1
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González R, Félix MA. Caenorhabditis elegans immune responses to microsporidia and viruses. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 154:105148. [PMID: 38325500 DOI: 10.1016/j.dci.2024.105148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 01/30/2024] [Accepted: 02/03/2024] [Indexed: 02/09/2024]
Abstract
The model organism Caenorhabditis elegans is susceptible to infection by obligate intracellular pathogens, specifically microsporidia and viruses. These intracellular pathogens infect intestinal cells, or, for some microsporidia, epidermal cells. Strikingly, intestinal cell infections by viruses or microsporidia trigger a common transcriptional response, activated in part by the ZIP-1 transcription factor. Among the strongest activated genes in this response are ubiquitin-pathway members and members of the pals family, an intriguing gene family with cross-regulations of different members of genomic clusters. Some of the induced genes participate in host defense against the pathogens, for example through ubiquitin-mediated inhibition. Other mechanisms defend the host specifically against viral infections, including antiviral RNA interference and uridylation. These various immune responses are altered by environmental factors and by intraspecific genetic variation of the host. These pathogens were first isolated 15 years ago and much remains to be discovered using C. elegans genetics; also, other intracellular pathogens of C. elegans may yet to be discovered.
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Affiliation(s)
- Rubén González
- Institut de Biologie de l'École Normale Supérieure, CNRS, INSERM, 75005, Paris, France.
| | - Marie-Anne Félix
- Institut de Biologie de l'École Normale Supérieure, CNRS, INSERM, 75005, Paris, France
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2
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Amoroso CR, Shepard LL, Gibson AK. Genetic variation in parasite avoidance, yet no evidence for constitutive fitness costs. Evolution 2024; 78:1005-1013. [PMID: 38416416 PMCID: PMC11136450 DOI: 10.1093/evolut/qpae030] [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: 10/09/2023] [Accepted: 02/26/2024] [Indexed: 02/29/2024]
Abstract
Behavioral avoidance of parasites is a widespread strategy among animal hosts and in human public health. Avoidance has repercussions for both individual and population-level infection risk. Although most cases of parasite avoidance are viewed as adaptive, there is little evidence that the basic assumptions of evolution by natural selection are met. This study addresses this gap by testing whether there is a heritable variation in parasite avoidance behavior. We quantified behavioral avoidance of the bacterial parasite Serratia marcescens for 12 strains of the nematode host Caenorhabditis elegans. We found that these strains varied in their magnitude of avoidance, and we estimated the broad-sense heritability of this behavior to be in the range of 11%-26%. We then asked whether avoidance carries a constitutive fitness cost. We did not find evidence of one. Rather, strains with higher avoidance had higher fitness, measured as population growth rate. Together, these results direct future theoretical and empirical work to identify the forces maintaining genetic variation in parasite avoidance.
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Affiliation(s)
| | - Leila L. Shepard
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Amanda K. Gibson
- Department of Biology, University of Virginia, Charlottesville, VA, USA
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3
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Mignerot L, Gimond C, Bolelli L, Bouleau C, Sandjak A, Boulin T, Braendle C. Natural variation in the Caenorhabditis elegans egg-laying circuit modulates an intergenerational fitness trade-off. eLife 2024; 12:RP88253. [PMID: 38564369 PMCID: PMC10987095 DOI: 10.7554/elife.88253] [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] [Indexed: 04/04/2024] Open
Abstract
Evolutionary transitions from egg laying (oviparity) to live birth (viviparity) are common across various taxa. Many species also exhibit genetic variation in egg-laying mode or display an intermediate mode with laid eggs containing embryos at various stages of development. Understanding the mechanistic basis and fitness consequences of such variation remains experimentally challenging. Here, we report highly variable intra-uterine egg retention across 316 Caenorhabditis elegans wild strains, some exhibiting strong retention, followed by internal hatching. We identify multiple evolutionary origins of such phenotypic extremes and pinpoint underlying candidate loci. Behavioral analysis and genetic manipulation indicates that this variation arises from genetic differences in the neuromodulatory architecture of the egg-laying circuitry. We provide experimental evidence that while strong egg retention can decrease maternal fitness due to in utero hatching, it may enhance offspring protection and confer a competitive advantage. Therefore, natural variation in C. elegans egg-laying behaviour can alter an apparent trade-off between different fitness components across generations. Our findings highlight underappreciated diversity in C. elegans egg-laying behavior and shed light on its fitness consequences. This behavioral variation offers a promising model to elucidate the molecular changes in a simple neural circuit underlying evolutionary shifts between alternative egg-laying modes in invertebrates.
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Affiliation(s)
| | | | | | | | - Asma Sandjak
- Université Côte d’Azur, CNRS, Inserm, IBVNiceFrance
| | - Thomas Boulin
- Institut NeuroMyoGène, CNRS, Inserm, Université de LyonLyonFrance
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4
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Gutnik S, You JE, Sawh AN, Andriollo A, Mango SE. Multiplex DNA fluorescence in situ hybridization to analyze maternal vs. paternal C. elegans chromosomes. Genome Biol 2024; 25:71. [PMID: 38486337 PMCID: PMC10941459 DOI: 10.1186/s13059-024-03199-6] [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: 09/29/2023] [Accepted: 02/15/2024] [Indexed: 03/17/2024] Open
Abstract
Recent advances in microscopy have enabled studying chromosome organization at the single-molecule level, yet little is known about inherited chromosome organization. Here we adapt single-molecule chromosome tracing to distinguish two C. elegans strains (N2 and HI) and find that while their organization is similar, the N2 chromosome influences the folding parameters of the HI chromosome, in particular the step size, across generations. Furthermore, homologous chromosomes overlap frequently, but alignment between homologous regions is rare, suggesting that transvection is unlikely. We present a powerful tool to investigate chromosome architecture and to track the parent of origin.
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Affiliation(s)
- Silvia Gutnik
- Biozentrum, University of Basel, 4056, Basel, Switzerland
- Current address: University Children's Hospital Zürich, Pediatric Oncology and Children's Research Center, Balgrist Campus AG, Lengghalde 5, 8008, Zürich, Switzerland
| | - Jia Emil You
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Ahilya N Sawh
- Biozentrum, University of Basel, 4056, Basel, Switzerland
- Current address: Department of Biochemistry, University of Toronto, Toronto, ON, M5G 1M1, Canada
| | - Aude Andriollo
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Susan E Mango
- Biozentrum, University of Basel, 4056, Basel, Switzerland.
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5
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Parée T, Noble L, Ferreira Gonçalves J, Teotónio H. rec-1 loss of function increases recombination in the central gene clusters at the expense of autosomal pairing centers. Genetics 2024; 226:iyad205. [PMID: 38001364 DOI: 10.1093/genetics/iyad205] [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: 10/03/2023] [Revised: 10/03/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Meiotic control of crossover (CO) number and position is critical for homologous chromosome segregation and organismal fertility, recombination of parental genotypes, and the generation of novel genetic combinations. We here characterize the recombination rate landscape of a rec-1 loss of function modifier of CO position in Caenorhabditis elegans, one of the first ever modifiers discovered. By averaging CO position across hermaphrodite and male meioses and by genotyping 203 single-nucleotide variants covering about 95% of the genome, we find that the characteristic chromosomal arm-center recombination rate domain structure is lost in the loss of function rec-1 mutant. The rec-1 loss of function mutant smooths the recombination rate landscape but is insufficient to eliminate the nonuniform position of CO. Lower recombination rates in the rec-1 mutant are particularly found in the autosomal arm domains containing the pairing centers. We further find that the rec-1 mutant is of little consequence for organismal fertility and egg viability and thus for rates of autosomal nondisjunction. It nonetheless increases X chromosome nondisjunction rates and thus male appearance. Our findings question the maintenance of recombination rate heritability and genetic diversity among C. elegans natural populations, and they further suggest that manipulating genetic modifiers of CO position will help find quantitative trait loci located in low-recombining genomic regions normally refractory to discovery.
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Affiliation(s)
- Tom Parée
- Institut de Biologie de l'École Normale Supérieure, CNRS UMR, 8197, Inserm U1024, PSL Research University, Paris F-75005, France
| | - Luke Noble
- Institut de Biologie de l'École Normale Supérieure, CNRS UMR, 8197, Inserm U1024, PSL Research University, Paris F-75005, France
- EnviroDNA, 95 Albert St., Brunswick, Victoria 3065, Australia
| | - João Ferreira Gonçalves
- Institut de Biologie de l'École Normale Supérieure, CNRS UMR, 8197, Inserm U1024, PSL Research University, Paris F-75005, France
| | - Henrique Teotónio
- Institut de Biologie de l'École Normale Supérieure, CNRS UMR, 8197, Inserm U1024, PSL Research University, Paris F-75005, France
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6
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Wolstenholme AJ, Andersen EC, Choudhary S, Ebner F, Hartmann S, Holden-Dye L, Kashyap SS, Krücken J, Martin RJ, Midha A, Nejsum P, Neveu C, Robertson AP, von Samson-Himmelstjerna G, Walker R, Wang J, Whitehead BJ, Williams PDE. Getting around the roundworms: Identifying knowledge gaps and research priorities for the ascarids. ADVANCES IN PARASITOLOGY 2024; 123:51-123. [PMID: 38448148 PMCID: PMC11143470 DOI: 10.1016/bs.apar.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
The ascarids are a large group of parasitic nematodes that infect a wide range of animal species. In humans, they cause neglected diseases of poverty; many animal parasites also cause zoonotic infections in people. Control measures include hygiene and anthelmintic treatments, but they are not always appropriate or effective and this creates a continuing need to search for better ways to reduce the human, welfare and economic costs of these infections. To this end, Le Studium Institute of Advanced Studies organized a two-day conference to identify major gaps in our understanding of ascarid parasites with a view to setting research priorities that would allow for improved control. The participants identified several key areas for future focus, comprising of advances in genomic analysis and the use of model organisms, especially Caenorhabditis elegans, a more thorough appreciation of the complexity of host-parasite (and parasite-parasite) communications, a search for novel anthelmintic drugs and the development of effective vaccines. The participants agreed to try and maintain informal links in the future that could form the basis for collaborative projects, and to co-operate to organize future meetings and workshops to promote ascarid research.
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Affiliation(s)
- Adrian J Wolstenholme
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Université de Tours, ISP, Nouzilly, France.
| | - Erik C Andersen
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
| | - Shivani Choudhary
- Department of Biomedical Sciences, Iowa State University, Ames, IA, United States
| | - Friederike Ebner
- Department of Molecular Life Sciences, School of Life Sciences, Technische Universität München, Freising, Germany
| | - Susanne Hartmann
- Institute for Immunology, Freie Universität Berlin, Berlin, Germany
| | - Lindy Holden-Dye
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Sudhanva S Kashyap
- Department of Biomedical Sciences, Iowa State University, Ames, IA, United States
| | - Jürgen Krücken
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Richard J Martin
- Department of Biomedical Sciences, Iowa State University, Ames, IA, United States
| | - Ankur Midha
- Institute for Immunology, Freie Universität Berlin, Berlin, Germany
| | - Peter Nejsum
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Cedric Neveu
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Université de Tours, ISP, Nouzilly, France
| | - Alan P Robertson
- Department of Biomedical Sciences, Iowa State University, Ames, IA, United States
| | | | - Robert Walker
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Jianbin Wang
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, United States
| | | | - Paul D E Williams
- Department of Biomedical Sciences, Iowa State University, Ames, IA, United States
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7
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Crombie TA, McKeown R, Moya ND, Evans K, Widmayer S, LaGrassa V, Roman N, Tursunova O, Zhang G, Gibson S, Buchanan C, Roberto N, Vieira R, Tanny R, Andersen E. CaeNDR, the Caenorhabditis Natural Diversity Resource. Nucleic Acids Res 2024; 52:D850-D858. [PMID: 37855690 PMCID: PMC10767927 DOI: 10.1093/nar/gkad887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/30/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
Studies of model organisms have provided important insights into how natural genetic differences shape trait variation. These discoveries are driven by the growing availability of genomes and the expansive experimental toolkits afforded to researchers using these species. For example, Caenorhabditis elegans is increasingly being used to identify and measure the effects of natural genetic variants on traits using quantitative genetics. Since 2016, the C. elegans Natural Diversity Resource (CeNDR) has facilitated many of these studies by providing an archive of wild strains, genome-wide sequence and variant data for each strain, and a genome-wide association (GWA) mapping portal for the C. elegans community. Here, we present an updated platform, the Caenorhabditis Natural Diversity Resource (CaeNDR), that enables quantitative genetics and genomics studies across the three Caenorhabditis species: C. elegans, C. briggsae and C. tropicalis. The CaeNDR platform hosts several databases that are continually updated by the addition of new strains, whole-genome sequence data and annotated variants. Additionally, CaeNDR provides new interactive tools to explore natural variation and enable GWA mappings. All CaeNDR data and tools are accessible through a freely available web portal located at caendr.org.
