1
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Teterina AA, Willis JH, Baer CF, Phillips PC. Pervasive conservation of intron number and other genetic elements revealed by a chromosome-level genomic assembly of the hyper-polymorphic nematode Caenorhabditis brenneri. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600681. [PMID: 38979286 PMCID: PMC11230420 DOI: 10.1101/2024.06.25.600681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
With within-species genetic diversity estimates that span the gambit of that seen across the entirety of animals, the Caenorhabditis genus of nematodes holds unique potential to provide insights into how population size and reproductive strategies influence gene and genome organization and evolution. Our study focuses on Caenorhabditis brenneri, currently known as one of the most genetically diverse nematodes within its genus and metazoan phyla. Here, we present a high-quality gapless genome assembly and annotation for C. brenneri, revealing a common nematode chromosome arrangement characterized by gene-dense central regions and repeat rich peripheral parts. Comparison of C. brenneri with other nematodes from the 'Elegans' group revealed conserved macrosynteny but a lack of microsynteny, characterized by frequent rearrangements and low correlation iof orthogroup sizes, indicative of high rates of gene turnover. We also assessed genome organization within corresponding syntenic blocks in selfing and outcrossing species, affirming that selfing species predominantly experience loss of both genes and intergenic DNA. Comparison of gene structures revealed strikingly small number of shared introns across species, yet consistent distributions of intron number and length, regardless of population size or reproductive mode, suggesting that their evolutionary dynamics are primarily reflective of functional constraints. Our study provides valuable insights into genome evolution and expands the nematode genome resources with the highly genetically diverse C. brenneri, facilitating research into various aspects of nematode biology and evolutionary processes.
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Affiliation(s)
- Anastasia A Teterina
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
- Center of Parasitology, Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
| | - John H Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Charles F Baer
- Department of Biology, University of Florida, Gainesville, USA
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
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2
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Shen Y, Lin SY, Harbin J, Amin R, Vassalotti A, Romanowski J, Schmidt E, Tierney A, Ellis RE. Rewiring the Sex-Determination Pathway During the Evolution of Self-Fertility. Mol Biol Evol 2024; 41:msae101. [PMID: 38880992 PMCID: PMC11180601 DOI: 10.1093/molbev/msae101] [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: 03/08/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 06/18/2024] Open
Abstract
Although evolution is driven by changes in how regulatory pathways control development, we know little about the molecular details underlying these transitions. The TRA-2 domain that mediates contact with TRA-1 is conserved in Caenorhabditis. By comparing the interaction of these proteins in two species, we identified a striking change in how sexual development is controlled. Identical mutations in this domain promote oogenesis in Caenorhabditis elegans but promote spermatogenesis in Caenorhabditis briggsae. Furthermore, the effects of these mutations involve the male-promoting gene fem-3 in C. elegans but are independent of fem-3 in C. briggsae. Finally, reciprocal mutations in these genes show that C. briggsae TRA-2 binds TRA-1 to prevent expression of spermatogenesis regulators. By contrast, in C. elegans TRA-1 sequesters TRA-2 in the germ line, allowing FEM-3 to initiate spermatogenesis. Thus, we propose that the flow of information within the sex determination pathway has switched directions during evolution. This result has important implications for how evolutionary change can occur.
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Affiliation(s)
- Yongquan Shen
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering and Science, Rowan-Virtua School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Shin-Yi Lin
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering and Science, Rowan-Virtua School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Jonathan Harbin
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering and Science, Rowan-Virtua School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Richa Amin
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering and Science, Rowan-Virtua School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Allison Vassalotti
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering and Science, Rowan-Virtua School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Joseph Romanowski
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering and Science, Rowan-Virtua School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Emily Schmidt
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering and Science, Rowan-Virtua School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Alexis Tierney
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering and Science, Rowan-Virtua School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Ronald E Ellis
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering and Science, Rowan-Virtua School of Osteopathic Medicine, Stratford, NJ 08084, USA
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3
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Portman DS. Behavioral evolution: No sex please, we're hermaphrodites. Curr Biol 2024; 34:R501-R504. [PMID: 38772338 DOI: 10.1016/j.cub.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Many 'hard-wired', innate animal behaviors are related to reproduction. So what happens when reproductive systems evolve? New research in nematodes has identified principles underlying the co-evolution of reproductive strategy and sexual behavior, revealing some surprises and raising intriguing new questions.
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Affiliation(s)
- Douglas S Portman
- Department of Biomedical Genetics and Ernest J. Del Monte Institute for Neuroscience, University of Rochester, Rochester, NY 14642, USA.
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4
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Banse SA, Jackson EG, Sedore CA, Onken B, Hall D, Coleman-Hulbert A, Huynh P, Garrett T, Johnson E, Harinath G, Inman D, Guo S, Morshead M, Xue J, Falkowski R, Chen E, Herrera C, Kirsch AJ, Perez VI, Guo M, Lithgow GJ, Driscoll M, Phillips PC. The coupling between healthspan and lifespan in Caenorhabditis depends on complex interactions between compound intervention and genetic background. Aging (Albany NY) 2024; 16:5829-5855. [PMID: 38613792 PMCID: PMC11042945 DOI: 10.18632/aging.205743] [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: 09/19/2023] [Accepted: 01/11/2024] [Indexed: 04/15/2024]
Abstract
Aging is characterized by declining health that results in decreased cellular resilience and neuromuscular function. The relationship between lifespan and health, and the influence of genetic background on that relationship, has important implications in the development of pharmacological anti-aging interventions. Here we assessed swimming performance as well as survival under thermal and oxidative stress across a nematode genetic diversity test panel to evaluate health effects for three compounds previously studied in the Caenorhabditis Intervention Testing Program and thought to promote longevity in different ways - NP1 (nitrophenyl piperazine-containing compound 1), propyl gallate, and resveratrol. Overall, we find the relationships among median lifespan, oxidative stress resistance, thermotolerance, and mobility vigor to be complex. We show that oxidative stress resistance and thermotolerance vary with compound intervention, genetic background, and age. The effects of tested compounds on swimming locomotion, in contrast, are largely species-specific. In this study, thermotolerance, but not oxidative stress or swimming ability, correlates with lifespan. Notably, some compounds exert strong impact on some health measures without an equally strong impact on lifespan. Our results demonstrate the importance of assessing health and lifespan across genetic backgrounds in the effort to identify reproducible anti-aging interventions, with data underscoring how personalized treatments might be required to optimize health benefits.
