur in genomic regions not covered by our markers, we conclude that LOH does not occur frequently during asexual reproduction in D. magna and ameiotic crossovers are very rare or absent. This finding suggests that clonal lineages of D. magna will remain genetically homogeneous at least over time periods typically relevant for experimental work.
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Affiliation(s)
- Marinela Dukić
- Zoological Institute, University of Basel, Basel, Switzerland.,Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Daniel Berner
- Zoological Institute, University of Basel, Basel, Switzerland
| | - Christoph R Haag
- Centre d'Ecologie Fonctionnelle et Evolutive-CEFE UMR 5175, CNRS-Université de Montpellier-Université Paul-Valéry Montpellier-EPHE, campus CNRS, Montpellier, France.,Department of Biology, Ecology and Evolution, University of Fribourg, Fribourg, Switzerland
| | - Dieter Ebert
- Zoological Institute, University of Basel, Basel, Switzerland
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Athanasio CG, Sommer U, Viant MR, Chipman JK, Mirbahai L. Use of 5-azacytidine in a proof-of-concept study to evaluate the impact of pre-natal and post-natal exposures, as well as within generation persistent DNA methylation changes in Daphnia. ECOTOXICOLOGY (LONDON, ENGLAND) 2018; 27:556-568. [PMID: 29623456 PMCID: PMC6010494 DOI: 10.1007/s10646-018-1927-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/14/2018] [Indexed: 05/28/2023]
Abstract
Short-term exposures at critical stages of development can lead to delayed adverse effects long after the initial stressor has been removed, a concept referred to as developmental origin of adult disease. This indicates that organisms' phenotypes may epigenetically reflect their past exposure history as well as reflecting chemicals currently present in their environment. This concept has significant implications for environmental monitoring. However, there is as yet little or no implementation of epigenetics in environmental risk assessment. In a proof-of-principle study we exposed Daphnia magna to 5-azacytidine, a known DNA de-methylating agent. Exposures covered combinations of prenatal and postnatal exposures as well as different exposure durations and recovery stages. Growth, the transcription of genes and levels of metabolites involved in regulating DNA methylation, and methylation levels of several genes were measured. Our data shows that prenatal exposures caused significant changes in the methylome of target genes, indicating that prenatal stages of Daphnia are also susceptible to same level of change as post-natal stages of Daphnia. While the combination of pre- and postnatal exposures caused the most extreme reduction in DNA methylation compared to the control group. Furthermore, some of the changes in the methylation patterns were persistent even after the initial stressor was removed. Our results suggest that epigenetic biomarkers have the potential to be used as indicators of past chemical exposure history of organisms and provide strong support for implementing changes to the current regimes for chemical risk assessment to mimic realistic environmental scenarios.
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Affiliation(s)
| | - Ulf Sommer
- NERC Biomolecular Analysis Facility-Metabolomics Node (NBAF-B), School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Mark R Viant
- NERC Biomolecular Analysis Facility-Metabolomics Node (NBAF-B), School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - James Kevin Chipman
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Leda Mirbahai
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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25
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Hiruta C, Kakui K, Tollefsen KE, Iguchi T. Targeted gene disruption by use of CRISPR/Cas9 ribonucleoprotein complexes in the water fleaDaphnia pulex. Genes Cells 2018; 23:494-502. [DOI: 10.1111/gtc.12589] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 03/30/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Chizue Hiruta
- Faculty of Science; Hokkaido University; Sapporo Japan
| | - Keiichi Kakui
- Faculty of Science; Hokkaido University; Sapporo Japan
| | - Knut E. Tollefsen
- Section of Ecotoxicology and Risk Assessment; Norwegian Institute for Water Research (NIVA); Oslo Norway
| | - Taisen Iguchi
- Graduate School of Nanobioscience; Yokohama City University; Yokohama Japan
- Department of Basic Biology; Faculty of Life Science; Okazaki Institute for Integrative Bioscience; National Institute for Basic Biology; National Institutes of Natural Sciences; SOKENDAI (Graduate University for Advanced Studies); Okazaki Japan
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26
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Haag CR, Theodosiou L, Zahab R, Lenormand T. Low recombination rates in sexual species and sex-asex transitions. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160461. [PMID: 29109224 PMCID: PMC5698623 DOI: 10.1098/rstb.2016.0461] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2017] [Indexed: 12/11/2022] Open
Abstract
In most sexual, diploid eukaryotes, at least one crossover occurs between each pair of homologous chromosomes during meiosis, presumably in order to ensure proper segregation. Well-known exceptions to this rule are species in which one sex does not recombine and specific chromosomes lacking crossover. We review other possible exceptions, including species with chromosome maps of less than 50 cM in one or both sexes. We discuss the idea that low recombination rates may favour sex-asex transitions, or, alternatively may be a consequence of it. We then show that a yet undescribed species of brine shrimp Artemia from Kazakhstan (A sp. Kazakhstan), the closest known relative of the asexual Artemia parthenogenetica, has one of the shortest genetic linkage maps known. Based on a family of 42 individuals and 589 RAD markers, we find that many linkage groups are considerably shorter than 50 cM, suggesting either no obligate crossover or crossovers concentrated at terminal positions with little effect on recombination. We contrast these findings with the published map of the more distantly related sexual congener, A. franciscana, and conclude that the study of recombination in non-model systems is important to understand the evolutionary causes and consequences of recombination.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'.