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Affiliation(s)
- Timothy A Crombie
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Ryan McKeown
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Nicolas D Moya
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
- Cell, Molecular, Developmental biology, and Biophysics Graduate Program, ohns Hopkins University, Baltimore, MD, USA
| | - Kathryn S Evans
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Samuel J Widmayer
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Vincent LaGrassa
- Northwestern University Information Technology, Media and Technology Innovation, Northwestern University, Evanston, IL USA
| | - Natalie Roman
- Northwestern University Information Technology, Media and Technology Innovation, Northwestern University, Evanston, IL USA
| | - Orzu Tursunova
- Northwestern University Information Technology, Media and Technology Innovation, Northwestern University, Evanston, IL USA
| | - Gaotian Zhang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Sophia B Gibson
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Claire M Buchanan
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Nicole M Roberto
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Rodolfo Vieira
- Northwestern University Information Technology, Media and Technology Innovation, Northwestern University, Evanston, IL USA
| | - Robyn E Tanny
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Erik C Andersen
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
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8
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Chou HT, Valencia F, Alexander JC, Bell AD, Deb D, Pollard DA, Paaby AB. Diversification of small RNA pathways underlies germline RNA interference incompetence in wild Caenorhabditis elegans strains. Genetics 2024; 226:iyad191. [PMID: 37865119 PMCID: PMC10763538 DOI: 10.1093/genetics/iyad191] [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: 07/09/2023] [Revised: 07/09/2023] [Accepted: 08/12/2023] [Indexed: 10/23/2023] Open
Abstract
The discovery that experimental delivery of dsRNA can induce gene silencing at target genes revolutionized genetics research, by both uncovering essential biological processes and creating new tools for developmental geneticists. However, the efficacy of exogenous RNA interference (RNAi) varies dramatically within the Caenorhabditis elegans natural population, raising questions about our understanding of RNAi in the lab relative to its activity and significance in nature. Here, we investigate why some wild strains fail to mount a robust RNAi response to germline targets. We observe diversity in mechanism: in some strains, the response is stochastic, either on or off among individuals, while in others, the response is consistent but delayed. Increased activity of the Argonaute PPW-1, which is required for germline RNAi in the laboratory strain N2, rescues the response in some strains but dampens it further in others. Among wild strains, genes known to mediate RNAi exhibited very high expression variation relative to other genes in the genome as well as allelic divergence and strain-specific instances of pseudogenization at the sequence level. Our results demonstrate functional diversification in the small RNA pathways in C. elegans and suggest that RNAi processes are evolving rapidly and dynamically in nature.
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Affiliation(s)
- Han Ting Chou
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Francisco Valencia
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jacqueline C Alexander
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Avery Davis Bell
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Diptodip Deb
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Janelia Research Campus, Ashburn, VA 20147, USA
| | - Daniel A Pollard
- Department of Biology, Western Washington University, Bellingham, WA 98225, USA
| | - Annalise B Paaby
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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9
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Villegas LI, Ferretti L, Wiehe T, Waldvogel A, Schiffer PH. Parthenogenomics: Insights on mutation rates and nucleotide diversity in parthenogenetic Panagrolaimus nematodes. Ecol Evol 2024; 14:e10831. [PMID: 38192904 PMCID: PMC10771965 DOI: 10.1002/ece3.10831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024] Open
Abstract
Asexual reproduction is assumed to lead to the accumulation of deleterious mutations, and reduced heterozygosity due to the absence of recombination. Panagrolaimid nematode species display different modes of reproduction. Sexual reproduction with distinct males and females, asexual reproduction through parthenogenesis in the genus Panagrolaimus, and hermaphroditism in Propanagrolaimus. Here, we compared genomic features of free-living nematodes in populations and species isolated from geographically distant regions to study diversity, and genome-wide differentiation under different modes of reproduction. We firstly estimated genome-wide spontaneous mutation rates in a triploid parthenogenetic Panagrolaimus, and a diploid hermaphroditic Propanagrolaimus via long-term mutation accumulation lines. Secondly, we calculated population genetic parameters including nucleotide diversity, and fixation index (F ST) between populations of asexually and sexually reproducing nematodes. Thirdly, we used phylogenetic network methods on sexually and asexually reproducing Panagrolaimus populations to understand evolutionary relationships between them. The estimated mutation rate was slightly lower for the asexual population, as expected for taxa with this reproductive mode. Natural polyploid asexual populations revealed higher nucleotide diversity. Despite their common ancestor, a gene network revealed a high level of genetic differentiation among asexual populations. The elevated heterozygosity found in the triploid parthenogens could be explained by the third genome copy. Given their tendentially lower mutation rates it can be hypothesized that this is part of the mechanism to evade Muller's ratchet. Our findings in parthenogenetic triploid nematode populations seem to challenge common expectations of evolution under asexuality.
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Affiliation(s)
| | | | - Thomas Wiehe
- Institute for GeneticsUniversity of CologneKölnGermany
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10
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Frézal L, Saglio M, Zhang G, Noble L, Richaud A, Félix MA. Genome-wide association and environmental suppression of the mortal germline phenotype of wild C. elegans. EMBO Rep 2023; 24:e58116. [PMID: 37983674 DOI: 10.15252/embr.202358116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/19/2023] [Accepted: 10/27/2023] [Indexed: 11/22/2023] Open
Abstract
The animal germline lineage needs to be maintained along generations. However, some Caenorhabditis elegans wild isolates display a mortal germline phenotype, leading to sterility after several generations at 25°C. Using a genome-wide association approach, we detect a significant peak on chromosome III around 5 Mb, confirmed by introgressions. Thus, a seemingly deleterious genotype is maintained at intermediate frequency in the species. Environmental rescue is a likely explanation, and indeed associated bacteria and microsporidia suppress the phenotype of wild isolates as well as mutants in small RNA inheritance (nrde-2) and histone modifications (set-2). Escherichia coli strains of the K-12 lineage suppress the phenotype compared to B strains. By shifting a wild strain from E. coli K-12 to E. coli B, we find that memory of the suppressing condition is maintained over several generations. Thus, the mortal germline phenotype of wild C. elegans is in part revealed by laboratory conditions and may represent variation in epigenetic inheritance and environmental interactions. This study also points to the importance of non-genetic memory in the face of environmental variation.
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Affiliation(s)
- Lise Frézal
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Marie Saglio
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Gaotian Zhang
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Luke Noble
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Aurélien Richaud
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Marie-Anne Félix
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
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11
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Bush ZD, Naftaly AFS, Dinwiddie D, Albers C, Hillers KJ, Libuda DE. Comprehensive detection of structural variation and transposable element differences between wild type laboratory lineages of C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.523974. [PMID: 37961628 PMCID: PMC10634987 DOI: 10.1101/2023.01.13.523974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Genomic structural variations (SVs) and transposable elements (TEs) can be significant contributors to genome evolution, altered gene expression, and risk of genetic diseases. Recent advancements in long-read sequencing have greatly improved the quality of de novo genome assemblies and enhanced the detection of sequence variants at the scale of hundreds or thousands of bases. Comparisons between two diverged wild isolates of Caenorhabditis elegans, the Bristol and Hawaiian strains, have been widely utilized in the analysis of small genetic variations. Genetic drift, including SVs and rearrangements of repeated sequences such as TEs, can occur over time from long-term maintenance of wild type isolates within the laboratory. To comprehensively detect both large and small structural variations as well as TEs due to genetic drift, we generated de novo genome assemblies and annotations for each strain from our lab collection using both long- and short-read sequencing and compared our assemblies and annotations with that of other lab wild type strains. Within our lab assemblies, we annotate over 3.1Mb of sequence divergence between the Bristol and Hawaiian isolates: 337,584 SNPs, 94,503 small insertion-deletions (<50bp), and 4,334 structural variations (>50bp). Further, we define the location and movement of specific DNA TEs between N2 Bristol and CB4856 Hawaiian wild type isolates. Specifically, we find the N2 Bristol genome has 20.6% more TEs from the Tc1/mariner family than the CB4856 Hawaiian genome. Moreover, we identified Zator elements as the most abundant and mobile TE family in the genome. Using specific TE sequences with unique SNPs, we also identify 38 TEs that moved intrachromosomally and 9 TEs that moved interchromosomally between the N2 Bristol and CB4856 Hawaiian genomes. By comparing the de novo genome assembly of our lab collection Bristol isolate to the VC2010 Bristol assembly, we also reveal that lab lineages display over 2 Mb of total variation: 1,162 SNPs, 1,528 indels, and 897 SVs with 95% of the variation due to SVs. Overall, our work demonstrates the unique contribution of SVs and TEs to variation and genetic drift between wild type laboratory strains assumed to be isogenic despite growing evidence of genetic drift and phenotypic variation.
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Affiliation(s)
- Zachary D. Bush
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Blvd Eugene, OR 97403, USA
| | - Alice F. S. Naftaly
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Blvd Eugene, OR 97403, USA
| | - Devin Dinwiddie
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Blvd Eugene, OR 97403, USA
| | - Cora Albers
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Blvd Eugene, OR 97403, USA
| | - Kenneth J. Hillers
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, California, USA
| | - Diana E. Libuda
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Blvd Eugene, OR 97403, USA
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12
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Saco A, Rey-Campos M, Gallardo-Escárate C, Gerdol M, Novoa B, Figueras A. Gene presence/absence variation in Mytilus galloprovincialis and its implications in gene expression and adaptation. iScience 2023; 26:107827. [PMID: 37744033 PMCID: PMC10514466 DOI: 10.1016/j.isci.2023.107827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/12/2023] [Accepted: 09/01/2023] [Indexed: 09/26/2023] Open
Abstract
Presence/absence variation (PAV) is a well-known phenomenon in prokaryotes that was described for the first time in bivalves in 2020 in Mytilus galloprovincialis. The objective of the present study was to further our understanding of the PAV phenomenon in mussel biology. The distribution of PAV was studied in a mussel chromosome-level genome assembly, revealing a widespread distribution but with hotspots of dispensability. Special attention was given to the effect of PAV in gene expression, since dispensable genes were found to be inherently subject to distortions due to their sparse distribution among individuals. Furthermore, the high expression and strong tissue specificity of some dispensable genes, such as myticins, strongly supported their biological relevance. The significant differences in the repertoire of dispensable genes associated with two geographically distinct populations suggest that PAV is involved in local adaptation. Overall, the PAV phenomenon would provide a key selective advantage at the population level.