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Affiliation(s)
- Stephen A. Banse
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - E. Grace Jackson
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Christine A. Sedore
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Brian Onken
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - David Hall
- The Buck Institute for Research on Aging, Novato, CA 94945, USA
| | | | - Phu Huynh
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Theo Garrett
- The Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Erik Johnson
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Girish Harinath
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Delaney Inman
- The Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Suzhen Guo
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | | | - Jian Xue
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ron Falkowski
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Esteban Chen
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Christopher Herrera
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Allie J. Kirsch
- 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
| | - Max Guo
- Division of Aging Biology, National Institute on Aging, Bethesda, MD 20892, USA
| | | | - Monica Driscoll
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Patrick C. Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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5
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Pliota P, Marvanova H, Koreshova A, Kaufman Y, Tikanova P, Krogull D, Hagmüller A, Widen SA, Handler D, Gokcezade J, Duchek P, Brennecke J, Ben-David E, Burga A. Selfish conflict underlies RNA-mediated parent-of-origin effects. Nature 2024; 628:122-129. [PMID: 38448590 PMCID: PMC10990930 DOI: 10.1038/s41586-024-07155-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/02/2024] [Indexed: 03/08/2024]
Abstract
Genomic imprinting-the non-equivalence of maternal and paternal genomes-is a critical process that has evolved independently in many plant and mammalian species1,2. According to kinship theory, imprinting is the inevitable consequence of conflictive selective forces acting on differentially expressed parental alleles3,4. Yet, how these epigenetic differences evolve in the first place is poorly understood3,5,6. Here we report the identification and molecular dissection of a parent-of-origin effect on gene expression that might help to clarify this fundamental question. Toxin-antidote elements (TAs) are selfish elements that spread in populations by poisoning non-carrier individuals7-9. In reciprocal crosses between two Caenorhabditis tropicalis wild isolates, we found that the slow-1/grow-1 TA is specifically inactive when paternally inherited. This parent-of-origin effect stems from transcriptional repression of the slow-1 toxin by the PIWI-interacting RNA (piRNA) host defence pathway. The repression requires PIWI Argonaute and SET-32 histone methyltransferase activities and is transgenerationally inherited via small RNAs. Remarkably, when slow-1/grow-1 is maternally inherited, slow-1 repression is halted by a translation-independent role of its maternal mRNA. That is, slow-1 transcripts loaded into eggs-but not SLOW-1 protein-are necessary and sufficient to counteract piRNA-mediated repression. Our findings show that parent-of-origin effects can evolve by co-option of the piRNA pathway and hinder the spread of selfish genes that require sex for their propagation.
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Affiliation(s)
- Pinelopi Pliota
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Hana Marvanova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Alevtina Koreshova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Yotam Kaufman
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Polina Tikanova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Daniel Krogull
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Andreas Hagmüller
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Sonya A Widen
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Dominik Handler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Joseph Gokcezade
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Peter Duchek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Eyal Ben-David
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Alejandro Burga
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
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6
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Ebert MS, Bargmann CI. Evolution remodels olfactory and mating-receptive behaviors in the transition from female to hermaphrodite reproduction. Curr Biol 2024; 34:969-979.e4. [PMID: 38340714 DOI: 10.1016/j.cub.2024.01.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/20/2023] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
Male/hermaphrodite species have arisen multiple times from a male/female ancestral state in nematodes, providing a model to study behavioral adaptations to different reproductive strategies. Here, we examined the mating behaviors of male/female (gonochoristic) Caenorhabditis species in comparison with male/hermaphrodite (androdiecious) close relatives. We find that females from two species in the Elegans group chemotax to volatile odor from males, but hermaphrodites do not. Females, but not hermaphrodites, also display known mating-receptive behaviors such as sedation when male reproductive structures contact the vulva. Focusing on the male/female species C. nigoni, we show that female chemotaxis to males is limited to adult females approaching adult or near-adult males and relies upon the AWA neuron-specific transcription factor ODR-7, as does male chemotaxis to female odor as previously shown in C. elegans. However, female receptivity during mating contact is odr-7 independent. All C. nigoni female behaviors are suppressed by mating and all are absent in young hermaphrodites from the sister species C. briggsae. However, latent receptivity during mating contact can be uncovered in mutant or aged C. briggsae hermaphrodites that lack self-sperm. These results reveal two mechanistically distinct components of the shift from female to hermaphrodite behavior: the loss of female-specific odr-7-dependent chemotaxis and a sperm-dependent state of reduced receptivity to mating contact. Hermaphrodites from a second androdioecious species, C. tropicalis, recover all female behaviors upon aging, including chemotaxis to males. Regaining mating receptivity after sperm depletion could maximize hermaphrodite fitness across their lifespan.
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Affiliation(s)
- Margaret S Ebert
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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7
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Indong RA, Park JM, Hong JK, Lyou ES, Han T, Hong JK, Lee TK, Lee JI. A simple protocol for cultivating the bacterivorous soil nematode Caenorhabditis elegans in its natural ecology in the laboratory. Front Microbiol 2024; 15:1347797. [PMID: 38476935 PMCID: PMC10929012 DOI: 10.3389/fmicb.2024.1347797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/09/2024] [Indexed: 03/14/2024] Open
Abstract
The complex interplay between an animal and its surrounding environment requires constant attentive observation in natural settings. Moreover, how ecological interactions are affected by an animal's genes is difficult to ascertain outside the laboratory. Genetic studies with the bacterivorous nematode Caenorhabditis elegans have elucidated numerous relationships between genes and functions, such as physiology, behaviors, and lifespan. However, these studies use standard laboratory culture that does not reflect C. elegans true ecology. C. elegans is found growing in nature and reproduced in large numbers in soils enriched with rotting fruit or vegetation, a source of abundant and diverse microbes that nourish the thriving populations of nematodes. We developed a simple mesocosm we call soil-fruit-natural-habitat that simulates the natural ecology of C. elegans in the laboratory. Apples were placed on autoclaved potted soils, and after a soil microbial solution was added, the mesocosm was subjected to day-night, temperature, and humidity cycling inside a growth chamber. After a period of apple-rotting, C elegans were added, and the growing worm population was observed. We determined optimal conditions for the growth of C. elegans and then performed an ecological succession experiment observing worm populations every few days. Our data showed that the mesocosm allows abundant growth and reproduction of C. elegans that resembles populations of the nematode found in rotting fruit in nature. Overall, our study presents a simple protocol that allows the cultivation of C. elegans in a natural habitat in the laboratory for a broad group of scientists to study various aspects of animal and microbial ecology.