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Affiliation(s)
- Christoph R Haag
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE)-Unité Mixte de Recherche 5175, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier-Université Paul-Valéry Montpellier-École Pratique des Hautes Études, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
| | - Loukas Theodosiou
- Research Group for Community Dynamics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany
| | - Roula Zahab
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE)-Unité Mixte de Recherche 5175, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier-Université Paul-Valéry Montpellier-École Pratique des Hautes Études, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
| | - Thomas Lenormand
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE)-Unité Mixte de Recherche 5175, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier-Université Paul-Valéry Montpellier-École Pratique des Hautes Études, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
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27
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Lenormand T, Engelstädter J, Johnston SE, Wijnker E, Haag CR. Evolutionary mysteries in meiosis. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2016.0001. [PMID: 27619705 DOI: 10.1098/rstb.2016.0001] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2016] [Indexed: 01/25/2023] Open
Abstract
Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these often 'weird' features. We discuss the origin of meiosis (origin of ploidy reduction and recombination, two-step meiosis), its secondary modifications (in polyploids or asexuals, inverted meiosis), its importance in punctuating life cycles (meiotic arrests, epigenetic resetting, meiotic asymmetry, meiotic fairness) and features associated with recombination (disjunction constraints, heterochiasmy, crossover interference and hotspots). We present the various evolutionary scenarios and selective pressures that have been proposed to account for these features, and we highlight that their evolutionary significance often remains largely mysterious. Resolving these mysteries will likely provide decisive steps towards understanding why sex and recombination are found in the majority of eukaryotes.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.
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Affiliation(s)
- Thomas Lenormand
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE)-Unité Mixte de Recherche 5175, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier-Université Paul-Valéry Montpellier-Ecole Pratique des Hautes Etudes (EPHE), 1919 Route de Mende, 34293 Montpellier Cedex 5, France
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Susan E Johnston
- Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Erik Wijnker
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Christoph R Haag
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE)-Unité Mixte de Recherche 5175, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier-Université Paul-Valéry Montpellier-Ecole Pratique des Hautes Etudes (EPHE), 1919 Route de Mende, 34293 Montpellier Cedex 5, France
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Engelstädter J. Asexual but Not Clonal: Evolutionary Processes in Automictic Populations. Genetics 2017; 206:993-1009. [PMID: 28381586 PMCID: PMC5499200 DOI: 10.1534/genetics.116.196873] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 03/21/2017] [Indexed: 11/18/2022] Open
Abstract
Many parthenogenetically reproducing animals produce offspring not clonally but through different mechanisms collectively referred to as automixis. Here, meiosis proceeds normally but is followed by a fusion of meiotic products that restores diploidy. This mechanism typically leads to a reduction in heterozygosity among the offspring compared to the mother. Following a derivation of the rate at which heterozygosity is lost at one and two loci, depending on the number of crossovers between loci and centromere, a number of models are developed to gain a better understanding of basic evolutionary processes in automictic populations. Analytical results are obtained for the expected neutral genetic variation, effective population size, mutation-selection balance, selection with overdominance, the spread of beneficial mutations, and selection on crossover rates. These results are complemented by numerical investigations elucidating how associative overdominance (two off-phase deleterious mutations at linked loci behaving like an overdominant locus) can in some cases maintain heterozygosity for prolonged times, and how clonal interference affects adaptation in automictic populations. These results suggest that although automictic populations are expected to suffer from the lack of gene shuffling with other individuals, they are nevertheless, in some respects, superior to both clonal and outbreeding sexual populations in the way they respond to beneficial and deleterious mutations. Implications for related genetic systems such as intratetrad mating, clonal reproduction, selfing, as well as different forms of mixed sexual and automictic reproduction are discussed.
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Affiliation(s)
- Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, 4072, Australia
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29
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Abstract
Using data from 83 isolates from a single population, the population genomics of the microcrustacean Daphnia pulex are described and compared to current knowledge for the only other well-studied invertebrate, Drosophila melanogaster These two species are quite similar with respect to effective population sizes and mutation rates, although some features of recombination appear to be different, with linkage disequilibrium being elevated at short ([Formula: see text] bp) distances in D. melanogaster and at long distances in D. pulex The study population adheres closely to the expectations under Hardy-Weinberg equilibrium, and reflects a past population history of no more than a twofold range of variation in effective population size. Fourfold redundant silent sites and a restricted region of intronic sites appear to evolve in a nearly neutral fashion, providing a powerful tool for population genetic analyses. Amino acid replacement sites are predominantly under strong purifying selection, as are a large fraction of sites in UTRs and intergenic regions, but the majority of SNPs at such sites that rise to frequencies [Formula: see text] appear to evolve in a nearly neutral fashion. All forms of genomic sites (including replacement sites within codons, and intergenic and UTR regions) appear to be experiencing an [Formula: see text] higher level of selection scaled to the power of drift in D. melanogaster, but this may in part be a consequence of recent demographic changes. These results establish D. pulex as an excellent system for future work on the evolutionary genomics of natural populations.