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Affiliation(s)
- Amaro Saco
- Institute of Marine Research, Spanish National Research Council, Vigo, Spain
| | - Magalí Rey-Campos
- Institute of Marine Research, Spanish National Research Council, Vigo, Spain
| | | | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Beatriz Novoa
- Institute of Marine Research, Spanish National Research Council, Vigo, Spain
| | - Antonio Figueras
- Institute of Marine Research, Spanish National Research Council, Vigo, Spain
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13
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Moya ND, Stevens L, Miller IR, Sokol CE, Galindo JL, Bardas AD, Koh ESH, Rozenich J, Yeo C, Xu M, Andersen EC. Novel and improved Caenorhabditis briggsae gene models generated by community curation. BMC Genomics 2023; 24:486. [PMID: 37626289 PMCID: PMC10463891 DOI: 10.1186/s12864-023-09582-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND The nematode Caenorhabditis briggsae has been used as a model in comparative genomics studies with Caenorhabditis elegans because of their striking morphological and behavioral similarities. However, the potential of C. briggsae for comparative studies is limited by the quality of its genome resources. The genome resources for the C. briggsae laboratory strain AF16 have not been developed to the same extent as C. elegans. The recent publication of a new chromosome-level reference genome for QX1410, a C. briggsae wild strain closely related to AF16, has provided the first step to bridge the gap between C. elegans and C. briggsae genome resources. Currently, the QX1410 gene models consist of software-derived gene predictions that contain numerous errors in their structure and coding sequences. In this study, a team of researchers manually inspected over 21,000 gene models and underlying transcriptomic data to repair software-derived errors. RESULTS We designed a detailed workflow to train a team of nine students to manually curate gene models using RNA read alignments. We manually inspected the gene models, proposed corrections to the coding sequences of over 8,000 genes, and modeled thousands of putative isoforms and untranslated regions. We exploited the conservation of protein sequence length between C. briggsae and C. elegans to quantify the improvement in protein-coding gene model quality and showed that manual curation led to substantial improvements in the protein sequence length accuracy of QX1410 genes. Additionally, collinear alignment analysis between the QX1410 and AF16 genomes revealed over 1,800 genes affected by spurious duplications and inversions in the AF16 genome that are now resolved in the QX1410 genome. CONCLUSIONS Community-based, manual curation using transcriptome data is an effective approach to improve the quality of software-derived protein-coding genes. The detailed protocols provided in this work can be useful for future large-scale manual curation projects in other species. Our manual curation efforts have brought the QX1410 gene models to a comparable level of quality as the extensively curated AF16 gene models. The improved genome resources for C. briggsae provide reliable tools for the study of Caenorhabditis biology and other related nematodes.
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Affiliation(s)
- Nicolas D Moya
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, 60208, USA
| | - Lewis Stevens
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Isabella R Miller
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Chloe E Sokol
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Joseph L Galindo
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Alexandra D Bardas
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Edward S H Koh
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Justine Rozenich
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Cassia Yeo
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Maryanne Xu
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA.
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14
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Bell AD, Chou HT, Valencia F, Paaby AB. Beyond the reference: gene expression variation and transcriptional response to RNA interference in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2023; 13:jkad112. [PMID: 37221008 PMCID: PMC10411595 DOI: 10.1093/g3journal/jkad112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/25/2023]
Abstract
Though natural systems harbor genetic and phenotypic variation, research in model organisms is often restricted to a reference strain. Focusing on a reference strain yields a great depth of knowledge but potentially at the cost of breadth of understanding. Furthermore, tools developed in the reference context may introduce bias when applied to other strains, posing challenges to defining the scope of variation within model systems. Here, we evaluate how genetic differences among 5 wild Caenorhabditis elegans strains affect gene expression and its quantification, in general and after induction of the RNA interference (RNAi) response. Across strains, 34% of genes were differentially expressed in the control condition, including 411 genes that were not expressed at all in at least 1 strain; 49 of these were unexpressed in reference strain N2. Reference genome mapping bias caused limited concern: despite hyperdiverse hotspots throughout the genome, 92% of variably expressed genes were robust to mapping issues. The transcriptional response to RNAi was highly strain- and target-gene-specific and did not correlate with RNAi efficiency, as the 2 RNAi-insensitive strains showed more differentially expressed genes following RNAi treatment than the RNAi-sensitive reference strain. We conclude that gene expression, generally and in response to RNAi, differs across C. elegans strains such that the choice of strain may meaningfully influence scientific inferences. Finally, we introduce a resource for querying gene expression variation in this dataset at https://wildworm.biosci.gatech.edu/rnai/.
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Affiliation(s)
- Avery Davis Bell
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr NW, EBB Building, Atlanta, GA 30332, USA
| | - Han Ting Chou
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr NW, EBB Building, Atlanta, GA 30332, USA
| | - Francisco Valencia
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr NW, EBB Building, Atlanta, GA 30332, USA
| | - Annalise B Paaby
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr NW, EBB Building, Atlanta, GA 30332, USA
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15
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Teterina AA, Willis JH, Lukac M, Jovelin R, Cutter AD, Phillips PC. Genomic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes. PLoS Genet 2023; 19:e1010879. [PMID: 37585484 PMCID: PMC10461856 DOI: 10.1371/journal.pgen.1010879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 08/28/2023] [Accepted: 07/21/2023] [Indexed: 08/18/2023] Open
Abstract
Caenorhabditis nematodes form an excellent model for studying how the mode of reproduction affects genetic diversity, as some species reproduce via outcrossing whereas others can self-fertilize. Currently, chromosome-level patterns of diversity and recombination are only available for self-reproducing Caenorhabditis, making the generality of genomic patterns across the genus unclear given the profound potential influence of reproductive mode. Here we present a whole-genome diversity landscape, coupled with a new genetic map, for the outcrossing nematode C. remanei. We demonstrate that the genomic distribution of recombination in C. remanei, like the model nematode C. elegans, shows high recombination rates on chromosome arms and low rates toward the central regions. Patterns of genetic variation across the genome are also similar between these species, but differ dramatically in scale, being tenfold greater for C. remanei. Historical reconstructions of variation in effective population size over the past million generations echo this difference in polymorphism. Evolutionary simulations demonstrate how selection, recombination, mutation, and selfing shape variation along the genome, and that multiple drivers can produce patterns similar to those observed in natural populations. The results illustrate how genome organization and selection play a crucial role in shaping the genomic pattern of diversity whereas demographic processes scale the level of diversity across the genome as a whole.
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Affiliation(s)
- Anastasia A. Teterina
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
- Center of Parasitology, Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
| | - John H. Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Matt Lukac
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Richard Jovelin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Asher D. Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Patrick C. Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
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16
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Moya ND, Stevens L, Miller IR, Sokol CE, Galindo JL, Bardas AD, Koh ESH, Rozenich J, Yeo C, Xu M, Andersen EC. Novel and improved Caenorhabditis briggsae gene models generated by community curation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541014. [PMID: 37292880 PMCID: PMC10245686 DOI: 10.1101/2023.05.16.541014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Background The nematode Caenorhabditis briggsae has been used as a model for genomics studies compared to Caenorhabditis elegans because of its striking morphological and behavioral similarities. These studies yielded numerous findings that have expanded our understanding of nematode development and evolution. However, the potential of C. briggsae to study nematode biology is limited by the quality of its genome resources. The reference genome and gene models for the C. briggsae laboratory strain AF16 have not been developed to the same extent as C. elegans . The recent publication of a new chromosome-level reference genome for QX1410, a C. briggsae wild strain closely related to AF16, has provided the first step to bridge the gap between C. elegans and C. briggsae genome resources. Currently, the QX1410 gene models consist of protein-coding gene predictions generated from short- and long-read transcriptomic data. Because of the limitations of gene prediction software, the existing gene models for QX1410 contain numerous errors in their structure and coding sequences. In this study, a team of researchers manually inspected over 21,000 software-derived gene models and underlying transcriptomic data to improve the protein-coding gene models of the C. briggsae QX1410 genome. Results We designed a detailed workflow to train a team of nine students to manually curate genes using RNA read alignments and predicted gene models. We manually inspected the gene models using the genome annotation editor, Apollo, and proposed corrections to the coding sequences of over 8,000 genes. Additionally, we modeled thousands of putative isoforms and untranslated regions. We exploited the conservation of protein sequence length between C. briggsae and C. elegans to quantify the improvement in protein-coding gene model quality before and after curation. Manual curation led to a substantial improvement in the protein sequence length accuracy of QX1410 genes. We also compared the curated QX1410 gene models against the existing AF16 gene models. The manual curation efforts yielded QX1410 gene models that are similar in quality to the extensively curated AF16 gene models in terms of protein-length accuracy and biological completeness scores. Collinear alignment analysis between the QX1410 and AF16 genomes revealed over 1,800 genes affected by spurious duplications and inversions in the AF16 genome that are now resolved in the QX1410 genome. Conclusions Community-based, manual curation using transcriptome data is an effective approach to improve the quality of software-derived protein-coding genes. Comparative genomic analysis using a related species with high-quality reference genome(s) and gene models can be used to quantify improvements in gene model quality in a newly sequenced genome. The detailed protocols provided in this work can be useful for future large-scale manual curation projects in other species. The chromosome-level reference genome for the C. briggsae strain QX1410 far surpasses the quality of the genome of the laboratory strain AF16, and our manual curation efforts have brought the QX1410 gene models to a comparable level of quality to the previous reference, AF16. The improved genome resources for C. briggsae provide reliable tools for the study of Caenorhabditis biology and other related nematodes.
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Affiliation(s)
- Nicolas D. Moya
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
| | - Lewis Stevens
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Isabella R. Miller
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Chloe E. Sokol
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Joseph L. Galindo
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Alexandra D. Bardas
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Edward S. H. Koh
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Justine Rozenich
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Cassia Yeo
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Maryanne Xu
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Erik C. Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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17
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Bell AD, Chou HT, Paaby AB. Beyond the reference: gene expression variation and transcriptional response to RNAi in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.533964. [PMID: 36993640 PMCID: PMC10055391 DOI: 10.1101/2023.03.24.533964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A universal feature of living systems is that natural variation in genotype underpins variation in phenotype. Yet, research in model organisms is often constrained to a single genetic background, the reference strain. Further, genomic studies that do evaluate wild strains typically rely on the reference strain genome for read alignment, leading to the possibility of biased inferences based on incomplete or inaccurate mapping; the extent of reference bias can be difficult to quantify. As an intermediary between genome and organismal traits, gene expression is well positioned to describe natural variability across genotypes generally and in the context of environmental responses, which can represent complex adaptive phenotypes. C. elegans sits at the forefront of investigation into small-RNA gene regulatory mechanisms, or RNA interference (RNAi), and wild strains exhibit natural variation in RNAi competency following environmental triggers. Here, we examine how genetic differences among five wild strains affect the C. elegans transcriptome in general and after inducing RNAi responses to two germline target genes. Approximately 34% of genes were differentially expressed across strains; 411 genes were not expressed at all in at least one strain despite robust expression in others, including 49 genes not expressed in reference strain N2. Despite the presence of hyper-diverse hotspots throughout the C. elegans genome, reference mapping bias was of limited concern: over 92% of variably expressed genes were robust to mapping issues. Overall, the transcriptional response to RNAi was strongly strain-specific and highly specific to the target gene, and the laboratory strain N2 was not representative of the other strains. Moreover, the transcriptional response to RNAi was not correlated with RNAi phenotypic penetrance; the two germline RNAi incompetent strains exhibited substantial differential gene expression following RNAi treatment, indicating an RNAi response despite failure to reduce expression of the target gene. We conclude that gene expression, both generally and in response to RNAi, differs across C. elegans strains such that choice of strain may meaningfully influence scientific conclusions. To provide a public, easily accessible resource for querying gene expression variation in this dataset, we introduce an interactive website at https://wildworm.biosci.gatech.edu/rnai/ .
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Affiliation(s)
- Avery Davis Bell
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA
| | - Han Ting Chou
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA
| | - Annalise B. Paaby
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA
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18
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da Silva EMG, Rebello KM, Choi YJ, Gregorio V, Paschoal AR, Mitreva M, McKerrow JH, Neves-Ferreira AGDC, Passetti F. Identification of Novel Genes and Proteoforms in Angiostrongylus costaricensis through a Proteogenomic Approach. Pathogens 2022; 11:1273. [PMID: 36365024 PMCID: PMC9694666 DOI: 10.3390/pathogens11111273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/15/2022] [Accepted: 10/20/2022] [Indexed: 07/22/2023] Open
Abstract
RNA sequencing (RNA-Seq) and mass-spectrometry-based proteomics data are often integrated in proteogenomic studies to assist in the prediction of eukaryote genome features, such as genes, splicing, single-nucleotide (SNVs), and single-amino-acid variants (SAAVs). Most genomes of parasite nematodes are draft versions that lack transcript- and protein-level information and whose gene annotations rely only on computational predictions. Angiostrongylus costaricensis is a roundworm species that causes an intestinal inflammatory disease, known as abdominal angiostrongyliasis (AA). Currently, there is no drug available that acts directly on this parasite, mostly due to the sparse understanding of its molecular characteristics. The available genome of A. costaricensis, specific to the Costa Rica strain, is a draft version that is not supported by transcript- or protein-level evidence. This study used RNA-Seq and MS/MS data to perform an in-depth annotation of the A. costaricensis genome. Our prediction improved the reference annotation with (a) novel coding and non-coding genes; (b) pieces of evidence of alternative splicing generating new proteoforms; and (c) a list of SNVs between the Brazilian (Crissiumal) and the Costa Rica strain. To the best of our knowledge, this is the first time that a multi-omics approach has been used to improve the genome annotation of A. costaricensis. We hope this improved genome annotation can assist in the future development of drugs, kits, and vaccines to treat, diagnose, and prevent AA caused by either the Brazil strain (Crissiumal) or the Costa Rica strain.