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Affiliation(s)
- Rocel Amor Indong
- Division of Biological Science and Technology, Yonsei University Mirae Campus, Wonju, Republic of Korea
| | - Jong Min Park
- Division of Biological Science and Technology, Yonsei University Mirae Campus, Wonju, Republic of Korea
| | - Jin-Kyung Hong
- Department of Environmental and Energy Engineering, Yonsei University Mirae Campus, Wonju, Republic of Korea
| | - Eun Sun Lyou
- Department of Environmental and Energy Engineering, Yonsei University Mirae Campus, Wonju, Republic of Korea
| | - Taeman Han
- Korea National Park Research Insitute, Korea National Park Service, Wonju, Republic of Korea
| | - Jong Kwang Hong
- Division of Biological Science and Technology, Yonsei University Mirae Campus, Wonju, Republic of Korea
| | - Tae Kwon Lee
- Department of Environmental and Energy Engineering, Yonsei University Mirae Campus, Wonju, Republic of Korea
| | - Jin I. Lee
- Division of Biological Science and Technology, Yonsei University Mirae Campus, Wonju, Republic of Korea
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8
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Woodruff GC, Willis JH, Phillips PC. Patterns of Genomic Diversity in a Fig-Associated Close Relative of Caenorhabditis elegans. Genome Biol Evol 2024; 16:evae020. [PMID: 38302111 PMCID: PMC10883733 DOI: 10.1093/gbe/evae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/03/2024] Open
Abstract
The evolution of reproductive mode is expected to have profound impacts on the genetic composition of populations. At the same time, ecological interactions can generate close associations among species, which can in turn generate a high degree of overlap in their spatial distributions. Caenorhabditis elegans is a hermaphroditic nematode that has enabled extensive advances in developmental genetics. Caenorhabditis inopinata, the sister species of C. elegans, is a gonochoristic nematode that thrives in figs and obligately disperses on fig wasps. Here, we describe patterns of genomic diversity in C. inopinata. We performed RAD-seq on individual worms isolated from the field across three Okinawan island populations. C. inopinata is about five times more diverse than C. elegans. Additionally, C. inopinata harbors greater differences in diversity among functional genomic regions (such as between genic and intergenic sequences) than C. elegans. Conversely, C. elegans harbors greater differences in diversity between high-recombining chromosome arms and low-recombining chromosome centers than C. inopinata. FST is low among island population pairs, and clear population structure could not be easily detected among islands, suggesting frequent migration of wasps between islands. These patterns of population differentiation appear comparable with those previously reported in its fig wasp vector. These results confirm many theoretical population genetic predictions regarding the evolution of reproductive mode and suggest C. inopinata population dynamics may be driven by wasp dispersal. This work sets the stage for future evolutionary genomic studies aimed at understanding the evolution of sex as well as the evolution of ecological interactions.
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Affiliation(s)
- Gavin C Woodruff
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
- Present address: Department of Biology, University of Oklahoma, Norman, OK 73019, USA
| | - John H Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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9
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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: 10] [Impact Index Per Article: 10.0] [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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10
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Bobinski M, Pilgrim D. A dominant dpy-10 co-transformation marker using CRISPR/Cas9 and a linear repair template in Caenorhabditis tropicalis. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000900. [PMID: 38021174 PMCID: PMC10656624 DOI: 10.17912/micropub.biology.000900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/10/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023]
Abstract
Caenorhabditis elegans is an excellent genetic model system with a large arsenal of forward and reverse genetic techniques. However, not all approaches are easily ported to related Caenorhabditis species (which are useful for gene conservation and gene pathway evolution studies). For CRISPR/Cas9 genetic editing, an easily screenable and dominant co-transformation marker is required - a secondary mutation that won't impact the phenotype of a desired mutation but is capable of being screened for in heterozygous mutants. We describe here the adaptation of a dominant dumpy/roller CRISPR/Cas9-induced mutation in the C. tropicalis dpy-10 orthologue.
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Affiliation(s)
- Montana Bobinski
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - David Pilgrim
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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11
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Susoy V, Samuel ADT. Evolutionarily conserved behavioral plasticity enables context-dependent mating in C. elegans. Curr Biol 2023; 33:4532-4537.e3. [PMID: 37769659 PMCID: PMC10615801 DOI: 10.1016/j.cub.2023.09.003] [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: 04/26/2023] [Revised: 07/20/2023] [Accepted: 09/01/2023] [Indexed: 10/03/2023]
Abstract
Behavioral plasticity helps humans and animals to achieve their goals by adapting their behaviors to different environments.1,2 Although behavioral plasticity is ubiquitous, many innate species-specific behaviors, such as mating, are often assumed to be stereotyped and unaffected by plasticity or learning, especially in invertebrates. Here, we describe a novel case of behavioral plasticity in the nematode C. elegans. Under standard lab conditions (agar plates with bacterial food), the male performs parallel mating,3,4,5 a largely two-dimensional behavioral strategy where his body and tail remain flat on the surface and slide alongside the partner's body from initial contact to copulation. But when placed in liquid media, the male performs spiral mating, a distinctly three-dimensional behavioral strategy where he winds around the partner's body in a helical embrace. The performance of spiral mating does not require a long-term change in growing conditions, but it does improve with experience. This experience-dependent improvement appears to involve a critical period-a time window around the L4 larval stage to the early adult stage-which coincides with the development of most male-specific neurons. We tested several wild isolates of C. elegans and other Caenorhabditis species and found that most were capable of parallel mating on surfaces and spiral mating in liquids. We suggest that two- and three-dimensional mating strategies in Caenorhabditis are plastic, conditionally expressed phenotypes conserved across the genus, which can be genetically "fixed" in some species.
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Affiliation(s)
- Vladislav Susoy
- Department of Physics and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA.
| | - Aravinthan D T Samuel
- Department of Physics and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA.
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12
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Sepulveda NB, Chen D, Petrella LN. Moderate heat stress-induced sterility is due to motility defects and reduced mating drive in Caenorhabditis elegans males. J Exp Biol 2023; 226:jeb245546. [PMID: 37724024 DOI: 10.1242/jeb.245546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023]
Abstract
Moderate heat stress negatively impacts fertility in sexually reproducing organisms at sublethal temperatures. These moderate heat stress effects are typically more pronounced in males. In some species, sperm production, quality and motility are the primary cause of male infertility during moderate heat stress. However, this is not the case in the model nematode Caenorhabditis elegans, where changes in mating behavior are the primary cause of fertility loss. We report that heat-stressed C. elegans males are more motivated to locate and remain on food and less motivated to leave food to find and mate with hermaphrodites than their unstressed counterparts. Heat-stressed males also demonstrate a reduction in motility that likely limits their ability to mate. Collectively these changes result in a dramatic reduction in reproductive success. The reduction in mate-searching behavior may be partially due to increased expression of the chemoreceptor odr-10 in the AWA sensory neurons, which is a marker for starvation in males. These results demonstrate that moderate heat stress may have profound and previously underappreciated effects on reproductive behaviors. As climate change continues to raise global temperatures, it will be imperative to understand how moderate heat stress affects behavioral and motility elements critical to reproduction.