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30
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Flynn JM, Chain FJ, Schoen DJ, Cristescu ME. Spontaneous Mutation Accumulation inDaphnia pulexin Selection-Free vs. Competitive Environments. Mol Biol Evol 2016; 34:160-173. [DOI: 10.1093/molbev/msw234] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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31
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Raborn RT, Spitze K, Brendel VP, Lynch M. Promoter Architecture and Sex-Specific Gene Expression in Daphnia pulex. Genetics 2016; 204:593-612. [PMID: 27585846 PMCID: PMC5068849 DOI: 10.1534/genetics.116.193334] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 07/29/2016] [Indexed: 11/18/2022] Open
Abstract
Large-scale transcription start site (TSS) profiling produces a high-resolution, quantitative picture of transcription initiation and core promoter locations within a genome. However, application of TSS profiling to date has largely been restricted to a small set of prominent model systems. We sought to characterize the cis-regulatory landscape of the water flea Daphnia pulex, an emerging model arthropod that reproduces both asexually (via parthenogenesis) and sexually (via meiosis). We performed Cap Analysis of Gene Expression (CAGE) with RNA isolated from D. pulex within three developmental states: sexual females, asexual females, and males. Identified TSSs were utilized to generate a "Daphnia Promoter Atlas," i.e., a catalog of active promoters across the surveyed states. Analysis of the distribution of promoters revealed evidence for widespread alternative promoter usage in D. pulex, in addition to a prominent fraction of compactly-arranged promoters in divergent orientations. We carried out de novo motif discovery using CAGE-defined TSSs and identified eight candidate core promoter motifs; this collection includes canonical promoter elements (e.g., TATA and Initiator) in addition to others lacking obvious orthologs. A comparison of promoter activities found evidence for considerable state-specific differential gene expression between states. Our work represents the first global definition of transcription initiation and promoter architecture in crustaceans. The Daphnia Promoter Atlas presented here provides a valuable resource for comparative study of cis-regulatory regions in metazoans, as well as for investigations into the circuitries that underpin meiosis and parthenogenesis.
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Affiliation(s)
- R Taylor Raborn
- Department of Biology, Indiana University, Bloomington, Indiana 47405 School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405
| | - Ken Spitze
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Volker P Brendel
- Department of Biology, Indiana University, Bloomington, Indiana 47405 School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, Indiana 47405
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Keith N, Tucker AE, Jackson CE, Sung W, Lucas Lledó JI, Schrider DR, Schaack S, Dudycha JL, Ackerman M, Younge AJ, Shaw JR, Lynch M. High mutational rates of large-scale duplication and deletion in Daphnia pulex. Genome Res 2016; 26:60-9. [PMID: 26518480 PMCID: PMC4691751 DOI: 10.1101/gr.191338.115] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 10/13/2015] [Indexed: 02/06/2023]
Abstract
Knowledge of the genome-wide rate and spectrum of mutations is necessary to understand the origin of disease and the genetic variation driving all evolutionary processes. Here, we provide a genome-wide analysis of the rate and spectrum of mutations obtained in two Daphnia pulex genotypes via separate mutation-accumulation (MA) experiments. Unlike most MA studies that utilize haploid, homozygous, or self-fertilizing lines, D. pulex can be propagated ameiotically while maintaining a naturally heterozygous, diploid genome, allowing the capture of the full spectrum of genomic changes that arise in a heterozygous state. While base-substitution mutation rates are similar to those in other multicellular eukaryotes (about 4 × 10(-9) per site per generation), we find that the rates of large-scale (>100 kb) de novo copy-number variants (CNVs) are significantly elevated relative to those seen in previous MA studies. The heterozygosity maintained in this experiment allowed for estimates of gene-conversion processes. While most of the conversion tract lengths we report are similar to those generated by meiotic processes, we also find larger tract lengths that are indicative of mitotic processes. Comparison of MA lines to natural isolates reveals that a majority of large-scale CNVs in natural populations are removed by purifying selection. The mutations observed here share similarities with disease-causing, complex, large-scale CNVs, thereby demonstrating that MA studies in D. pulex serve as a system for studying the processes leading to such alterations.
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Affiliation(s)
- Nathan Keith
- School of Public and Environmental Affairs, Indiana University, Bloomington, Indiana 47405, USA
| | - Abraham E Tucker
- Biology Department, Southern Arkansas University, Magnolia, Arkansas 71753, USA
| | - Craig E Jackson
- School of Public and Environmental Affairs, Indiana University, Bloomington, Indiana 47405, USA
| | - Way Sung
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | | | - Daniel R Schrider
- Department of Genetics, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Sarah Schaack
- Biology Department, Reed College, Portland, Oregon 97202, USA
| | - Jeffry L Dudycha
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Matthew Ackerman
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Andrew J Younge
- School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405, USA
| | - Joseph R Shaw
- School of Public and Environmental Affairs, Indiana University, Bloomington, Indiana 47405, USA; School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
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Gómez R, Van Damme K, Gosálvez J, Morán ES, Colbourne JK. Male meiosis in Crustacea: synapsis, recombination, epigenetics and fertility in Daphnia magna. Chromosoma 2015; 125:769-87. [PMID: 26685998 PMCID: PMC5023733 DOI: 10.1007/s00412-015-0558-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 10/28/2015] [Accepted: 11/09/2015] [Indexed: 11/28/2022]
Abstract
We present the first detailed cytological study of male meiosis in Daphnia (Crustacea: Branchiopoda: Cladocera)—an aquatic microcrustacean with a cyclical parthenogenetic life cycle. Using immunostaining of the testes in Daphnia magna for baseline knowledge, we characterized the different stages of meiotic division and spermiogenesis in relation to the distribution of proteins involved in synapsis, early recombination events and sister chromatid cohesion. We also studied post-translational histone modifications in male spermatocytes, in relation to the dynamic chromatin progression of meiosis. Finally, we applied a DNA fragmentation test to measure sperm quality of D. magna, with respect to levels of inbreeding. As a proxy for fertility, this technique may be used to assess the reproductive health of a sentinel species of aquatic ecosystems. Daphnia proves to be a model species for comparative studies of meiosis that is poised to improve our understanding of the cytological basis of sexual and asexual reproduction.