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Affiliation(s)
- Esdras Matheus Gomes da Silva
- Instituto Carlos Chagas, Fiocruz, Curitiba 81350-010, PR, Brazil
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Karina Mastropasqua Rebello
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
- Laboratory of Integrated Studies in Protozoology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil
| | - Young-Jun Choi
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Vitor Gregorio
- Bioinformatics and Pattern Recognition Group (Bioinfo-CP), Department of Computer Science (DACOM), Federal University of Technology-Parana (UTFPR), Cornélio Procópio 86300-000, PR, Brazil
| | - Alexandre Rossi Paschoal
- Bioinformatics and Pattern Recognition Group (Bioinfo-CP), Department of Computer Science (DACOM), Federal University of Technology-Parana (UTFPR), Cornélio Procópio 86300-000, PR, Brazil
| | - Makedonka Mitreva
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - James H. McKerrow
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA 92093, USA
| | | | - Fabio Passetti
- Instituto Carlos Chagas, Fiocruz, Curitiba 81350-010, PR, Brazil
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19
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Servello FA, Fernandes R, Eder M, Harris N, Martin OMF, Oswal N, Lindberg A, Derosiers N, Sengupta P, Stroustrup N, Apfeld J. Neuronal temperature perception induces specific defenses that enable C. elegans to cope with the enhanced reactivity of hydrogen peroxide at high temperature. eLife 2022; 11:e78941. [PMID: 36226814 PMCID: PMC9635881 DOI: 10.7554/elife.78941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 10/12/2022] [Indexed: 11/30/2022] Open
Abstract
Hydrogen peroxide is the most common reactive chemical that organisms face on the microbial battlefield. The rate with which hydrogen peroxide damages biomolecules required for life increases with temperature, yet little is known about how organisms cope with this temperature-dependent threat. Here, we show that Caenorhabditis elegans nematodes use temperature information perceived by sensory neurons to cope with the temperature-dependent threat of hydrogen peroxide produced by the pathogenic bacterium Enterococcus faecium. These nematodes preemptively induce the expression of specific hydrogen peroxide defenses in response to perception of high temperature by a pair of sensory neurons. These neurons communicate temperature information to target tissues expressing those defenses via an insulin/IGF1 hormone. This is the first example of a multicellular organism inducing their defenses to a chemical when they sense an inherent enhancer of the reactivity of that chemical.
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Affiliation(s)
| | - Rute Fernandes
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Matthias Eder
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Nathan Harris
- Department of Biology, Brandeis UniversityWalthamUnited States
| | - Olivier MF Martin
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Natasha Oswal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Anders Lindberg
- Biology Department, Northeastern UniversityBostonUnited States
| | | | - Piali Sengupta
- Department of Biology, Brandeis UniversityWalthamUnited States
| | - Nicholas Stroustrup
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Javier Apfeld
- Biology Department, Northeastern UniversityBostonUnited States
- Bioengineering Department, Northeastern UniversityBostonUnited States
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20
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Widmayer SJ, Evans KS, Zdraljevic S, Andersen EC. Evaluating the power and limitations of genome-wide association studies in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2022; 12:6583190. [PMID: 35536194 PMCID: PMC9258552 DOI: 10.1093/g3journal/jkac114] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/02/2022] [Indexed: 11/30/2022]
Abstract
Quantitative genetics in Caenorhabditis elegans seeks to identify naturally segregating genetic variants that underlie complex traits. Genome-wide association studies scan the genome for individual genetic variants that are significantly correlated with phenotypic variation in a population, or quantitative trait loci. Genome-wide association studies are a popular choice for quantitative genetic analyses because the quantitative trait loci that are discovered segregate in natural populations. Despite numerous successful mapping experiments, the empirical performance of genome-wide association study has not, to date, been formally evaluated in C. elegans. We developed an open-source genome-wide association study pipeline called NemaScan and used a simulation-based approach to provide benchmarks of mapping performance in collections of wild C. elegans strains. Simulated trait heritability and complexity determined the spectrum of quantitative trait loci detected by genome-wide association studies. Power to detect smaller-effect quantitative trait loci increased with the number of strains sampled from the C. elegans Natural Diversity Resource. Population structure was a major driver of variation in mapping performance, with populations shaped by recent selection exhibiting significantly lower false discovery rates than populations composed of more divergent strains. We also recapitulated previous genome-wide association studies of experimentally validated quantitative trait variants. Our simulation-based evaluation of performance provides the community with critical context to pursue quantitative genetic studies using the C. elegans Natural Diversity Resource to elucidate the genetic basis of complex traits in C. elegans natural populations.
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Affiliation(s)
- Samuel J Widmayer
- Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Kathryn S Evans
- Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Stefan Zdraljevic
- Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - Erik C Andersen
- Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
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21
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Sloat SA, Noble LM, Paaby AB, Bernstein M, Chang A, Kaur T, Yuen J, Tintori SC, Jackson JL, Martel A, Salome Correa JA, Stevens L, Kiontke K, Blaxter M, Rockman MV. Caenorhabditis nematodes colonize ephemeral resource patches in neotropical forests. Ecol Evol 2022; 12:e9124. [PMID: 35898425 PMCID: PMC9309040 DOI: 10.1002/ece3.9124] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/17/2022] [Accepted: 06/23/2022] [Indexed: 01/09/2023] Open
Abstract
Factors shaping the distribution and abundance of species include life-history traits, population structure, and stochastic colonization-extinction dynamics. Field studies of model species groups help reveal the roles of these factors. Species of Caenorhabditis nematodes are highly divergent at the sequence level but exhibit highly conserved morphology, and many of these species live in sympatry on microbe-rich patches of rotten material. Here, we use field experiments and large-scale opportunistic collections to investigate species composition, abundance, and colonization efficiency of Caenorhabditis species in two of the world's best-studied lowland tropical field sites: Barro Colorado Island in Panamá and La Selva in Sarapiquí, Costa Rica. We observed seven species of Caenorhabditis, four of them known only from these collections. We formally describe two species and place them within the Caenorhabditis phylogeny. While these localities contain species from many parts of the phylogeny, both localities were dominated by globally distributed androdiecious species. We found that Caenorhabditis individuals were able to colonize baits accessible only through phoresy and preferentially colonized baits that were in direct contact with the ground. We estimate the number of colonization events per patch to be low.
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Affiliation(s)
- Solomon A. Sloat
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Luke M. Noble
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Annalise B. Paaby
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
- School of Biological SciencesGeorgia Institute of TechnologyAtlantaGeorgiaUSA
| | - Max Bernstein
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Audrey Chang
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Taniya Kaur
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - John Yuen
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
- Renaissance School of MedicineStony Brook UniversityStony BrookNew YorkUSA
| | - Sophia C. Tintori
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Jacqueline L. Jackson
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Arielle Martel
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Jose A. Salome Correa
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | | | - Karin Kiontke
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger InstituteHinxtonUK
| | - Matthew V. Rockman
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
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22
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Pallotto LM, Dilks CM, Park YJ, Smit RB, Lu B, Gopalakrishnan C, Gilleard JS, Andersen EC, Mains PE. Interactions of C. elegans β-tubulins with the microtubule inhibitor and anthelmintic drug albendazole. Genetics 2022; 221:6613138. [PMID: 35731216 DOI: 10.1093/genetics/iyac093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/08/2022] [Indexed: 11/14/2022] Open
Abstract
Parasitic nematodes are major human and agricultural pests, and benzimidazoles are amongst the most important broad spectrum anthelmintic drug class used for their control. Benzimidazole resistance is now widespread in many species of parasitic nematodes in livestock globally and an emerging concern for the sustainable control of human soil transmitted helminths. β-tubulin is the major benzimidazole target, although other genes may influence resistance. Among the six C. elegans β-tubulin genes, loss of ben-1 causes resistance without other apparent defects. Here, we explored the genetics of C. elegans β-tubulin genes in relation to the response to the benzimidazole derivative albendazole. The most highly expressed β-tubulin isotypes, encoded by tbb-1 and tbb-2, were known to be redundant with each other for viability, and their products are predicted not to bind benzimidazoles. We found that tbb-2 mutants, and to a lesser extent tbb-1 mutants, were hypersensitive to albendazole. The double mutant tbb-2 ben-1 is uncoordinated and short, resembling the wild type exposed to albendazole, but the tbb-1 ben-1 double mutant did not show the same phenotypes. These results suggest that tbb-2 is a modifier of ABZ sensitivity. To better understand how BEN-1 mutates to cause benzimidazole resistance, we isolated mutants resistant to albendazole and found that 15 of 16 mutations occurred in the ben-1 coding region. Mutations ranged from likely nulls to hypomorphs, and several corresponded to residues that cause resistance in other organisms. Null alleles of ben-1 are albendazole-resistant and BEN-1 shows high sequence identity with tubulins from other organisms, suggesting that many amino acid changes could cause resistance. However, our results suggest that missense mutations conferring resistance are not evenly distributed across all possible conserved sites. Independent of their roles in benzimidazole resistance, tbb-1 and tbb-2 may have specialized functions as null mutants of tbb-1 or tbb-2 were cold or heat sensitive, respectively.
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Affiliation(s)
- Linda M Pallotto
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Clayton M Dilks
- Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, 60208, USA
| | - Ye-Jean Park
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Ryan B Smit
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Brian Lu
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | | | - John S Gilleard
- Department of Comparative Biology and Experimental Medicine, Host-Parasite Interactions (HPI) Program, Faculty of Veterinary Medicine, University of Calgary, Alberta, T2N 4N1 Canada
| | - Erik C Andersen
- Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Paul E Mains
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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23
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The impact of species-wide gene expression variation on Caenorhabditis elegans complex traits. Nat Commun 2022; 13:3462. [PMID: 35710766 PMCID: PMC9203580 DOI: 10.1038/s41467-022-31208-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/08/2022] [Indexed: 12/15/2022] Open
Abstract
Phenotypic variation in organism-level traits has been studied in Caenorhabditis elegans wild strains, but the impacts of differences in gene expression and the underlying regulatory mechanisms are largely unknown. Here, we use natural variation in gene expression to connect genetic variants to differences in organismal-level traits, including drug and toxicant responses. We perform transcriptomic analyses on 207 genetically distinct C. elegans wild strains to study natural regulatory variation of gene expression. Using this massive dataset, we perform genome-wide association mappings to investigate the genetic basis underlying gene expression variation and reveal complex genetic architectures. We find a large collection of hotspots enriched for expression quantitative trait loci across the genome. We further use mediation analysis to understand how gene expression variation could underlie organism-level phenotypic variation for a variety of complex traits. These results reveal the natural diversity in gene expression and possible regulatory mechanisms in this keystone model organism, highlighting the promise of using gene expression variation to understand how phenotypic diversity is generated.
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24
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Lee BY, Kim J, Lee J. Intraspecific de novo gene birth revealed by presence-absence variant genes in Caenorhabditis elegans. NAR Genom Bioinform 2022; 4:lqac031. [PMID: 35464238 PMCID: PMC9022459 DOI: 10.1093/nargab/lqac031] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 03/30/2022] [Accepted: 04/13/2022] [Indexed: 12/24/2022] Open
Abstract
Genes embed their evolutionary history in the form of various alleles. Presence-absence variants (PAVs) are extreme cases of such alleles, where a gene present in one haplotype does not exist in another. Because PAVs may result from either birth or death of a gene, PAV genes and their alternative alleles, if available, can represent a basis for rapid intraspecific gene evolution. Using long-read sequencing technologies, this study traced the possible evolution of PAV genes in the PD1074 and CB4856 C. elegans strains as well as their alternative alleles in 14 other wild strains. We updated the CB4856 genome by filling 18 gaps and identified 46 genes and 7,460 isoforms from both strains not annotated previously. We verified 328 PAV genes, out of which 46 were C. elegans-specific. Among these possible newly born genes, 12 had alternative alleles in other wild strains; in particular, the alternative alleles of three genes showed signatures of active transposons. Alternative alleles of three other genes showed another type of signature reflected in accumulation of small insertions or deletions. Research on gene evolution using both species-specific PAV genes and their alternative alleles may provide new insights into the process of gene evolution.