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Affiliation(s)
- Nicholas B Sepulveda
- Department of Biological Sciences, Marquette University, 1428 W Clybourn St., Milwaukee, WI 53217, USA
| | - Donald Chen
- Department of Biological Sciences, Marquette University, 1428 W Clybourn St., Milwaukee, WI 53217, USA
| | - Lisa N Petrella
- Department of Biological Sciences, Marquette University, 1428 W Clybourn St., Milwaukee, WI 53217, USA
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13
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Tandingan De Ley I, Kiontke K, Bert W, Sudhaus W, Fitch DHA. Pellioditis pelhamensis n. sp. (Nematoda: Rhabditidae) and Pellioditis pellio (Schneider, 1866), earthworm associates from different subclades within Pellioditis (syn. Phasmarhabditis Andrássy, 1976). PLoS One 2023; 18:e0288196. [PMID: 37672545 PMCID: PMC10482300 DOI: 10.1371/journal.pone.0288196] [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: 06/20/2023] [Accepted: 07/27/2023] [Indexed: 09/08/2023] Open
Abstract
Recently, much attention has been focused on a group of rhabditid nematodes called Phasmarhabditis, a junior synonym of Pellioditis, as a promising source of biocontrol agents for invasive slugs. Pellioditis pelhamensis n. sp. was first isolated from earthworms near Pelham Bay Park in Bronx, New York, USA, in 1990 and has been found to be pathogenic to slugs as well as some earthworms. It has also been used in several comparative developmental studies. Here, we provide a description of this species, as well as a redescription of a similar earthworm-associated nematode, Pellioditis pellio Schneider, 1866, re-isolated from the type locality. Although P. pelhamensis n. sp. and P. pellio are morphologically similar, they are reproductively isolated. Molecular phylogenetic analysis places both species in a clade that includes all species previously described as Phasmarhabditis which are associated with gastropods. Phasmarhabditis Andrássy, 1976 is therefore a junior synonym of Pellioditis Dougherty, 1953. Also, Pellioditis bohemica Nermut', Půža, Mekete & Mráček, 2017, described to be a facultative parasite of slugs, is found to be a junior synonym of Pellioditis pellio (Schneider, 1866), adding to evidence that P. pellio is associated with both slugs and earthworms. The earthworm-associated species P. pelhamensis n. sp. and P. pellio represent different subclades within Pellioditis, suggesting that Pellioditis species in general have a broader host range than just slugs. Because of this, caution is warranted in using these species as biological control agents until more is understood about their ecology.
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Affiliation(s)
- Irma Tandingan De Ley
- Department of Nematology, University of California, Riverside, CA, United States of America
| | - Karin Kiontke
- Department of Biology, New York University, New York, NY, United States of America
| | - Wim Bert
- Nematology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Walter Sudhaus
- Institut für Biologie/Zoologie, Freie Universität Berlin, Berlin, Germany
| | - David H. A. Fitch
- Department of Biology, New York University, New York, NY, United States of America
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14
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Jourdan J, Bundschuh M, Copilaș-Ciocianu D, Fišer C, Grabowski M, Hupało K, Jemec Kokalj A, Kabus J, Römbke J, Soose LJ, Oehlmann J. Cryptic Species in Ecotoxicology. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:1889-1914. [PMID: 37314101 DOI: 10.1002/etc.5696] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/20/2023] [Accepted: 06/12/2023] [Indexed: 06/15/2023]
Abstract
The advent of genetic methods has led to the discovery of an increasing number of species that previously could not be distinguished from each other on the basis of morphological characteristics. Even though there has been an exponential growth of publications on cryptic species, such species are rarely considered in ecotoxicology. Thus, the particular question of ecological differentiation and the sensitivity of closely related cryptic species is rarely addressed. Tackling this question, however, is of key importance for evolutionary ecology, conservation biology, and, in particular, regulatory ecotoxicology. At the same time, the use of species with (known or unknown) cryptic diversity might be a reason for the lack of reproducibility of ecotoxicological experiments and implies a false extrapolation of the findings. Our critical review includes a database and literature search through which we investigated how many of the species most frequently used in ecotoxicological assessments show evidence of cryptic diversity. We found a high proportion of reports indicating overlooked species diversity, especially in invertebrates. In terrestrial and aquatic realms, at least 67% and 54% of commonly used species, respectively, were identified as cryptic species complexes. The issue is less prominent in vertebrates, in which we found evidence for cryptic species complexes in 27% of aquatic and 6.7% of terrestrial vertebrates. We further exemplified why different evolutionary histories may significantly determine cryptic species' ecology and sensitivity to pollutants. This in turn may have a major impact on the results of ecotoxicological tests and, consequently, the outcome of environmental risk assessments. Finally, we provide a brief guideline on how to deal practically with cryptic diversity in ecotoxicological studies in general and its implementation in risk assessment procedures in particular. Environ Toxicol Chem 2023;42:1889-1914. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Jonas Jourdan
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Mirco Bundschuh
- iES Landau, Institute for Environmental Sciences, University of Kaiserslautern-Landau, Landau, Germany
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Denis Copilaș-Ciocianu
- Laboratory of Evolutionary Ecology of Hydrobionts, Nature Research Centre, Vilnius, Lithuania
| | - Cene Fišer
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Michał Grabowski
- Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
| | - Kamil Hupało
- Department of Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Anita Jemec Kokalj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jana Kabus
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Jörg Römbke
- ECT Oekotoxikologie, Flörsheim am Main, Germany
| | - Laura J Soose
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Jörg Oehlmann
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
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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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Kern CC, Srivastava S, Ezcurra M, Hsiung KC, Hui N, Townsend S, Maczik D, Zhang B, Tse V, Konstantellos V, Bähler J, Gems D. C. elegans ageing is accelerated by a self-destructive reproductive programme. Nat Commun 2023; 14:4381. [PMID: 37474586 PMCID: PMC10359416 DOI: 10.1038/s41467-023-40088-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 07/12/2023] [Indexed: 07/22/2023] Open
Abstract
In post-reproductive C. elegans, destructive somatic biomass repurposing supports production of yolk which, it was recently shown, is vented and can serve as a foodstuff for larval progeny. This is reminiscent of the suicidal reproductive effort (reproductive death) typical of semelparous organisms such as Pacific salmon. To explore the possibility that C. elegans exhibits reproductive death, we have compared sibling species pairs of the genera Caenorhabditis and Pristionchus with hermaphrodites and females. We report that yolk venting and constitutive, early pathology involving major anatomical changes occur only in hermaphrodites, which are also shorter lived. Moreover, only in hermaphrodites does germline removal suppress senescent pathology and markedly increase lifespan. This is consistent with the hypothesis that C. elegans exhibit reproductive death that is suppressed by germline ablation. If correct, this would imply a major difference in the ageing process between C. elegans and most higher organisms, and potentially explain the exceptional plasticity in C. elegans ageing.
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Affiliation(s)
- Carina C Kern
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Shivangi Srivastava
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Marina Ezcurra
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
- School of Biosciences, Stacey Building, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Kuei Ching Hsiung
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Nancy Hui
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - StJohn Townsend
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Dominik Maczik
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Bruce Zhang
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Victoria Tse
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Viktoras Konstantellos
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Jürg Bähler
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - David Gems
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK.