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Affiliation(s)
- Rocío Gómez
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, E-28049, Madrid, Spain. .,Environmental Genomics Group. School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK. .,Chromosome Dynamics Group. School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK.
| | - Kay Van Damme
- Environmental Genomics Group. School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Jaime Gosálvez
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, E-28049, Madrid, Spain
| | - Eugenio Sánchez Morán
- Chromosome Dynamics Group. School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - John K Colbourne
- Environmental Genomics Group. School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
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34
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Xu S, Spitze K, Ackerman MS, Ye Z, Bright L, Keith N, Jackson CE, Shaw JR, Lynch M. Hybridization and the Origin of Contagious Asexuality in Daphnia pulex. Mol Biol Evol 2015; 32:3215-25. [PMID: 26351296 PMCID: PMC4840848 DOI: 10.1093/molbev/msv190] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Hybridization plays a potentially important role in the origin of obligate parthenogenesis (OP) in many organisms. However, it remains controversial whether hybridization directly triggers the transition from sexual reproduction to obligate asexuality or a hybrid genetic background enables asexual species to persist. Furthermore, we know little about the specific genetic elements from the divergent, yet still hybridizing lineages responsible for this transition and how these elements are further spread to create other OP lineages. In this study, we address these questions in Daphnia pulex, where cyclically parthenogenetic (CP) and OP lineages coexist. Ancestry estimates and whole-genome association mapping using 32 OP isolates suggest that a complex hybridization history between the parental species D. pulex and D. pulicaria is responsible for the introgression of a set of 647 D. pulicaria single nucleotide polymorphism alleles that show perfect association with OP. Crossing experiments using males of OP lineages and females of CP lineages strongly support a polygenic basis for OP. Single-sperm analyses show that although normal meiotic recombination occurs in the production of haploid sperm by males of OP lineages, a significant proportion of such sperm are polyploid, suggesting that the spread of asexual elements through these males (i.e., contagious asexuality) is much less efficient than previously envisioned. Although the current Daphnia genome annotation does not provide mechanistic insight into the nature of the asexuality-associated alleles, these alleles should be considered as candidates for future investigations on the genetic underpinnings of OP.
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Affiliation(s)
- Sen Xu
- Department of Biology, Indiana University, Bloomington
| | - Ken Spitze
- Department of Biology, Indiana University, Bloomington
| | | | - Zhiqiang Ye
- Department of Biology, Indiana University, Bloomington
| | - Lydia Bright
- Department of Biology, Indiana University, Bloomington
| | - Nathan Keith
- School of Public and Environmental Affairs, Indiana University, Bloomington
| | - Craig E Jackson
- School of Public and Environmental Affairs, Indiana University, Bloomington
| | - Joseph R Shaw
- School of Public and Environmental Affairs, Indiana University, Bloomington School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington
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Svendsen N, Reisser CMO, Dukić M, Thuillier V, Ségard A, Liautard-Haag C, Fasel D, Hürlimann E, Lenormand T, Galimov Y, Haag CR. Uncovering Cryptic Asexuality in Daphnia magna by RAD Sequencing. Genetics 2015; 201:1143-55. [PMID: 26341660 PMCID: PMC4649641 DOI: 10.1534/genetics.115.179879] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 08/29/2015] [Indexed: 02/06/2023] Open
Abstract
The breeding systems of many organisms are cryptic and difficult to investigate with observational data, yet they have profound effects on a species' ecology, evolution, and genome organization. Genomic approaches offer a novel, indirect way to investigate breeding systems, specifically by studying the transmission of genetic information from parents to offspring. Here we exemplify this method through an assessment of self-fertilization vs. automictic parthenogenesis in Daphnia magna. Self-fertilization reduces heterozygosity by 50% compared to the parents, but under automixis, whereby two haploid products from a single meiosis fuse, the expected heterozygosity reduction depends on whether the two meiotic products are separated during meiosis I or II (i.e., central vs. terminal fusion). Reviewing the existing literature and incorporating recombination interference, we derive an interchromosomal and an intrachromosomal prediction of how to distinguish various forms of automixis from self-fertilization using offspring heterozygosity data. We then test these predictions using RAD-sequencing data on presumed automictic diapause offspring of so-called nonmale producing strains and compare them with "self-fertilized" offspring produced by within-clone mating. The results unequivocally show that these offspring were produced by automixis, mostly, but not exclusively, through terminal fusion. However, the results also show that this conclusion was only possible owing to genome-wide heterozygosity data, with phenotypic data as well as data from microsatellite markers yielding inconclusive or even misleading results. Our study thus demonstrates how to use the power of genomic approaches for elucidating breeding systems, and it provides the first demonstration of automictic parthenogenesis in Daphnia.