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Affiliation(s)
- Bo Yun Lee
- Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Korea
| | - Jun Kim
- Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Korea
| | - Junho Lee
- Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Korea
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25
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Stevens L, Moya ND, Tanny RE, Gibson SB, Tracey A, Na H, Chitrakar R, Dekker J, Walhout AJ, Baugh LR, Andersen EC. Chromosome-level reference genomes for two strains of Caenorhabditis briggsae: an improved platform for comparative genomics. Genome Biol Evol 2022; 14:6554914. [PMID: 35348662 PMCID: PMC9011032 DOI: 10.1093/gbe/evac042] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
The publication of the Caenorhabditis briggsae reference genome in 2003 enabled the first comparative genomics studies between C. elegans and C. briggsae, shedding light on the evolution of genome content and structure in the Caenorhabditis genus. However, despite being widely used, the currently available C. briggsae reference genome is substantially less complete and structurally accurate than the C. elegans reference genome. Here, we used high-coverage Oxford Nanopore long-read and chromosome conformation capture data to generate chromosome-level reference genomes for two C. briggsae strains: QX1410, a new reference strain closely related to the laboratory AF16 strain, and VX34, a highly divergent strain isolated in China. We also sequenced 99 recombinant inbred lines (RILs) generated from reciprocal crosses between QX1410 and VX34 to create a recombination map and identify chromosomal domains. Additionally, we used both short- and long-read RNA sequencing (RNA-seq) data to generate high-quality gene annotations. By comparing these new reference genomes to the current reference, we reveal that hyper-divergent haplotypes cover large portions of the C. briggsae genome, similar to recent reports in C. elegans and C. tropicalis. We also show that the genomes of selfing Caenorhabditis species have undergone more rearrangement than their outcrossing relatives, which has biased previous estimates of rearrangement rate in Caenorhabditis. These new genomes provide a substantially improved platform for comparative genomics in Caenorhabditis and narrow the gap between the quality of genomic resources available for C. elegans and C. briggsae.
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Affiliation(s)
- Lewis Stevens
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Nicolas D. Moya
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
| | - Robyn E. Tanny
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Sophia B. Gibson
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Huimin Na
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Albertha J.M. Walhout
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - L. Ryan Baugh
- Department of Biology, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Erik C. Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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26
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Crombie TA, Battlay P, Tanny RE, Evans KS, Buchanan CM, Cook DE, Dilks CM, Stinson LA, Zdraljevic S, Zhang G, Roberto NM, Lee D, Ailion M, Hodgins KA, Andersen EC. Local adaptation and spatiotemporal patterns of genetic diversity revealed by repeated sampling of Caenorhabditis elegans across the Hawaiian Islands. Mol Ecol 2022; 31:2327-2347. [PMID: 35167162 PMCID: PMC9306471 DOI: 10.1111/mec.16400] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/23/2022] [Accepted: 02/03/2022] [Indexed: 11/28/2022]
Abstract
The nematode Caenorhabditis elegans is among the most widely studied organisms, but relatively little is known about its natural ecology. Genetic diversity is low across much of the globe but high in the Hawaiian Islands and across the Pacific Rim. To characterize the niche and genetic diversity of C. elegans on the Hawaiian Islands and to explore how genetic diversity might be influenced by local adaptation, we repeatedly sampled nematodes over a three‐year period, measured various environmental parameters at each sampling site, and whole‐genome sequenced the C. elegans isolates that we identified. We found that the typical Hawaiian C. elegans niche comprises moderately moist native forests at high elevations (500–1,500 m) where ambient air temperatures are cool (15–20°C). Compared to other Caenorhabditis species found on the Hawaiian Islands (e.g., Caenorhabditis briggsae and Caenorhabditis tropicalis), we found that C. elegans were enriched in native habitats. We measured levels of genetic diversity and differentiation among Hawaiian C. elegans and found evidence of seven genetically distinct groups distributed across the islands. Then, we scanned these genomes for signatures of local adaptation and identified 18 distinct regions that overlap with hyper‐divergent regions, which may be maintained by balancing selection and are enriched for genes related to environmental sensing, xenobiotic detoxification, and pathogen resistance. These results provide strong evidence of local adaptation among Hawaiian C. elegans and contribute to our understanding of the forces that shape genetic diversity on the most remote volcanic archipelago in the world.
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Affiliation(s)
- Timothy A Crombie
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Paul Battlay
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Robyn E Tanny
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Kathryn S Evans
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Claire M Buchanan
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Daniel E Cook
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Clayton M Dilks
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Loraina A Stinson
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Stefan Zdraljevic
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Gaotian Zhang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Nicole M Roberto
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Daehan Lee
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Michael Ailion
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
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27
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Tintori SC, Sloat SA, Rockman MV. Rapid Isolation of Wild Nematodes by Baermann Funnel. J Vis Exp 2022:10.3791/63287. [PMID: 35156660 PMCID: PMC8857960 DOI: 10.3791/63287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023] Open
Abstract
Beyond being robust experimental model organisms, Caenorhabditis elegans and its relatives are also real animals that live in nature. Studies of wild nematodes in their natural environments are valuable for understanding many aspects of biology, including the selective regimes in which distinctive genomic and phenotypic characters evolve, the genetic basis for complex trait variation, and the natural genetic diversity fundamental to all animal populations. This manuscript describes a simple and efficient method for extracting nematodes from their natural substrates, including rotting fruits, flowers, fungi, leaf litter, and soil. The Baermann funnel method, a classical nematology technique, selectively isolates active nematodes from their substrates. Because it recovers nearly all active worms from the sample, the Baermann funnel technique allows for the recovery of rare and slow-growing genotypes that co-occur with abundant and fast-growing genotypes, which might be missed in extraction methods that involve multiple generations of reproduction. The technique is also well suited to addressing metagenetic, population-genetic, and ecological questions. It captures the entire population in a sample simultaneously, allowing an unbiased view of the natural distribution of ages, sexes, and genotypes. The protocol allows for deployment at scale in the field, rapidly converting substrates into worm plates, and the authors have validated it through fieldwork on multiple continents.
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Affiliation(s)
- Sophia C Tintori
- Department of Biology and Center for Genomics & Systems Biology, New York University
| | - Solomon A Sloat
- Department of Biology and Center for Genomics & Systems Biology, New York University
| | - Matthew V Rockman
- Department of Biology and Center for Genomics & Systems Biology, New York University;
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28
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van Sluijs L, Bosman KJ, Pankok F, Blokhina T, Wilten JIHA, te Molder DM, Riksen JAG, Snoek BL, Pijlman GP, Kammenga JE, Sterken MG. Balancing Selection of the Intracellular Pathogen Response in Natural Caenorhabditis elegans Populations. Front Cell Infect Microbiol 2022; 11:758331. [PMID: 35174100 PMCID: PMC8841876 DOI: 10.3389/fcimb.2021.758331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/21/2021] [Indexed: 12/17/2022] Open
Abstract
Genetic variation in host populations may lead to differential viral susceptibilities. Here, we investigate the role of natural genetic variation in the Intracellular Pathogen Response (IPR), an important antiviral pathway in the model organism Caenorhabditis elegans against Orsay virus (OrV). The IPR involves transcriptional activity of 80 genes including the pals-genes. We examine the genetic variation in the pals-family for traces of selection and explore the molecular and phenotypic effects of having distinct pals-gene alleles. Genetic analysis of 330 global C. elegans strains reveals that genetic diversity within the IPR-related pals-genes can be categorized in a few haplotypes worldwide. Importantly, two key IPR regulators, pals-22 and pals-25, are in a genomic region carrying signatures of balancing selection, suggesting that different evolutionary strategies exist in IPR regulation. We infected eleven C. elegans strains that represent three distinct pals-22 pals-25 haplotypes with Orsay virus to determine their susceptibility. For two of these strains, N2 and CB4856, the transcriptional response to infection was also measured. The results indicate that pals-22 pals-25 haplotype shapes the defense against OrV and host genetic variation can result in constitutive activation of IPR genes. Our work presents evidence for balancing genetic selection of immunity genes in C. elegans and provides a novel perspective on the functional diversity that can develop within a main antiviral response in natural host populations.
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Affiliation(s)
- Lisa van Sluijs
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
- Laboratory of Virology, Wageningen University and Research, Wageningen, Netherlands
| | - Kobus J. Bosman
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Frederik Pankok
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Tatiana Blokhina
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Jop I. H. A. Wilten
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Dennie M. te Molder
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Joost A. G. Riksen
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Basten L. Snoek
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Gorben P. Pijlman
- Laboratory of Virology, Wageningen University and Research, Wageningen, Netherlands
| | - Jan E. Kammenga
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Mark G. Sterken
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
- Laboratory of Virology, Wageningen University and Research, Wageningen, Netherlands
- *Correspondence: Mark G. Sterken,
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29
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Teterina AA, Coleman-Hulbert AL, Banse SA, Willis JH, Perez VI, Lithgow GJ, Driscoll M, Phillips PC. Genetic diversity estimates for the Caenorhabditis Intervention Testing Program screening panel. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000518. [PMID: 35098051 PMCID: PMC8796004 DOI: 10.17912/micropub.biology.000518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/15/2021] [Accepted: 01/11/2022] [Indexed: 11/06/2022]
Abstract
The Caenorhabditis Intervention Testing Program (CITP) was founded on the principle that compounds with positive effects across a genetically diverse test-set should have an increased probability of engaging conserved biochemical pathways with mammalian translational potential. To fulfill its mandate, the CITP uses a genetic diversity panel of Caenorhabditis strains for assaying longevity effects of candidate compounds. The panel comprises 22 strains from three different species, collected globally, to achieve inter-population genetic diversity. The three represented species, C. elegans, C. briggsae, and C. tropicalis, are all sequential hermaphrodites, which simplifies experimental procedures while maximizing intra-population homogeneity. Here, we present estimates of the genetic diversity encapsulated by the constituent strains in the panel based on their most recently published and publicly available whole-genome sequences, as well as two newly generated genomic data sets. We observed average genome-wide nucleotide diversity (π) within the C. elegans (1.2e-3), C. briggsae (7.5e-3), and C. tropicalis strains (2.6e-3) greater than estimates for human populations, and comparable to that found in mouse populations. Our analysis supports the assumption that the CITP screening panel encompasses broad genetic diversity, suggesting that lifespan-extending chemicals with efficacy across the panel should be enriched for interventions that function on conserved processes that are shared across genetic backgrounds. While the diversity panel was established by the CITP for studying longevity interventions, the panel may prove useful for the broader research community when seeking broadly efficacious interventions for any phenotype with potential genetic background effects.
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Affiliation(s)
- Anastasia A Teterina
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA,
Center of Parasitology, Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
| | | | - Stephen A Banse
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - John H Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Viviana I Perez
- Division of Aging Biology, National Institute on Aging, Bethesda, MD, 20892, USA
| | - Gordon J Lithgow
- The Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Monica Driscoll
- Rutgers University, Dept. of Molecular Biology and Biochemistry, Piscataway, NJ, 08854, USA
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA,
Correspondence to: Patrick C Phillips ()
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30
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Abstract
Wild populations of the model organism C. elegans represent a valuable resource, allowing for genetic characterization underlying natural phenotypic variation. Here we provide a simple protocol on how to sample and rapidly identify C. elegans wild isolates. We outline how to find suitable habitats and organic substrates, followed by describing isolation and identification of C. elegans live cultures based on easily recognizable morphological characteristics, molecular barcodes, and mating tests. This protocol uses standard laboratory equipment and requires little prior knowledge of C. elegans biology.