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17
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Broitman-Maduro G, Maduro MF. Evolutionary Change in Gut Specification in Caenorhabditis Centers on the GATA Factor ELT-3 in an Example of Developmental System Drift. J Dev Biol 2023; 11:32. [PMID: 37489333 PMCID: PMC10366740 DOI: 10.3390/jdb11030032] [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: 06/02/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/26/2023] Open
Abstract
Cells in a developing animal embryo become specified by the activation of cell-type-specific gene regulatory networks. The network that specifies the gut in the nematode Caenorhabditis elegans has been the subject of study for more than two decades. In this network, the maternal factors SKN-1/Nrf and POP-1/TCF activate a zygotic GATA factor cascade consisting of the regulators MED-1,2 → END-1,3 → ELT-2,7, leading to the specification of the gut in early embryos. Paradoxically, the MED, END, and ELT-7 regulators are present only in species closely related to C. elegans, raising the question of how the gut can be specified without them. Recent work found that ELT-3, a GATA factor without an endodermal role in C. elegans, acts in a simpler ELT-3 → ELT-2 network to specify gut in more distant species. The simpler ELT-3 → ELT-2 network may thus represent an ancestral pathway. In this review, we describe the elucidation of the gut specification network in C. elegans and related species and propose a model by which the more complex network might have formed. Because the evolution of this network occurred without a change in phenotype, it is an example of the phenomenon of Developmental System Drift.
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Affiliation(s)
- Gina Broitman-Maduro
- Department of Molecular, Cell, and Systems Biology, University of California-Riverside, Riverside, CA 92521, USA
| | - Morris F Maduro
- Department of Molecular, Cell, and Systems Biology, University of California-Riverside, Riverside, CA 92521, USA
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18
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Widen SA, Bes IC, Koreshova A, Pliota P, Krogull D, Burga A. Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities. Science 2023; 380:eade0705. [PMID: 37384706 DOI: 10.1126/science.ade0705] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 05/17/2023] [Indexed: 07/01/2023]
Abstract
Horizontal gene transfer, the movement of genetic material between species, has been reported across all major eukaryotic lineages. However, the underlying mechanisms of transfer and their impact on genome evolution are still poorly understood. While studying the evolutionary origin of a selfish element in the nematode Caenorhabditis briggsae, we discovered that Mavericks, ancient virus-like transposons related to giant viruses and virophages, are one of the long-sought vectors of horizontal gene transfer. We found that Mavericks gained a novel herpesvirus-like fusogen in nematodes, leading to the widespread exchange of cargo genes between extremely divergent species, bypassing sexual and genetic barriers spanning hundreds of millions of years. Our results show how the union between viruses and transposons causes horizontal gene transfer and ultimately genetic incompatibilities in natural populations.
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Affiliation(s)
- Sonya A Widen
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Israel Campo Bes
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Alevtina Koreshova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030 Vienna, Austria
| | - Pinelopi Pliota
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Daniel Krogull
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030 Vienna, Austria
| | - Alejandro Burga
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
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19
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Huang Y, Lo YH, Hsu JC, Le TS, Yang FJ, Chang T, Braendle C, Wang J. Widespread sex ratio polymorphism in Caenorhabditis nematodes. ROYAL SOCIETY OPEN SCIENCE 2023; 10:221636. [PMID: 36938539 PMCID: PMC10014251 DOI: 10.1098/rsos.221636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Although equal sex ratio is ubiquitous and represents an equilibrium in evolutionary theory, biased sex ratios are predicted for certain local conditions. Cases of sex ratio bias have been mostly reported for single species, but little is known about its evolution above the species level. Here, we surveyed progeny sex ratios in 23 species of the nematode genus Caenorhabditis, including 19 for which we tested multiple strains. For the species with multiple strains, five species had female-biased and two had non-biased sex ratios in all strains, respectively. The other 12 species showed polymorphic sex ratios across strains. Female-biased sex ratios could be due to sperm competition whereby X-bearing sperm outcompete nullo-X sperm during fertilization. In this model, when sperm are limited allowing all sperm to be used, sex ratios are expected to be equal. However, in assays limiting mating to a few hours, most strains showed similarly biased sex ratios compared with unlimited mating experiments, except that one C. becei strain showed significantly reduced female bias compared with unlimited mating. Our study shows frequent polymorphism in sex ratios within Caenorhabditis species and that sperm competition alone cannot explain the sex ratio bias.
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Affiliation(s)
- Yun Huang
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yun-Hua Lo
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Jung-Chen Hsu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Tho Son Le
- Department of Molecular Genetics and Gene Technology, College of Forestry Biotechnology, Vietnam National University of Forestry, Hanoi, Vietnam
| | - Fang-Jung Yang
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Tiffany Chang
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | | | - John Wang
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
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20
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Courtot É, Boisseau M, Dhorne-Pollet S, Serreau D, Gesbert A, Reigner F, Basiaga M, Kuzmina T, Lluch J, Annonay G, Kuchly C, Diekmann I, Krücken J, von Samson-Himmelstjerna G, Mach N, Sallé G. Comparison of two molecular barcodes for the study of equine strongylid communities with amplicon sequencing. PeerJ 2023; 11:e15124. [PMID: 37070089 PMCID: PMC10105562 DOI: 10.7717/peerj.15124] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 03/03/2023] [Indexed: 04/19/2023] Open
Abstract
Basic knowledge on the biology and epidemiology of equine strongylid species still needs to be improved to contribute to the design of better parasite control strategies. Nemabiome metabarcoding is a convenient tool to quantify and identify species in bulk samples that could overcome the hurdle that cyathostomin morphological identification represents. To date, this approach has relied on the internal transcribed spacer 2 (ITS-2) of the ribosomal RNA gene, with a limited investigation of its predictive performance for cyathostomin communities. Using DNA pools of single cyathostomin worms, this study aimed to provide the first elements to compare performances of the ITS-2 and a cytochrome c oxidase subunit I (COI) barcode newly developed in this study. Barcode predictive abilities were compared across various mock community compositions of two, five and 11 individuals from distinct species. The amplification bias of each barcode was estimated. Results were also compared between various types of biological samples, i.e., eggs, infective larvae or adults. Bioinformatic parameters were chosen to yield the closest representation of the cyathostomin community for each barcode, underscoring the need for communities of known composition for metabarcoding purposes. Overall, the proposed COI barcode was suboptimal relative to the ITS-2 rDNA region, because of PCR amplification biases, reduced sensitivity and higher divergence from the expected community composition. Metabarcoding yielded consistent community composition across the three sample types. However, imperfect correlations were found between relative abundances from infective larvae and other life-stages for Cylicostephanus species using the ITS-2 barcode. While the results remain limited by the considered biological material, they suggest that additional improvements are needed for both the ITS-2 and COI barcodes.