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Affiliation(s)
- Nils Svendsen
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE)-Unité Mixte de Recherche 5175, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier-Université Paul-Valéry Montpellier-Ecole Pratique des Hautes Etudes (EPHE), campus CNRS, 19, 34293 Montpellier Cedex 5, France
| | - Celine M O Reisser
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE)-Unité Mixte de Recherche 5175, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier-Université Paul-Valéry Montpellier-Ecole Pratique des Hautes Etudes (EPHE), campus CNRS, 19, 34293 Montpellier Cedex 5, France Ecology and Evolution, University of Fribourg, 1700 Fribourg, Switzerland
| | - Marinela Dukić
- Zoology Institute, Evolutionary Biology, University of Basel, 4051 Basel, Switzerland
| | - Virginie Thuillier
- Ecology and Evolution, University of Fribourg, 1700 Fribourg, Switzerland
| | - Adeline Ségard
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE)-Unité Mixte de Recherche 5175, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier-Université Paul-Valéry Montpellier-Ecole Pratique des Hautes Etudes (EPHE), campus CNRS, 19, 34293 Montpellier Cedex 5, France
| | | | - Dominique Fasel
- Ecology and Evolution, University of Fribourg, 1700 Fribourg, Switzerland
| | - Evelin Hürlimann
- Ecology and Evolution, University of Fribourg, 1700 Fribourg, Switzerland
| | - Thomas Lenormand
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE)-Unité Mixte de Recherche 5175, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier-Université Paul-Valéry Montpellier-Ecole Pratique des Hautes Etudes (EPHE), campus CNRS, 19, 34293 Montpellier Cedex 5, France
| | - Yan Galimov
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Christoph R Haag
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE)-Unité Mixte de Recherche 5175, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier-Université Paul-Valéry Montpellier-Ecole Pratique des Hautes Etudes (EPHE), campus CNRS, 19, 34293 Montpellier Cedex 5, France Ecology and Evolution, University of Fribourg, 1700 Fribourg, Switzerland
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Nougué O, Rode NO, Jabbour-zahab R, Ségard A, Chevin LM, Haag CR, Lenormand T. Automixis in Artemia: solving a century-old controversy. J Evol Biol 2015; 28:2337-48. [DOI: 10.1111/jeb.12757] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 08/26/2015] [Accepted: 09/07/2015] [Indexed: 12/11/2022]
Affiliation(s)
- O. Nougué
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry - EPHE; Montpellier Cedex 5 France
| | - N. O. Rode
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry - EPHE; Montpellier Cedex 5 France
- INRA - UMR 1334 AGAP; Montpellier France
| | - R. Jabbour-zahab
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry - EPHE; Montpellier Cedex 5 France
| | - A. Ségard
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry - EPHE; Montpellier Cedex 5 France
| | - L.-M. Chevin
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry - EPHE; Montpellier Cedex 5 France
| | - C. R. Haag
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry - EPHE; Montpellier Cedex 5 France
| | - T. Lenormand
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry - EPHE; Montpellier Cedex 5 France
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Möst M, Oexle S, Marková S, Aidukaite D, Baumgartner L, Stich HB, Wessels M, Martin-Creuzburg D, Spaak P. Population genetic dynamics of an invasion reconstructed from the sediment egg bank. Mol Ecol 2015; 24:4074-93. [PMID: 26122166 DOI: 10.1111/mec.13298] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 06/23/2015] [Accepted: 06/25/2015] [Indexed: 01/16/2023]
Abstract
Biological invasions are a global issue with far-reaching consequences for single species, communities and whole ecosystems. Our understanding of modes and mechanisms of biological invasions requires knowledge of the genetic processes associated with successful invasions. In many instances, this information is particularly difficult to obtain as the initial phases of the invasion process often pass unnoticed and we rely on inferences from contemporary population genetic data. Here, we combined historic information with the genetic analysis of resting eggs to reconstruct the invasion of Daphnia pulicaria into Lower Lake Constance (LLC) in the 1970s from the resting egg bank in the sediments. We identified the invader as 'European D. pulicaria' originating from meso- and eutrophic lowland lakes and ponds in Central Europe. The founding population was characterized by extremely low genetic variation in the resting egg bank that increased considerably over time. Furthermore, strong evidence for selfing and/or biparental inbreeding was found during the initial phase of the invasion, followed by a drop of selfing rate to low levels in subsequent decades. Moreover, the increase in genetic variation was most pronounced during early stages of the invasion, suggesting additional introductions during this period. Our study highlights that genetic data covering the entire invasion process from its beginning can be crucial to accurately reconstruct the invasion history of a species. We show that propagule banks can preserve such information enabling the study of population genetic dynamics and sources of genetic variation in successful invasive populations.
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Affiliation(s)
- Markus Möst
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600, Dübendorf, Switzerland.,Institute of Integrative Biology, ETH Zurich, CH-8092, Zurich, Switzerland.,Department of Zoology, University of Cambridge, CB2 3EJ, Cambridge, UK
| | - Sarah Oexle
- Limnological Institute, University of Konstanz, D-78464, Konstanz, Germany.,Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, B-3000, Leuven, Belgium
| | - Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburská 89, 27721, Liběchov, Czech Republic
| | - Dalia Aidukaite
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600, Dübendorf, Switzerland
| | - Livia Baumgartner
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600, Dübendorf, Switzerland
| | | | - Martin Wessels
- Institute for Lake Research, D-88085, Langenargen, Germany
| | | | - Piet Spaak
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600, Dübendorf, Switzerland.,Institute of Integrative Biology, ETH Zurich, CH-8092, Zurich, Switzerland
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38
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Cloning and expression of a Chk1 gene in Daphnia pulex during different modes of reproduction. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0310-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Bonandin L, Scavariello C, Luchetti A, Mantovani B. Evolutionary dynamics of R2 retroelement and insertion inheritance in the genome of bisexual and parthenogenetic Bacillus rossius populations (Insecta Phasmida). INSECT MOLECULAR BIOLOGY 2014; 23:808-820. [PMID: 25134735 DOI: 10.1111/imb.12126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Theoretical and empirical studies have shown differential management of transposable elements in organisms with different reproductive strategies. To investigate this issue, we analysed the R2 retroelement structure and variability in parthenogenetic and bisexual populations of Bacillus rossius stick insects, as well as insertions inheritance in the offspring of parthenogenetic isolates and of crosses. The B. rossius genome hosts a functional (R2Br(fun) ) and a degenerate (R2Br(deg) ) element, their presence correlating with neither reproductive strategies nor population distribution. The median-joining network method indicated that R2Br(fun) duplicates through a multiple source model, while R2Br(deg) is apparently still duplicating via a master gene model. Offspring analyses showed that unisexual and bisexual offspring have a similar number of R2Br-occupied sites. Multiple or recent shifts from gonochoric to parthenogenetic reproduction may explain the observed data. Moreover, insertion frequency spectra show that higher-frequency insertions in unisexual offspring significantly outnumber those in bisexual offspring. This suggests that unisexual offspring eliminate insertions with lower efficiency. A comparison with simulated insertion frequencies shows that inherited insertions in unisexual and bisexual offspring are significantly different from the expectation. On the whole, different mechanisms of R2 elimination in unisexual vs bisexual offspring and a complex interplay between recombination effectiveness, natural selection and time can explain the observed data.