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Affiliation(s)
| | - Nausicaa Poullet
- Université Côte d'Azur, CNRS, Inserm, IBV, Nice, France
- URZ, INRAE, Petit-Bourg (Guadeloupe), France
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31
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Pujol N, Ewbank JJ. C. elegans: out on an evolutionary limb. Immunogenetics 2021; 74:63-73. [PMID: 34761293 DOI: 10.1007/s00251-021-01231-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/22/2021] [Indexed: 12/18/2022]
Abstract
The natural environment of the free-living nematode Caenorhabditis elegans is rich in pathogenic microbes. There is now ample evidence to indicate that these pathogens exert a strong selection pressure on C. elegans, and have shaped its genome, physiology, and behaviour. In this short review, we concentrate on how C. elegans stands out from other animals in terms of its immune repertoire and innate immune signalling pathways. We discuss how C. elegans often detects pathogens because of their effects on essential cellular processes, or organelle integrity, in addition to direct microbial recognition. We illustrate the extensive molecular plasticity that is characteristic of immune defences in C. elegans and highlight some remarkable instances of lineage-specific innovation in innate immune mechanisms.
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Affiliation(s)
- Nathalie Pujol
- Aix Marseille Univ, CNRS, INSERM, CIML, Turing Centre for Living Systems, Marseille, France.
| | - Jonathan J Ewbank
- Aix Marseille Univ, CNRS, INSERM, CIML, Turing Centre for Living Systems, Marseille, France
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32
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easyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application. PLoS One 2021; 16:e0254293. [PMID: 34613959 PMCID: PMC8494344 DOI: 10.1371/journal.pone.0254293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/21/2021] [Indexed: 11/23/2022] Open
Abstract
Large-scale ecological sampling can be difficult and costly, especially for organisms that are too small to be easily identified in a natural environment by eye. Typically, these microscopic floral and fauna are sampled by collecting substrates from nature and then separating organisms from substrates in the laboratory. In many cases, diverse organisms can be identified to the species-level using molecular barcodes. To facilitate large-scale ecological sampling of microscopic organisms, we used a geographic data-collection platform for mobile devices called Fulcrum that streamlines the organization of geospatial sampling data, substrate photographs, and environmental data at natural sampling sites. These sampling data are then linked to organism isolation data from the laboratory. Here, we describe the easyFulcrum R package, which can be used to clean, process, and visualize ecological field sampling and isolation data exported from the Fulcrum mobile application. We developed this package for wild nematode sampling, but it can be used with other organisms. The advantages of using Fulcrum combined with easyFulcrum are (1) the elimination of transcription errors by replacing manual data entry and/or spreadsheets with a mobile application, (2) the ability to clean, process, and visualize sampling data using a standardized set of functions in the R software environment, and (3) the ability to join disparate data to each other, including environmental data from the field and the molecularly defined identities of individual specimens isolated from samples.
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33
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Gilbert KJ, Zdraljevic S, Cook DE, Cutter AD, Andersen EC, Baer CF. The distribution of mutational effects on fitness in Caenorhabditis elegans inferred from standing genetic variation. Genetics 2021; 220:6383146. [PMID: 34791202 DOI: 10.1093/genetics/iyab166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/27/2021] [Indexed: 11/14/2022] Open
Abstract
The distribution of fitness effects (DFE) for new mutations is one of the most theoretically important but difficult to estimate properties in population genetics. A crucial challenge to inferring the DFE from natural genetic variation is the sensitivity of the site frequency spectrum to factors like population size change, population substructure, genome structure, and nonrandom mating. Although inference methods aim to control for population size changes, the influence of nonrandom mating remains incompletely understood, despite being a common feature of many species. We report the DFE estimated from 326 genomes of Caenorhabditis elegans, a nematode roundworm with a high rate of self-fertilization. We evaluate the robustness of DFE inferences using simulated data that mimics the genomic structure and reproductive life history of C. elegans. Our observations demonstrate how the combined influence of self-fertilization, genome structure, and natural selection on linked sites can conspire to compromise estimates of the DFE from extant polymorphisms with existing methods. These factors together tend to bias inferences toward weakly deleterious mutations, making it challenging to have full confidence in the inferred DFE of new mutations as deduced from standing genetic variation in species like C. elegans. Improved methods for inferring the DFE are needed to appropriately handle strong linked selection and selfing. These results highlight the importance of understanding the combined effects of processes that can bias our interpretations of evolution in natural populations.
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Affiliation(s)
| | - Stefan Zdraljevic
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.,Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, USA
| | - Daniel E Cook
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Asher D Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Charles F Baer
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA.,University of Florida Genetics Institute, Gainesville, FL 32611, USA
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34
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Mattick J, Libro S, Bromley R, Chaicumpa W, Chung M, Cook D, Khan MB, Kumar N, Lau YL, Misra-Bhattacharya S, Rao R, Sadzewicz L, Saeung A, Shahab M, Sparklin BC, Steven A, Turner JD, Tallon LJ, Taylor MJ, Moorhead AR, Michalski M, Foster JM, Dunning Hotopp JC. X-treme loss of sequence diversity linked to neo-X chromosomes in filarial nematodes. PLoS Negl Trop Dis 2021; 15:e0009838. [PMID: 34705823 PMCID: PMC8575316 DOI: 10.1371/journal.pntd.0009838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 11/08/2021] [Accepted: 09/24/2021] [Indexed: 11/19/2022] Open
Abstract
The sequence diversity of natural and laboratory populations of Brugia pahangi and Brugia malayi was assessed with Illumina resequencing followed by mapping in order to identify single nucleotide variants and insertions/deletions. In natural and laboratory Brugia populations, there is a lack of sequence diversity on chromosome X relative to the autosomes (πX/πA = 0.2), which is lower than the expected (πX/πA = 0.75). A reduction in diversity is also observed in other filarial nematodes with neo-X chromosome fusions in the genera Onchocerca and Wuchereria, but not those without neo-X chromosome fusions in the genera Loa and Dirofilaria. In the species with neo-X chromosome fusions, chromosome X is abnormally large, containing a third of the genetic material such that a sizable portion of the genome is lacking sequence diversity. Such profound differences in genetic diversity can be consequential, having been associated with drug resistance and adaptability, with the potential to affect filarial eradication.
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Affiliation(s)
- John Mattick
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
| | - Silvia Libro
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Robin Bromley
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
| | - Wanpen Chaicumpa
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Matthew Chung
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
| | - Darren Cook
- Centre for Neglected Tropical Diseases, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Mohammad Behram Khan
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Nikhil Kumar
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
| | - Yee-Ling Lau
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Ramakrishna Rao
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Lisa Sadzewicz
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
| | - Atiporn Saeung
- Center of Insect Vector Study, Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Mohd Shahab
- Division of Parasitology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Benjamin C. Sparklin
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
| | - Andrew Steven
- Centre for Neglected Tropical Diseases, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Joseph D. Turner
- Centre for Neglected Tropical Diseases, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Luke J. Tallon
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
| | - Mark J. Taylor
- Centre for Neglected Tropical Diseases, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Andrew R. Moorhead
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Michelle Michalski
- University of Wisconsin Oshkosh, Oshkosh, Wisconsin, United States of America
| | - Jeremy M. Foster
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Julie C. Dunning Hotopp
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland, Baltimore, Maryland, United States of America
- Greenebaum Cancer Center, University of Maryland, Baltimore, Maryland, United States of America
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35
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Lim J, Kim J, Lee J. Natural variation in reproductive timing and X-chromosome non-disjunction in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2021; 11:6373895. [PMID: 34550364 PMCID: PMC8664432 DOI: 10.1093/g3journal/jkab327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 09/02/2021] [Indexed: 11/12/2022]
Abstract
Caenorhabditis elegans hermaphrodites first produce a limited number of sperm cells, before their germline switches to oogenesis. Production of progeny then ensues until sperm is depleted. Male production in the self-progeny of hermaphrodites occurs following X-chromosome non-disjunction during gametogenesis, and in the reference strain increases with age of the hermaphrodite parent. To enhance our understanding of the reproductive timecourse in Caenorhabditis elegans, we measured and compared progeny production and male proportion during the early and late reproductive periods of hermaphrodites for 96 wild Caenorhabditis elegans strains. We found that the two traits exhibited natural phenotypic variation with few outliers and a similar reproductive timing pattern as previous reports. Progeny number and male proportion were not correlated in the wild isolates, implying that isolates with a large brood size did not produce males at a higher rate. We also identified loci and candidate genetic variants significantly associated with male-production rate in the late and total reproductive periods. Our results provide an insight into life history traits in wild Caenorhabditis elegans strains.
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Affiliation(s)
- Jiseon Lim
- Department of Biological Sciences, Seoul National University, Seoul, Korea 08826.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea 08826
| | - Jun Kim
- Department of Biological Sciences, Seoul National University, Seoul, Korea 08826.,Research Institute of Basic Sciences, Seoul National University, Seoul, Korea 08826
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Seoul, Korea 08826.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea 08826.,Research Institute of Basic Sciences, Seoul National University, Seoul, Korea 08826
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36
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Wang W, Flury AG, Garrison JL, Brem RB. Cold Survival and Its Molecular Mechanisms in a Locally Adapted Nematode Population. Genome Biol Evol 2021; 13:evab188. [PMID: 34383891 PMCID: PMC8449824 DOI: 10.1093/gbe/evab188] [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] [Accepted: 08/09/2021] [Indexed: 11/25/2022] Open
Abstract
Since Darwin, evolutionary biologists have sought to understand the drivers and mechanisms of natural trait diversity. The field advances toward this goal with the discovery of phenotypes that vary in the wild, their relationship to ecology, and their underlying genes. Here, we established resistance to extreme low temperature in the free-living nematode Caenorhabditis briggsae as an ecological and evolutionary model system. We found that C. briggsae strains of temperate origin were strikingly more cold-resistant than those isolated from tropical localities. Transcriptional profiling revealed expression patterns unique to the resistant temperate ecotype, including dozens of genes expressed at high levels even after multiple days of cold-induced physiological slowdown. Mutational analysis validated a role in cold resistance for seven such genes. These findings highlight a candidate case of robust, genetically complex adaptation in an emerging model nematode, and shed light on the mechanisms at play.
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Affiliation(s)
- Wenke Wang
- Buck Institute for Research on Aging, Novato, California, USA
- Department of Plant and Microbial Biology, UC Berkeley, USA
| | - Anna G Flury
- Buck Institute for Research on Aging, Novato, California, USA
- Department of Plant and Microbial Biology, UC Berkeley, USA
| | - Jennifer L Garrison
- Buck Institute for Research on Aging, Novato, California, USA
- Leonard Davis School of Gerontology, University of Southern California, USA
- Department of Cellular and Molecular Pharmacology, UC San Francisco, USA
- Global Consortium for Reproductive Longevity & Equality, Novato, California, USA
| | - Rachel B Brem
- Buck Institute for Research on Aging, Novato, California, USA
- Department of Plant and Microbial Biology, UC Berkeley, USA
- Leonard Davis School of Gerontology, University of Southern California, USA
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37
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Zhang G, Mostad JD, Andersen EC. Natural variation in fecundity is correlated with species-wide levels of divergence in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2021; 11:jkab168. [PMID: 33983439 PMCID: PMC8496234 DOI: 10.1093/g3journal/jkab168] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/03/2021] [Indexed: 01/08/2023]
Abstract
Life history traits underlie the fitness of organisms and are under strong natural selection. A new mutation that positively impacts a life history trait will likely increase in frequency and become fixed in a population (e.g., a selective sweep). The identification of the beneficial alleles that underlie selective sweeps provides insights into the mechanisms that occurred during the evolution of a species. In the global population of Caenorhabditis elegans, we previously identified selective sweeps that have drastically reduced chromosomal-scale genetic diversity in the species. Here, we measured the fecundity of 121 wild C. elegans strains, including many recently isolated divergent strains from the Hawaiian islands and found that strains with larger swept genomic regions have significantly higher fecundity than strains without evidence of the recent selective sweeps. We used genome-wide association (GWA) mapping to identify three quantitative trait loci (QTL) underlying the fecundity variation. In addition, we mapped previous fecundity data from wild C. elegans strains and C. elegans recombinant inbred advanced intercross lines that were grown in various conditions and detected eight QTL using GWA and linkage mappings. These QTL show the genetic complexity of fecundity across this species. Moreover, the haplotype structure in each GWA QTL region revealed correlations with recent selective sweeps in the C. elegans population. North American and European strains had significantly higher fecundity than most strains from Hawaii, a hypothesized origin of the C. elegans species, suggesting that beneficial alleles that caused increased fecundity could underlie the selective sweeps during the worldwide expansion of C. elegans.