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Affiliation(s)
- Élise Courtot
- Animal Health, UMR1282 Infectiologie et Santé Publique, INRAE, Nouzilly, France
| | - Michel Boisseau
- Animal Health, UMR1282 Infectiologie et Santé Publique, INRAE, Nouzilly, France
- Animal Health, UMR1225 IHAP, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse, France
| | | | - Delphine Serreau
- Animal Health, UMR1282 Infectiologie et Santé Publique, INRAE, Nouzilly, France
| | - Amandine Gesbert
- Animal Physiology, UEPAO, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nouzilly, France
| | - Fabrice Reigner
- Animal Physiology, UEPAO, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nouzilly, France
| | | | - Tetiana Kuzmina
- Schmalhausen Institute of Zoology NAS of Ukraine, Kyiv, Ukraine
- Institute of Parasitology, Slovak Academy of Sciences, Košice, Slovak Republic
| | - Jérôme Lluch
- GeT-PlaGe, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse, France
| | - Gwenolah Annonay
- GeT-PlaGe, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse, France
| | - Claire Kuchly
- GeT-PlaGe, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse, France
| | - Irina Diekmann
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Jürgen Krücken
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | | | - Nuria Mach
- Animal Health, UMR1225 IHAP, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse, France
| | - Guillaume Sallé
- Animal Health, UMR1282 Infectiologie et Santé Publique, INRAE, Nouzilly, France
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21
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Pandey T, Ma DK. Stress-Induced Phenoptosis: Mechanistic Insights and Evolutionary Implications. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1504-1511. [PMID: 36717459 DOI: 10.1134/s0006297922120082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Evolution by natural selection results in biological traits that enable organismic adaptation and survival under various stressful environments. External stresses can be sometimes too severe to overcome, leading to organismic death either because of failure in adapting to such stress, or alternatively, through a regulated form of organismic death (phenoptosis). While regulated cell deaths, including apoptosis, have been extensively studied, little is known about the molecular and cellular mechanisms underlying phenoptosis and its evolutionary significance for multicellular organisms. In this article, we review documented phenomena and mechanistic evidence emerging from studies of stress-induced phenoptosis in the multicellular organism C. elegans and stress-induced deaths at cellular levels in organisms ranging from bacteria to mammals, focusing on abiotic and pathogen stresses. Genes and signaling pathways involved in phenoptosis appear to promote organismic death during severe stress and aging, while conferring fitness and immune defense during mild stress and early life, consistent with their antagonistic pleiotropy actions. As cell apoptosis during development can shape tissues and organs, stress-induced phenoptosis may also contribute to possible benefits at the population level, through mechanisms including kin selection, abortive infection, and soma-to-germline resource allocation. Current models can generate experimentally testable predictions and conceptual frameworks with implications for understanding both stress-induced phenoptosis and natural aging.
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Affiliation(s)
- Taruna Pandey
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, USA.
| | - Dengke K Ma
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, USA. .,Innovative Genomics Institute, University of California, Berkeley, USA
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22
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Sun S, Kanzaki N, Dayi M, Maeda Y, Yoshida A, Tanaka R, Kikuchi T. The compact genome of Caenorhabditis niphades n. sp., isolated from a wood-boring weevil, Niphades variegatus. BMC Genomics 2022; 23:765. [PMID: 36418933 PMCID: PMC9682657 DOI: 10.1186/s12864-022-09011-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The first metazoan genome sequenced, that of Caenorhabditis elegans, has motivated animal genome evolution studies. To date > 50 species from the genus Caenorhabditis have been sequenced, allowing research on genome variation. RESULTS In the present study, we describe a new gonochoristic species, Caenorhabditis niphades n. sp., previously referred as C. sp. 36, isolated from adult weevils (Niphades variegatus), with whom they appear to be tightly associated during its life cycle. Along with a species description, we sequenced the genome of C. niphades n. sp. and produced a chromosome-level assembly. A genome comparison highlighted that C. niphades n. sp. has the smallest genome (59 Mbp) so far sequenced in the Elegans supergroup, despite being closely related to a species with an exceptionally large genome, C. japonica. CONCLUSIONS The compact genome of C. niphades n. sp. can serve as a key resource for comparative evolutionary studies of genome and gene number expansions in Caenorhabditis species.
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Affiliation(s)
- Simo Sun
- grid.26999.3d0000 0001 2151 536XDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan ,grid.410849.00000 0001 0657 3887Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Miyazaki, 889-1692 Japan
| | - Natsumi Kanzaki
- grid.417935.d0000 0000 9150 188XKansai Research Center, Forestry and Forest Products Research Institute, 68 Nagaikyutaroh, Momoyama, Fushimi, Kyoto, 612-0855 Japan
| | - Mehmet Dayi
- grid.26999.3d0000 0001 2151 536XDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan ,grid.412121.50000 0001 1710 3792Forestry Vocational School, Duzce University, 81620 Duzce, Türkiye
| | - Yasunobu Maeda
- grid.26999.3d0000 0001 2151 536XDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan ,grid.410849.00000 0001 0657 3887Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Miyazaki, 889-1692 Japan
| | - Akemi Yoshida
- grid.410849.00000 0001 0657 3887Genomics and Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Miyazaki, 889-1692 Japan
| | - Ryusei Tanaka
- grid.410849.00000 0001 0657 3887Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Miyazaki, 889-1692 Japan
| | - Taisei Kikuchi
- grid.26999.3d0000 0001 2151 536XDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan ,grid.410849.00000 0001 0657 3887Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Miyazaki, 889-1692 Japan
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23
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Wang B, Pandey T, Long Y, Delgado-Rodriguez SE, Daugherty MD, Ma DK. Co-opted genes of algal origin protect C. elegans against cyanogenic toxins. Curr Biol 2022; 32:4941-4948.e3. [PMID: 36223775 PMCID: PMC9691542 DOI: 10.1016/j.cub.2022.09.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/31/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022]
Abstract
Amygdalin is a cyanogenic glycoside enriched in the tissues of many edible plants, including seeds of stone fruits such as cherry (Prunus avium), peach (Prunus persica), and apple (Malus domestica). These plants biosynthesize amygdalin in defense against herbivore animals, as amygdalin generates poisonous cyanide upon plant tissue destruction.1,2,3,4 Poisonous to many animals, amygdalin-derived cyanide is detoxified by potent enzymes commonly found in bacteria and plants but not most animals.5 Here we show that the nematode C. elegans can detoxify amygdalin by a genetic pathway comprising cysl-1, egl-9, hif-1, and cysl-2. A screen of a natural product library for hypoxia-independent regulators of HIF-1 identifies amygdalin as a potent activator of cysl-2, a HIF-1 transcriptional target that encodes a cyanide detoxification enzyme in C. elegans. As a cysl-2 paralog similarly essential for amygdalin resistance, cysl-1 encodes a protein homologous to cysteine biosynthetic enzymes in bacteria and plants but functionally co-opted in C. elegans. We identify exclusively HIF-activating egl-9 mutations in a cysl-1 suppressor screen and show that cysl-1 confers amygdalin resistance by regulating HIF-1-dependent cysl-2 transcription to protect against amygdalin toxicity. Phylogenetic analysis indicates that cysl-1 and cysl-2 were likely acquired from green algae through horizontal gene transfer (HGT) and functionally co-opted in protection against amygdalin. Since acquisition, these two genes evolved division of labor in a cellular circuit to detect and detoxify cyanide. Thus, algae-to-nematode HGT and subsequent gene function co-option events may facilitate host survival and adaptation to adverse environmental stresses and biogenic toxins.