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Affiliation(s)
- L Bonandin
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
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Hiruta C, Ogino Y, Sakuma T, Toyota K, Miyagawa S, Yamamoto T, Iguchi T. Targeted gene disruption by use of transcription activator-like effector nuclease (TALEN) in the water flea Daphnia pulex. BMC Biotechnol 2014; 14:95. [PMID: 25404042 PMCID: PMC4239399 DOI: 10.1186/s12896-014-0095-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 10/28/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The cosmopolitan microcrustacean Daphnia pulex provides a model system for both human health research and monitoring ecosystem integrity. It is the first crustacean to have its complete genome sequenced, an unprecedented ca. 36% of which has no known homologs with any other species. Moreover, D. pulex is ideally suited for experimental manipulation because of its short reproductive cycle, large numbers of offspring, synchronization of oocyte maturation, and other life history characteristics. However, existing gene manipulation techniques are insufficient to accurately define gene functions. Although our previous investigations developed an RNA interference (RNAi) system in D. pulex, the possible time period of functional analysis was limited because the effectiveness of RNAi is transient. Thus, in this study, we developed a genome editing system for D. pulex by first microinjecting transcription activator-like effector nuclease (TALEN) mRNAs into early embryos and then evaluating TALEN activity and mutation phenotypes. RESULTS We assembled a TALEN construct specific to the Distal-less gene (Dll), which is a homeobox transcription factor essential for distal limb development in invertebrates and vertebrates, and evaluated its activity in vitro by single-strand annealing assay. Then, we injected TALEN mRNAs into eggs within 1 hour post-ovulation. Injected embryos presented with defects in the second antenna and altered appendage development, and indel mutations were detected in Dll loci, indicating that this technique successfully knocked out the target gene. CONCLUSIONS We succeeded, for the first time in D. pulex, in targeted mutagenesis by use of Platinum TALENs. This genome editing technique makes it possible to conduct reverse genetic analysis in D. pulex, making this species an even more appropriate model organism for environmental, evolutionary, and developmental genomics.
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Affiliation(s)
- Chizue Hiruta
- Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, Higashiyama 5-1, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
| | - Yukiko Ogino
- Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, Higashiyama 5-1, Myodaiji, Okazaki, Aichi, 444-8787, Japan. .,Faculty of Life Science, Graduate University for Advanced Studies (SOKENDAI), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan.
| | - Kenji Toyota
- Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, Higashiyama 5-1, Myodaiji, Okazaki, Aichi, 444-8787, Japan. .,Faculty of Life Science, Graduate University for Advanced Studies (SOKENDAI), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
| | - Shinichi Miyagawa
- Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, Higashiyama 5-1, Myodaiji, Okazaki, Aichi, 444-8787, Japan. .,Faculty of Life Science, Graduate University for Advanced Studies (SOKENDAI), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan.
| | - Taisen Iguchi
- Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, Higashiyama 5-1, Myodaiji, Okazaki, Aichi, 444-8787, Japan. .,Faculty of Life Science, Graduate University for Advanced Studies (SOKENDAI), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
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41
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Sumiya E, Ogino Y, Miyakawa H, Hiruta C, Toyota K, Miyagawa S, Iguchi T. Roles of ecdysteroids for progression of reproductive cycle in the fresh water crustacean Daphnia magna. Front Zool 2014. [DOI: 10.1186/s12983-014-0060-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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Hiruta C, Tochinai S. Formation and structure of the ephippium (resting egg case) in relation to molting and egg laying in the water flea Daphnia pulex De Geer (Cladocera: Daphniidae). J Morphol 2014; 275:760-7. [PMID: 24500908 DOI: 10.1002/jmor.20255] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 01/04/2014] [Accepted: 01/11/2014] [Indexed: 11/08/2022]
Abstract
Resting eggs produced by daphnid species in response to environmental deterioration play an important role in colonizing new habitats or in re-establishing extinct populations. Females lay resting eggs into the space within the dorsal part of their carapace and form an egg case called the ephippium to protect them. Previous studies mainly reported the morphology of the completely formed ephippium and/or the forming ephippium of an uncertain stage. To understand ephippium formation and to clarify key transitions in the formation of resting eggs, we examined the structure and formation of the ephippium in the water flea Daphnia pulex De Geer (Cladocera: Daphniidae) by stereomicroscopy, histology, and scanning electron microscopy. The females used in this study produced resting eggs by obligate parthenogenesis. We divided ephippium formation into four stages based on two molts and a single ovulation, as follows. Stage I begins 13 min after molting in adult females that do not ovulate. In Stage II, immediately after the first molt, a protuberance appears beneath the neck region and the carapace begins to thicken. In Stage III, the resting eggs ovulate and the carapace in the area of the forming ephippium becomes much thicker than the normal carapace and accumulates dark pigmentation. In Stage IV, following the second molt, the female sheds the ephippium with the enclosed resting eggs and forms a new carapace. These stages will provide a useful reference for future studies on resting egg formation.