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Affiliation(s)
- Gaotian Zhang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Jake D Mostad
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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38
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Wit J, Rodriguez BC, Andersen EC. Natural variation in Caenorhabditis elegans responses to the anthelmintic emodepside. Int J Parasitol Drugs Drug Resist 2021; 16:1-8. [PMID: 33878514 PMCID: PMC8079822 DOI: 10.1016/j.ijpddr.2021.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 11/19/2022]
Abstract
Treatment of parasitic nematode infections depends primarily on the use of anthelmintics. However, this drug arsenal is limited, and resistance against most anthelmintics is widespread. Emodepside is a new anthelmintic drug effective against gastrointestinal and filarial nematodes. Nematodes that are resistant to other anthelmintic drug classes are susceptible to emodepside, indicating that the emodepside mode of action is distinct from previous anthelmintics. The laboratory-adapted Caenorhabditis elegans strain N2 is sensitive to emodepside, and genetic selection and in vitro experiments implicated slo-1, a large K+ conductance (BK) channel gene, in emodepside mode of action. In an effort to understand how natural populations will respond to emodepside, we measured brood sizes and developmental rates of wild C. elegans strains after exposure to the drug and found natural variation across the species. Some of the observed variation in C. elegans emodepside responses correlates with amino acid substitutions in slo-1, but genetic mechanisms other than slo-1 coding variants likely underlie emodepside resistance in wild C. elegans strains. Additionally, the assayed strains have higher offspring production in low concentrations of emodepside (a hormetic effect). We find that natural variation affects emodepside sensitivity, supporting the suitability of C. elegans as a model system to study emodepside responses across natural nematode populations.
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Affiliation(s)
- Janneke Wit
- Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Briana C Rodriguez
- Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Erik C Andersen
- Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.
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39
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Noble LM, Rockman MV, Teotónio H. Gene-level quantitative trait mapping in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2021; 11:6114457. [PMID: 33693602 PMCID: PMC8022935 DOI: 10.1093/g3journal/jkaa061] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 12/13/2020] [Indexed: 02/06/2023]
Abstract
The Caenorhabditis elegans multiparental experimental evolution (CeMEE) panel is a collection of genome-sequenced, cryopreserved recombinant inbred lines useful for mapping the evolution and genetic basis of quantitative traits. We have expanded the resource with new lines and new populations, and here report the genotype and haplotype composition of CeMEE version 2, including a large set of putative de novo mutations, and updated additive and epistatic mapping simulations. Additive quantitative trait loci explaining 4% of trait variance are detected with >80% power, and the median detection interval approaches single-gene resolution on the highly recombinant chromosome arms. Although CeMEE populations are derived from a long-term evolution experiment, genetic structure is dominated by variation present in the ancestral population.
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Affiliation(s)
- Luke M Noble
- Institut de Biologie, École Normale Supérieure, CNRS 8197, Inserm U1024, PSL Research University, F-75005 Paris, France.,Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Matthew V Rockman
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Henrique Teotónio
- Institut de Biologie, École Normale Supérieure, CNRS 8197, Inserm U1024, PSL Research University, F-75005 Paris, France
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40
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Evans KS, van Wijk MH, McGrath PT, Andersen EC, Sterken MG. From QTL to gene: C. elegans facilitates discoveries of the genetic mechanisms underlying natural variation. Trends Genet 2021; 37:933-947. [PMID: 34229867 DOI: 10.1016/j.tig.2021.06.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 11/15/2022]
Abstract
Although many studies have examined quantitative trait variation across many species, only a small number of genes and thereby molecular mechanisms have been discovered. Without these data, we can only speculate about evolutionary processes that underlie trait variation. Here, we review how quantitative and molecular genetics in the nematode Caenorhabditis elegans led to the discovery and validation of 37 quantitative trait genes over the past 15 years. Using these data, we can start to make inferences about evolution from these quantitative trait genes, including the roles that coding versus noncoding variation, gene family expansion, common versus rare variants, pleiotropy, and epistasis play in trait variation across this species.
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Affiliation(s)
- Kathryn S Evans
- Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
| | - Marijke H van Wijk
- Laboratory of Nematology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Patrick T McGrath
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Erik C Andersen
- Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands.
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41
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Lee D, Zdraljevic S, Stevens L, Wang Y, Tanny RE, Crombie TA, Cook DE, Webster AK, Chirakar R, Baugh LR, Sterken MG, Braendle C, Félix MA, Rockman MV, Andersen EC. Balancing selection maintains hyper-divergent haplotypes in Caenorhabditis elegans. Nat Ecol Evol 2021; 5:794-807. [PMID: 33820969 PMCID: PMC8202730 DOI: 10.1038/s41559-021-01435-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 02/26/2021] [Indexed: 12/16/2022]
Abstract
Across diverse taxa, selfing species have evolved independently from outcrossing species thousands of times. The transition from outcrossing to selfing decreases the effective population size, effective recombination rate and heterozygosity within a species. These changes lead to a reduction in genetic diversity, and therefore adaptive potential, by intensifying the effects of random genetic drift and linked selection. Within the nematode genus Caenorhabditis, selfing has evolved at least three times, and all three species, including the model organism Caenorhabditis elegans, show substantially reduced genetic diversity relative to outcrossing species. Selfing and outcrossing Caenorhabditis species are often found in the same niches, but we still do not know how selfing species with limited genetic diversity can adapt to these environments. Here, we examine the whole-genome sequences from 609 wild C. elegans strains isolated worldwide and show that genetic variation is concentrated in punctuated hyper-divergent regions that cover 20% of the C. elegans reference genome. These regions are enriched in environmental response genes that mediate sensory perception, pathogen response and xenobiotic stress response. Population genomic evidence suggests that genetic diversity in these regions has been maintained by long-term balancing selection. Using long-read genome assemblies for 15 wild strains, we show that hyper-divergent haplotypes contain unique sets of genes and show levels of divergence comparable to levels found between Caenorhabditis species that diverged millions of years ago. These results provide an example of how species can avoid the evolutionary dead end associated with selfing.
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Affiliation(s)
- Daehan Lee
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Stefan Zdraljevic
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
- Department of Human Genetics, University of California, Los Angeles, CA, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, USA
| | - Lewis Stevens
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Ye Wang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, People's Republic of China
| | - Robyn E Tanny
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Timothy A Crombie
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Daniel E Cook
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Amy K Webster
- Department of Biology, Duke University, Durham, NC, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | | | - L Ryan Baugh
- Department of Biology, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University and Research, Wageningen, the Netherlands
| | | | - Marie-Anne Félix
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, INSERM, École Normale Supérieure, Paris Sciences et Lettres, Paris, France
| | - Matthew V Rockman
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
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42
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Koneru SL, Hintze M, Katsanos D, Barkoulas M. Cryptic genetic variation in a heat shock protein modifies the outcome of a mutation affecting epidermal stem cell development in C. elegans. Nat Commun 2021; 12:3263. [PMID: 34059684 PMCID: PMC8166903 DOI: 10.1038/s41467-021-23567-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 04/29/2021] [Indexed: 12/13/2022] Open
Abstract
A fundamental question in medical genetics is how the genetic background modifies the phenotypic outcome of mutations. We address this question by focusing on the seam cells, which display stem cell properties in the epidermis of Caenorhabditis elegans. We demonstrate that a putative null mutation in the GATA transcription factor egl-18, which is involved in seam cell fate maintenance, is more tolerated in the CB4856 isolate from Hawaii than the lab reference strain N2 from Bristol. We identify multiple quantitative trait loci (QTLs) underlying the difference in phenotype expressivity between the two isolates. These QTLs reveal cryptic genetic variation that reinforces seam cell fate through potentiating Wnt signalling. Within one QTL region, a single amino acid deletion in the heat shock protein HSP-110 in CB4856 is sufficient to modify Wnt signalling and seam cell development, highlighting that natural variation in conserved heat shock proteins can shape phenotype expressivity. How the genetic background modifies the expression of mutations is a key question that is addressed in this study in the context of seam cell development in Caenorhabditis elegans isolates. One amino acid deletion in a conserved heat shock protein is sufficient to shape phenotype expressivity upon mutation of a GATA transcription factor.
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Affiliation(s)
- Sneha L Koneru
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Mark Hintze
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Dimitris Katsanos
- Department of Life Sciences, Imperial College, London, United Kingdom
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43
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Calcino AD, Kenny NJ, Gerdol M. Single individual structural variant detection uncovers widespread hemizygosity in molluscs. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200153. [PMID: 33813894 PMCID: PMC8059565 DOI: 10.1098/rstb.2020.0153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2021] [Indexed: 11/12/2022] Open
Abstract
The advent of complete genomic sequencing has opened a window into genomic phenomena obscured by fragmented assemblies. A good example of these is the existence of hemizygous regions of autosomal chromosomes, which can result in marked differences in gene content between individuals within species. While these hemizygous regions, and presence/absence variation of genes that can result, are well known in plants, firm evidence has only recently emerged for their existence in metazoans. Here, we use recently published, complete genomes from wild-caught molluscs to investigate the prevalence of hemizygosity across a well-known and ecologically important clade. We show that hemizygous regions are widespread in mollusc genomes, not clustered in individual chromosomes, and often contain genes linked to transposition, DNA repair and stress response. With targeted investigations of HSP70-12 and C1qDC, we also show how individual gene families are distributed within pan-genomes. This work suggests that extensive pan-genomes are widespread across the conchiferan Mollusca, and represent useful tools for genomic evolution, allowing the maintenance of additional genetic diversity within the population. As genomic sequencing and re-sequencing becomes more routine, the prevalence of hemizygosity, and its impact on selection and adaptation, are key targets for research across the tree of life. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Affiliation(s)
- Andrew D. Calcino
- Department of Evolutionary Biology, Integrative Zoology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Nathan J. Kenny
- Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
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44
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Le TS, Nguyen TTH, Thi Mai Huong B, Nguyen HG, Ha BH, Nguyen VS, Nguyen MH, Nguyen HH, Wang J. Cultivation of Caenorhabditis elegans on new cheap monoxenic media without peptone. J Nematol 2021; 53:e2021-36. [PMID: 33860269 PMCID: PMC8040142 DOI: 10.21307/jofnem-2021-036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Indexed: 01/30/2023] Open
Abstract
The study of species biodiversity within the Caenorhabditis genus of nematodes would be facilitated by the isolation of as many species as possible. So far, over 50 species have been found, usually associated with decaying vegetation or soil samples, with many from Africa, South America and Southeast Asia. Scientists based in these regions can contribute to Caenorhabditis sampling and their proximity would allow intensive sampling, which would be useful for understanding the natural history of these species. However, severely limited research budgets are often a constraint for these local scientists. In this study, we aimed to find a more economical, alternative growth media to rear Caenorhabditis and related species. We tested 25 media permutations using cheaper substitutes for the reagents found in the standard nematode growth media (NGM) and found three media combinations that performed comparably to NGM with respect to the reproduction and longevity of C. elegans. These new media should facilitate the isolation and characterization of Caenorhabditis and other free-living nematodes for the researchers in the poorer regions such as Africa, South America, and Southeast Asia where nematode diversity appears high.