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Affiliation(s)
- Bingying Wang
- Cardiovascular Research Institute and Department of Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Taruna Pandey
- Cardiovascular Research Institute and Department of Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Yong Long
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | | | - Matthew D Daugherty
- Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA.
| | - Dengke K Ma
- Cardiovascular Research Institute and Department of Physiology, University of California, San Francisco, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
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24
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Broitman-Maduro G, Sun S, Kikuchi T, Maduro MF. The GATA factor ELT-3 specifies endoderm in Caenorhabditis angaria in an ancestral gene network. Development 2022; 149:277064. [PMID: 36196618 PMCID: PMC9720673 DOI: 10.1242/dev.200984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022]
Abstract
ABSTRACT
Endoderm specification in Caenorhabditis elegans occurs through a network in which maternally provided SKN-1/Nrf, with additional input from POP-1/TCF, activates the GATA factor cascade MED-1,2→END-1,3→ELT-2,7. Orthologues of the MED, END and ELT-7 factors are found only among nematodes closely related to C. elegans, raising the question of how gut is specified in their absence in more distant species in the genus. We find that the C. angaria, C. portoensis and C. monodelphis orthologues of the GATA factor gene elt-3 are expressed in the early E lineage, just before their elt-2 orthologues. In C. angaria, Can-pop-1(RNAi), Can-elt-3(RNAi) and a Can-elt-3 null mutation result in a penetrant ‘gutless’ phenotype. Can-pop-1 is necessary for Can-elt-3 activation, showing that it acts upstream. Forced early E lineage expression of Can-elt-3 in C. elegans can direct the expression of a Can-elt-2 transgene and rescue an elt-7 end-1 end-3; elt-2 quadruple mutant strain to viability. Our results demonstrate an ancestral mechanism for gut specification and differentiation in Caenorhabditis involving a simpler POP-1→ELT-3→ELT-2 gene network.
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Affiliation(s)
- Gina Broitman-Maduro
- University of California 1 Department of Molecular, Cell and Systems Biology , , Riverside, CA 92521 , USA
| | - Simo Sun
- Faculty of Medicine, University of Miyazaki 2 Department of Infectious Diseases , , 5200 Kihara, Miyazaki 889-1692 , Japan
- Graduate School of Frontier Sciences, The University of Tokyo 3 Department of Integrated Biosciences , , Chiba 277-8562 , Japan
| | - Taisei Kikuchi
- Faculty of Medicine, University of Miyazaki 2 Department of Infectious Diseases , , 5200 Kihara, Miyazaki 889-1692 , Japan
- Graduate School of Frontier Sciences, The University of Tokyo 3 Department of Integrated Biosciences , , Chiba 277-8562 , Japan
| | - Morris F. Maduro
- University of California 1 Department of Molecular, Cell and Systems Biology , , Riverside, CA 92521 , USA
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25
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Salas A, Rusconi JM, Rocca M, Lucas FD, Balcazar D, Achinelly MF. A new wild strain of Caenorhabditis elegans associated with Allograpta exotica (Syrphidae) in Argentina: an update of its ecological niche and worldwide distribution. AN ACAD BRAS CIENC 2022; 94:e20201440. [PMID: 35920483 DOI: 10.1590/0001-3765202220201440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 09/06/2021] [Indexed: 11/21/2022] Open
Abstract
Caenorhabditis elegans is a free-living nematode, belonging to the bacterivorous trophic group. Although it was cited in several countries, in different types of ecosystems and in associations with other organisms, the wild habitats of this nematode have not yet been precisely defined. In Argentina, C. elegans was recently isolated from the hoverfly Allograpta exotica, a voracious predator with potential biological control against aphids in horticultural crops. In this frame, the objectives of this study were (i) to characterize it molecularly and morphologically (ii) to report a wild strain of C. elegans for the first time from Argentina, (iii) to present a new ecological niche by associating it with A. exotica and (iv) to evaluate the pathogenicity against these insects. The results of the morphological and molecular analyses made it possible to determine that the isolated nematode was C. elegans, thus establishing the ARGLP1900 wild strain as the first record of this nematode for Argentina. A new association was described, since there are no records of interaction between C. elegans and A. exotica, providing information on a new ecological niche. The new wild strain found in this work, could be appropriate for comparative genomic studies with other C. elegans strains.
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Affiliation(s)
- Augusto Salas
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola, L de la Torre, s/n, G lvez, G lvez, Argentina
| | - José M Rusconi
- Centro de Estudios Parasitológicos y de Vectores CEPAVE (CCT La Plata, CONICET/UNLP), Blvd. 120 1900, La Plata, Provincia de Buenos Aires, Argentina
| | - Margarita Rocca
- Centro de Estudios Parasitológicos y de Vectores CEPAVE (CCT La Plata, CONICET/UNLP), Blvd. 120 1900, La Plata, Provincia de Buenos Aires, Argentina
| | - Florencia D Lucas
- Centro de Estudios Parasitológicos y de Vectores CEPAVE (CCT La Plata, CONICET/UNLP), Blvd. 120 1900, La Plata, Provincia de Buenos Aires, Argentina
| | - Darío Balcazar
- Centro de Estudios Parasitológicos y de Vectores CEPAVE (CCT La Plata, CONICET/UNLP), Blvd. 120 1900, La Plata, Provincia de Buenos Aires, Argentina
| | - María Fernanda Achinelly
- Centro de Estudios Parasitológicos y de Vectores CEPAVE (CCT La Plata, CONICET/UNLP), Blvd. 120 1900, La Plata, Provincia de Buenos Aires, Argentina
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26
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Hammerschmith EW, Woodruff GC, Moser KA, Johnson E, Phillips PC. Opposing directions of stage-specific body shape change in a close relative of C. elegans. BMC ZOOL 2022; 7:38. [PMID: 37170380 PMCID: PMC10127021 DOI: 10.1186/s40850-022-00131-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 05/04/2022] [Indexed: 11/17/2022] Open
Abstract
Abstract
Background
Body size is a fundamental organismal trait. However, as body size and ecological contexts change across developmental time, evolutionary divergence may cause unexpected patterns of body size diversity among developmental stages. This may be particularly evident in polyphenic developmental stages specialized for dispersal. The dauer larva is such a stage in nematodes, and Caenorhabditis species disperse by traveling on invertebrate carriers. Here, we describe the morphology of a stress-resistant, dauer-like larval stage of the nematode Caenorhabditis inopinata, whose adults can grow to be nearly twice as long as its close relative, the model organism C. elegans.
Results
We find that a dauer-like, stress-resistant larval stage in two isolates of C. inopinata is on average 13% shorter and 30% wider than the dauer larvae of C. elegans, despite its much longer adult stage. Additionally, many C. inopinata dauer-like larvae were ensheathed, a possible novelty in this lineage reminiscent of the infective juveniles of parasitic nematodes. Variation in dauer-like larva formation frequency among twenty-four wild isolates of C. inopinata was also observed, although frequencies were low across all isolates (< 2%), with many isolates unable to produce dauer-like larvae under conventional laboratory conditions.
Conclusion
Most Caenorhabditis species thrive on rotting plants and disperse on snails, slugs, or isopods (among others) whereas C. inopinata is ecologically divergent and thrives in fresh Ficus septica figs and disperses on their pollinating wasps. While there is some unknown factor of the fig environment that promotes elongated body size in C. inopinata adults, the small size or unique life history of its fig wasp carrier may be driving the divergent morphology of its stress-resistant larval stages. Further characterization of the behavior, development, and morphology of this stage will refine connections to homologous developmental stages in other species and determine whether ecological divergence across multiple developmental stages can promote unexpected and opposing changes in body size dimensions within a single species.