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Affiliation(s)
- Chizue Hiruta
- Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan; Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan
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Hiruta C, Toyota K, Miyakawa H, Ogino Y, Miyagawa S, Tatarazako N, Shaw JR, Iguchi T. Development of a microinjection system for RNA interference in the water flea Daphnia pulex. BMC Biotechnol 2013; 13:96. [PMID: 24188141 PMCID: PMC4228505 DOI: 10.1186/1472-6750-13-96] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 10/31/2013] [Indexed: 11/25/2022] Open
Abstract
Background The ubiquitous, freshwater microcrustacean Daphnia pulex provides a model system for both human health research and monitoring ecosystem integrity. It is the first crustacean to have a well annotated, reference genome assembly that revealed an unusually high gene count highlighted by a large gene orphanage,-i.e., previously uncharacterized genes. Daphnia are capable of either clonal or sexual reproduction, making them ideally suited for genetic manipulation, but the establishment of gene manipulation techniques is needed to accurately define gene functions. Although previous investigations developed an RNA interference (RNAi) system for one congener D. magna, these methods are not appropriate for D. pulex because of the smaller size of their early embryos. In these studies, we develop RNAi techniques for D. pulex by first determining the optimum culture conditions of their isolated embryos and then applying these conditions to the development of microinjection techniques and proof-of-principle RNAi experiments. Results We found that isolated embryos were best cultured on a 2% agar plate bathed in 60 mM sucrose dissolved in M4 media, providing optimal conditions for microinjections. Then, we injected double-stranded (ds)RNA specific to the Distal-less gene (Dll), which is a homeobox transcription factor essential for limb development in invertebrates and vertebrates. Injected embryos presented with defects in the second antenna and appendage development, and dsRNA induced the degradation of Dll mRNAs, indicating that this technique successfully inhibited transcription of the target gene. Conclusions We developed a microinjection system for RNAi studies in D. pulex. These techniques add to the growing genomic toolbox and enhance the genetic tractability of this important model for environmental, evolutionary, and developmental genomics.
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Affiliation(s)
| | | | | | | | | | | | | | - Taisen Iguchi
- Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.
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Xu S, Innes DJ, Lynch M, Cristescu ME. The role of hybridization in the origin and spread of asexuality in Daphnia. Mol Ecol 2013; 22:4549-61. [PMID: 23879327 DOI: 10.1111/mec.12407] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 05/16/2013] [Accepted: 05/26/2013] [Indexed: 11/27/2022]
Abstract
The molecular mechanisms leading to asexuality remain little understood despite their substantial bearing on why sexual reproduction is dominant in nature. Here, we examine the role of hybridization in the origin and spread of obligate asexuality in Daphnia pulex, arguably the best-documented case of contagious asexuality. Obligately parthenogenetic (OP) clones of D. pulex have traditionally been separated into 'hybrid' (Ldh SF) and 'nonhybrid' (Ldh SS) forms because the lactase dehydrogenase (Ldh) locus distinguishes the cyclically parthenogenetic (CP) lake dwelling Daphnia pulicaria (Ldh FF) from its ephemeral pond dwelling sister species D. pulex (Ldh SS). The results of our population genetic analyses based on microsatellite loci suggest that both Ldh SS and SF OP individuals can originate from the crossing of CP female F1 (D. pulex × D. pulicaria) and backcross with males from OP lineages carrying genes that suppress meiosis specifically in female offspring. In previous studies, a suite of diagnostic markers was found to be associated with OP in Ldh SS D. pulex lineages. Our association mapping supports a similar genetic mechanism for the spread of obligate parthenogenesis in Ldh SF OP individuals. Interestingly, our study shows that CP D. pulicaria carry many of the diagnostic microsatellite alleles associated with obligate parthenogenesis. We argue that the assemblage of mutations that suppress meiosis and underlie obligate parthenogenesis in D. pulex originated due to a unique historical hybridization and introgression event between D. pulex and D. pulicaria.
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Affiliation(s)
- Sen Xu
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada N9B 3P4.