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Affiliation(s)
- Tho Son Le
- College of Forestry Biotechnology, Vietnam National University of Forestry, Hanoi, Vietnam
| | - T. T. Hang Nguyen
- College of Forestry Biotechnology, Vietnam National University of Forestry, Hanoi, Vietnam
| | - Bui Thi Mai Huong
- College of Forestry Biotechnology, Vietnam National University of Forestry, Hanoi, Vietnam
| | - H. Gam Nguyen
- College of Forestry Biotechnology, Vietnam National University of Forestry, Hanoi, Vietnam
| | - B. Hong Ha
- College of Forestry Biotechnology, Vietnam National University of Forestry, Hanoi, Vietnam
| | - Van Sang Nguyen
- Faculty of Biology, VNU University of Science, Vietnam National University, Hanoi, Vietnam
| | - Minh Hung Nguyen
- Center for Molecular Biology, Institute of Research and Development, Duy Tan University, Da Nang, Vietnam
| | - Huy-Hoang Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - John Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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45
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Evans KS, Wit J, Stevens L, Hahnel SR, Rodriguez B, Park G, Zamanian M, Brady SC, Chao E, Introcaso K, Tanny RE, Andersen EC. Two novel loci underlie natural differences in Caenorhabditis elegans abamectin responses. PLoS Pathog 2021; 17:e1009297. [PMID: 33720993 PMCID: PMC7993787 DOI: 10.1371/journal.ppat.1009297] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/25/2021] [Accepted: 03/02/2021] [Indexed: 11/18/2022] Open
Abstract
Parasitic nematodes cause a massive worldwide burden on human health along with a loss of livestock and agriculture productivity. Anthelmintics have been widely successful in treating parasitic nematodes. However, resistance is increasing, and little is known about the molecular and genetic causes of resistance for most of these drugs. The free-living roundworm Caenorhabditis elegans provides a tractable model to identify genes that underlie resistance. Unlike parasitic nematodes, C. elegans is easy to maintain in the laboratory, has a complete and well annotated genome, and has many genetic tools. Using a combination of wild isolates and a panel of recombinant inbred lines constructed from crosses of two genetically and phenotypically divergent strains, we identified three genomic regions on chromosome V that underlie natural differences in response to the macrocyclic lactone (ML) abamectin. One locus was identified previously and encodes an alpha subunit of a glutamate-gated chloride channel (glc-1). Here, we validate and narrow two novel loci using near-isogenic lines. Additionally, we generate a list of prioritized candidate genes identified in C. elegans and in the parasite Haemonchus contortus by comparison of ML resistance loci. These genes could represent previously unidentified resistance genes shared across nematode species and should be evaluated in the future. Our work highlights the advantages of using C. elegans as a model to better understand ML resistance in parasitic nematodes.
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Affiliation(s)
- Kathryn S. Evans
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois, United States of America
| | - Janneke Wit
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Lewis Stevens
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Steffen R. Hahnel
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Briana Rodriguez
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Grace Park
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Mostafa Zamanian
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Shannon C. Brady
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois, United States of America
| | - Ellen Chao
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Katherine Introcaso
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Robyn E. Tanny
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Erik C. Andersen
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- * E-mail:
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46
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Ma F, Lau CY, Zheng C. Large genetic diversity and strong positive selection in F-box and GPCR genes among the wild isolates of Caenorhabditis elegans. Genome Biol Evol 2021; 13:6163285. [PMID: 33693740 PMCID: PMC8120010 DOI: 10.1093/gbe/evab048] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 02/17/2021] [Accepted: 03/03/2021] [Indexed: 01/05/2023] Open
Abstract
The F-box and chemosensory GPCR (csGPCR) gene families are greatly expanded in nematodes, including the model organism Caenorhabditis elegans, compared with insects and vertebrates. However, the intraspecific evolution of these two gene families in nematodes remain unexamined. In this study, we analyzed the genomic sequences of 330 recently sequenced wild isolates of C. elegans using a range of population genetics approaches. We found that F-box and csGPCR genes, especially the Srw family csGPCRs, showed much more diversity than other gene families. Population structure analysis and phylogenetic analysis divided the wild strains into eight non-Hawaiian and three Hawaiian subpopulations. Some Hawaiian strains appeared to be more ancestral than all other strains. F-box and csGPCR genes maintained a great amount of the ancestral variants in the Hawaiian subpopulation and their divergence among the non-Hawaiian subpopulations contributed significantly to population structure. F-box genes are mostly located at the chromosomal arms and high recombination rate correlates with their large polymorphism. Moreover, using both neutrality tests and extended haplotype homozygosity analysis, we identified signatures of strong positive selection in the F-box and csGPCR genes among the wild isolates, especially in the non-Hawaiian population. Accumulation of high-frequency-derived alleles in these genes was found in non-Hawaiian population, leading to divergence from the ancestral genotype. In summary, we found that F-box and csGPCR genes harbor a large pool of natural variants, which may be subjected to positive selection. These variants are mostly mapped to the substrate-recognition domains of F-box proteins and the extracellular and intracellular regions of csGPCRs, possibly resulting in advantages during adaptation by affecting protein degradation and the sensing of environmental cues, respectively.
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Affiliation(s)
- Fuqiang Ma
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Chun Yin Lau
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Chaogu Zheng
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
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47
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Hartman JH, Widmayer SJ, Bergemann CM, King DE, Morton KS, Romersi RF, Jameson LE, Leung MCK, Andersen EC, Taubert S, Meyer JN. Xenobiotic metabolism and transport in Caenorhabditis elegans. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART B, CRITICAL REVIEWS 2021; 24:51-94. [PMID: 33616007 PMCID: PMC7958427 DOI: 10.1080/10937404.2021.1884921] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Caenorhabditis elegans has emerged as a major model in biomedical and environmental toxicology. Numerous papers on toxicology and pharmacology in C. elegans have been published, and this species has now been adopted by investigators in academic toxicology, pharmacology, and drug discovery labs. C. elegans has also attracted the interest of governmental regulatory agencies charged with evaluating the safety of chemicals. However, a major, fundamental aspect of toxicological science remains underdeveloped in C. elegans: xenobiotic metabolism and transport processes that are critical to understanding toxicokinetics and toxicodynamics, and extrapolation to other species. The aim of this review was to initially briefly describe the history and trajectory of the use of C. elegans in toxicological and pharmacological studies. Subsequently, physical barriers to chemical uptake and the role of the worm microbiome in xenobiotic transformation were described. Then a review of what is and is not known regarding the classic Phase I, Phase II, and Phase III processes was performed. In addition, the following were discussed (1) regulation of xenobiotic metabolism; (2) review of published toxicokinetics for specific chemicals; and (3) genetic diversity of these processes in C. elegans. Finally, worm xenobiotic transport and metabolism was placed in an evolutionary context; key areas for future research highlighted; and implications for extrapolating C. elegans toxicity results to other species discussed.
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Affiliation(s)
- Jessica H Hartman
- Nicholas School of the Environment, Duke University, Durham, North Carolina
| | - Samuel J Widmayer
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States
| | | | - Dillon E King
- Nicholas School of the Environment, Duke University, Durham, North Carolina
| | - Katherine S Morton
- Nicholas School of the Environment, Duke University, Durham, North Carolina
| | - Riccardo F Romersi
- Nicholas School of the Environment, Duke University, Durham, North Carolina
| | - Laura E Jameson
- School of Mathematical and Natural Sciences, Arizona State University - West Campus, Glendale, Arizona, United States
| | - Maxwell C K Leung
- School of Mathematical and Natural Sciences, Arizona State University - West Campus, Glendale, Arizona, United States
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States
| | - Stefan Taubert
- Dept. Of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, the University of British Colombia, Vancouver, BC, Canada
| | - Joel N Meyer
- Nicholas School of the Environment, Duke University, Durham, North Carolina
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48
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Noble LM, Yuen J, Stevens L, Moya N, Persaud R, Moscatelli M, Jackson JL, Zhang G, Chitrakar R, Baugh LR, Braendle C, Andersen EC, Seidel HS, Rockman MV. Selfing is the safest sex for Caenorhabditis tropicalis. eLife 2021; 10:e62587. [PMID: 33427200 PMCID: PMC7853720 DOI: 10.7554/elife.62587] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 01/08/2021] [Indexed: 12/30/2022] Open
Abstract
Mating systems have profound effects on genetic diversity and compatibility. The convergent evolution of self-fertilization in three Caenorhabditis species provides a powerful lens to examine causes and consequences of mating system transitions. Among the selfers, Caenorhabditis tropicalis is the least genetically diverse and most afflicted by outbreeding depression. We generated a chromosomal-scale genome for C. tropicalis and surveyed global diversity. Population structure is very strong, and islands of extreme divergence punctuate a genomic background that is highly homogeneous around the globe. Outbreeding depression in the laboratory is caused largely by multiple Medea-like elements, genetically consistent with maternal toxin/zygotic antidote systems. Loci with Medea activity harbor novel and duplicated genes, and their activity is modified by mito-nuclear background. Segregating Medea elements dramatically reduce fitness, and simulations show that selfing limits their spread. Frequent selfing in C. tropicalis may therefore be a strategy to avoid Medea-mediated outbreeding depression.
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Affiliation(s)
- Luke M Noble
- Department of Biology and Center for Genomics & Systems Biology, New York UniversityNew YorkUnited States
- Institute de Biologie, École Normale Supérieure, CNRS, InsermParisFrance
| | - John Yuen
- Department of Biology and Center for Genomics & Systems Biology, New York UniversityNew YorkUnited States
| | - Lewis Stevens
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Nicolas Moya
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Riaad Persaud
- Department of Biology and Center for Genomics & Systems Biology, New York UniversityNew YorkUnited States
| | - Marc Moscatelli
- Department of Biology and Center for Genomics & Systems Biology, New York UniversityNew YorkUnited States
| | - Jacqueline L Jackson
- Department of Biology and Center for Genomics & Systems Biology, New York UniversityNew YorkUnited States
| | - Gaotian Zhang
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | | | - L Ryan Baugh
- Department of Biology, Duke UniversityDurhamUnited States
| | - Christian Braendle
- Institut de Biologie Valrose, Université Côte d’Azur, CNRS, InsermNiceFrance
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Hannah S Seidel
- Department of Biology, Eastern Michigan UniversityYpsilantiUnited States
| | - Matthew V Rockman
- Department of Biology and Center for Genomics & Systems Biology, New York UniversityNew YorkUnited States
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49
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Wit J, Dilks CM, Andersen EC. Complementary Approaches with Free-living and Parasitic Nematodes to Understanding Anthelmintic Resistance. Trends Parasitol 2020; 37:240-250. [PMID: 33317926 DOI: 10.1016/j.pt.2020.11.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/11/2022]
Abstract
Anthelmintic drugs are the major line of defense against parasitic nematode infections, but the arsenal is limited and resistance threatens sustained efficacy of the available drugs. Discoveries of the modes of action of these drugs and mechanisms of resistance have predominantly come from studies of a related nonparasitic nematode species, Caenorhabditis elegans, and the parasitic nematode Haemonchus contortus. Here, we discuss how our understanding of anthelmintic resistance and modes of action came from the interplay of results from each of these species. We argue that this 'cycle of discovery', where results from one species inform the design of experiments in the other, can use the complementary strengths of both to understand anthelmintic modes of action and mechanisms of resistance.
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Affiliation(s)
- Janneke Wit
- Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Clayton M Dilks
- Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
| | - Erik C Andersen
- Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
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50
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Evans KS, Zdraljevic S, Stevens L, Collins K, Tanny RE, Andersen EC. Natural variation in the sequestosome-related gene, sqst-5, underlies zinc homeostasis in Caenorhabditis elegans. PLoS Genet 2020; 16:e1008986. [PMID: 33175833 PMCID: PMC7682890 DOI: 10.1371/journal.pgen.1008986] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 11/23/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022] Open
Abstract
Zinc is an essential trace element that acts as a co-factor for many enzymes and transcription factors required for cellular growth and development. Altering intracellular zinc levels can produce dramatic effects ranging from cell proliferation to cell death. To avoid such fates, cells have evolved mechanisms to handle both an excess and a deficiency of zinc. Zinc homeostasis is largely maintained via zinc transporters, permeable channels, and other zinc-binding proteins. Variation in these proteins might affect their ability to interact with zinc, leading to either increased sensitivity or resistance to natural zinc fluctuations in the environment. We can leverage the power of the roundworm nematode Caenorhabditis elegans as a tractable metazoan model for quantitative genetics to identify genes that could underlie variation in responses to zinc. We found that the laboratory-adapted strain (N2) is resistant and a natural isolate from Hawaii (CB4856) is sensitive to micromolar amounts of exogenous zinc supplementation. Using a panel of recombinant inbred lines, we identified two large-effect quantitative trait loci (QTL) on the left arm of chromosome III and the center of chromosome V that are associated with zinc responses. We validated and refined both QTL using near-isogenic lines (NILs) and identified a naturally occurring deletion in sqst-5, a sequestosome-related gene, that is associated with resistance to high exogenous zinc. We found that this deletion is relatively common across strains within the species and that variation in sqst-5 is associated with zinc resistance. Our results offer a possible mechanism for how organisms can respond to naturally high levels of zinc in the environment and how zinc homeostasis varies among individuals.
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Affiliation(s)
- Kathryn S. Evans
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois, United States of America
| | - Stefan Zdraljevic
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois, United States of America
| | - Lewis Stevens
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Kimberly Collins
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Robyn E. Tanny
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Erik C. Andersen
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, United States of America
- * E-mail:
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