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Hanson SJ, Stelzer CP, Welch DBM, Logsdon JM. Comparative transcriptome analysis of obligately asexual and cyclically sexual rotifers reveals genes with putative functions in sexual reproduction, dormancy, and asexual egg production. BMC Genomics 2013; 14:412. [PMID: 23782598 PMCID: PMC3701536 DOI: 10.1186/1471-2164-14-412] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Accepted: 05/31/2013] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Sexual reproduction is a widely studied biological process because it is critically important to the genetics, evolution, and ecology of eukaryotes. Despite decades of study on this topic, no comprehensive explanation has been accepted that explains the evolutionary forces underlying its prevalence and persistence in nature. Monogonont rotifers offer a useful system for experimental studies relating to the evolution of sexual reproduction due to their rapid reproductive rate and close relationship to the putatively ancient asexual bdelloid rotifers. However, little is known about the molecular underpinnings of sex in any rotifer species. RESULTS We generated mRNA-seq libraries for obligate parthenogenetic (OP) and cyclical parthenogenetic (CP) strains of the monogonont rotifer, Brachionus calyciflorus, to identify genes specific to both modes of reproduction. Our differential expression analysis identified receptors with putative roles in signaling pathways responsible for the transition from asexual to sexual reproduction. Differential expression of a specific copy of the duplicated cell cycle regulatory gene CDC20 and specific copies of histone H2A suggest that such duplications may underlie the phenotypic plasticity required for reproductive mode switch in monogononts. We further identified differential expression of genes involved in the formation of resting eggs, a process linked exclusively to sex in this species. Finally, we identified transcripts from the bdelloid rotifer Adineta ricciae that have significant sequence similarity to genes with higher expression in CP strains of B. calyciflorus. CONCLUSIONS Our analysis of global gene expression differences between facultatively sexual and exclusively asexual populations of B. calyciflorus provides insights into the molecular nature of sexual reproduction in rotifers. Furthermore, our results offer insight into the evolution of obligate asexuality in bdelloid rotifers and provide indicators important for the use of monogononts as a model system for investigating the evolution of sexual reproduction.
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Affiliation(s)
- Sara J Hanson
- Department of Biology and Interdisciplinary Program in Genetics, University of Iowa, 301 Biology Building, Iowa City, IA 52242, USA
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46
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Hanson SJ, Schurko AM, Hecox-Lea B, Welch DBM, Stelzer CP, Logsdon JM. Inventory and phylogenetic analysis of meiotic genes in monogonont rotifers. J Hered 2013; 104:357-70. [PMID: 23487324 PMCID: PMC3622358 DOI: 10.1093/jhered/est011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 12/17/2012] [Accepted: 02/11/2013] [Indexed: 12/22/2022] Open
Abstract
A long-standing question in evolutionary biology is how sexual reproduction has persisted in eukaryotic lineages. As cyclical parthenogens, monogonont rotifers are a powerful model for examining this question, yet the molecular nature of sexual reproduction in this lineage is currently understudied. To examine genes involved in meiosis, we generated partial genome assemblies for 2 distantly related monogonont species, Brachionus calyciflorus and B. manjavacas. Here we present an inventory of 89 meiotic genes, of which 80 homologs were identified and annotated from these assemblies. Using phylogenetic analysis, we show that several meiotic genes have undergone relatively recent duplication events that appear to be specific to the monogonont lineage. Further, we compare the expression of "meiosis-specific" genes involved in recombination and all annotated copies of the cell cycle regulatory gene CDC20 between obligate parthenogenetic (OP) and cyclical parthenogenetic (CP) strains of B. calyciflorus. We show that "meiosis-specific" genes are expressed in both CP and OP strains, whereas the expression of one of the CDC20 genes is specific to cyclical parthenogenesis. The data presented here provide insights into mechanisms of cyclical parthenogenesis and establish expectations for studies of obligate asexual relatives of monogononts, the bdelloid rotifer lineage.
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Affiliation(s)
- Sara J Hanson
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
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47
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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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Hiruta C, Tochinai S. Spindle assembly and spatial distribution of γ-tubulin during abortive meiosis and cleavage division in the parthenogenetic water flea Daphnia pulex. Zoolog Sci 2013; 29:733-7. [PMID: 23106557 DOI: 10.2108/zsj.29.733] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In most animal species, centrosomes, the main microtubule-organizing centers, usually disintegrate in oocytes during meiosis and are reconstructed from sperm-provided centrioles before the first cleavage division. In parthenogenetic oocytes, however, no sperm-derived centrosome-dependent microtubule nucleation is expected, as fertilization does not occur. The water flea Daphnia pulex undergoes parthenogenesis and sexual reproduction differentially in response to environmental cues. We used immunofluorescence microscopy with anti-α-tubulin and anti-γ-tubulin antibodies to examine spindle formation and the occurrence of centrosomes during parthenogenetic oogenesis and the subsequent cleavage division in D. pulex. The spindle formed in abortive meiosis in parthenogenesis is barrel-shaped and lacks centrosomes, whereas the spindle in the subsequent cleavage division is typically spindle-shaped, with centrosomes. During abortive meiosis, γ-tubulin is localized along the spindle, while in the first cleavage division it is localized only at the spindle poles. Thus, D. pulex should provide a useful comparative model system for elucidating mechanisms of spindle formation and improving our understanding of how evolutionary modification of these mechanisms is involved in the switch from sexual to parthenogenetic reproduction.
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Affiliation(s)
- Chizue Hiruta
- Department of Natural History Sciences, Hokkaido University, Sapporo, Japan.
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Stenberg P, Saura A. Meiosis and Its Deviations in Polyploid Animals. Cytogenet Genome Res 2013; 140:185-203. [DOI: 10.1159/000351731] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Georgantzopoulou A, Balachandran YL, Rosenkranz P, Dusinska M, Lankoff A, Wojewodzka M, Kruszewski M, Guignard C, Audinot JN, Girija S, Hoffmann L, Gutleb AC. Ag nanoparticles: size- and surface-dependent effects on model aquatic organisms and uptake evaluation with NanoSIMS. Nanotoxicology 2012; 7:1168-78. [DOI: 10.3109/17435390.2012.715312] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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