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27
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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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28
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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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29
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HODDA M. Phylum Nematoda: trends in species descriptions, the documentation of diversity, systematics, and the species concept. Zootaxa 2022; 5114:290-317. [DOI: 10.11646/zootaxa.5114.1.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Indexed: 11/04/2022]
Abstract
This paper summarizes the trends in nematode species description and systematics emerging from a comparison of the latest comprehensive classification and census of Phylum Nematoda (Hodda 2022a, b) with earlier classifications (listed in Hodda 2007). It also offers some general observations on trends in nematode systematics emerging from the review of the voluminous literature used to produce the classification. The trends in nematodes can be compared with developments in the systematics of other organisms to shed light on many of the general issues confronting systematists now and into the future.
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30
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Ellis RE. Sex Determination in Nematode Germ Cells. Sex Dev 2022:1-18. [PMID: 35172320 PMCID: PMC9378769 DOI: 10.1159/000520872] [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: 09/10/2021] [Accepted: 11/02/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Animal germ cells differentiate as sperm or as oocytes. These sexual fates are controlled by complex regulatory pathways to ensure that the proper gametes are made at the appropriate times. SUMMARY Nematodes like Caenorhabditis elegans and its close relatives are ideal models for studying how this regulation works, because the XX animals are self-fertile hermaphrodites that produce both sperm and oocytes. In these worms, germ cells use the same signal transduction pathway that functions in somatic cells. This pathway determines the activity of the transcription factor TRA-1, a Gli protein that can repress male genes. However, the pathway is extensively modified in germ cells, largely by the action of translational regulators like the PUF proteins. Many of these modifications play critical roles in allowing the XX hermaphrodites to make sperm in an otherwise female body. Finally, TRA-1 cooperates with chromatin regulators in the germ line to control the activity of fog-1 and fog-3, which are essential for spermatogenesis. FOG-1 and FOG-3 work together to determine germ cell fates by blocking the translation of oogenic transcripts. Key Messages: Although there is great diversity in how germ cell fates are controlled in other animals, many of the key nematode genes are conserved, and the critical role of translational regulators may be universal.
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Affiliation(s)
- Ronald E Ellis
- Department of Molecular Biology, Rowan University SOM, Stratford, New Jersey, USA
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31
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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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32
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Brand JN, Harmon LJ, Schärer L. Mating behavior and reproductive morphology predict macroevolution of sex allocation in hermaphroditic flatworms. BMC Biol 2022; 20:35. [PMID: 35130880 PMCID: PMC8822660 DOI: 10.1186/s12915-022-01234-1] [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: 11/08/2021] [Accepted: 01/18/2022] [Indexed: 11/10/2022] Open
Abstract
Background Sex allocation is the distribution of resources to male or female reproduction. In hermaphrodites, this concerns an individual’s resource allocation to, for example, the production of male or female gametes. Macroevolutionary studies across hermaphroditic plants have revealed that the self-pollination rate and the pollination mode are strong predictors of sex allocation. Consequently, we expect similar factors such as the selfing rate and aspects of the reproductive biology, like the mating behaviour and the intensity of postcopulatory sexual selection, to predict sex allocation in hermaphroditic animals. However, comparative work on hermaphroditic animals is limited. Here, we study sex allocation in 120 species of the hermaphroditic free-living flatworm genus Macrostomum. We ask how hypodermic insemination, a convergently evolved mating behaviour where sperm are traumatically injected through the partner’s epidermis, affects the evolution of sex allocation. We also test the commonly-made assumption that investment into male and female reproduction should trade-off. Finally, we ask if morphological indicators of the intensity of postcopulatory sexual selection (female genital complexity, male copulatory organ length, and sperm length) can predict sex allocation. Results We find that the repeated evolution of hypodermic insemination predicts a more female-biased sex allocation (i.e., a relative shift towards female allocation). Moreover, transcriptome-based estimates of heterozygosity reveal reduced heterozygosity in hypodermically mating species, indicating that this mating behavior is linked to increased selfing or biparental inbreeding. Therefore, hypodermic insemination could represent a selfing syndrome. Furthermore, across the genus, allocation to male and female gametes is negatively related, and larger species have a more female-biased sex allocation. Finally, increased female genital complexity, longer sperm, and a longer male copulatory organ predict a more male-biased sex allocation. Conclusions Selfing syndromes have repeatedly originated in plants. Remarkably, this macroevolutionary pattern is replicated in Macrostomum flatworms and linked to repeated shifts in reproductive behavior. We also find a trade-off between male and female reproduction, a fundamental assumption of most theories of sex allocation. Beyond that, no theory predicts a more female-biased allocation in larger species, suggesting avenues for future work. Finally, morphological indicators of more intense postcopulatory sexual selection appear to predict more intense sperm competition. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01234-1.
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Affiliation(s)
- Jeremias N Brand
- Department of Environmental Sciences, Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland. .,Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany.
| | - Luke J Harmon
- Department of Biological Sciences, University of Idaho, Life Sciences South 252, 875 Perimeter Dr MS 3051, Moscow, ID, USA
| | - Lukas Schärer
- Department of Environmental Sciences, Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
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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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34
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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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35
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Diano MA, Dalan L, Singh PR, Sumaya NH. First report, morphological and molecular characterization of Caenorhabditis brenneri (Nematoda: Rhabditidae) isolated from the giant African land snail Achatina fulica (Gastropoda: Achatinidae). Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-021-00972-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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36
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Andersen EC, Rockman MV. Natural genetic variation as a tool for discovery in Caenorhabditis nematodes. Genetics 2022; 220:iyab156. [PMID: 35134197 PMCID: PMC8733454 DOI: 10.1093/genetics/iyab156] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 09/11/2021] [Indexed: 11/12/2022] Open
Abstract
Over the last 20 years, studies of Caenorhabditis elegans natural diversity have demonstrated the power of quantitative genetic approaches to reveal the evolutionary, ecological, and genetic factors that shape traits. These studies complement the use of the laboratory-adapted strain N2 and enable additional discoveries not possible using only one genetic background. In this chapter, we describe how to perform quantitative genetic studies in Caenorhabditis, with an emphasis on C. elegans. These approaches use correlations between genotype and phenotype across populations of genetically diverse individuals to discover the genetic causes of phenotypic variation. We present methods that use linkage, near-isogenic lines, association, and bulk-segregant mapping, and we describe the advantages and disadvantages of each approach. The power of C. elegans quantitative genetic mapping is best shown in the ability to connect phenotypic differences to specific genes and variants. We will present methods to narrow genomic regions to candidate genes and then tests to identify the gene or variant involved in a quantitative trait. The same features that make C. elegans a preeminent experimental model animal contribute to its exceptional value as a tool to understand natural phenotypic variation.
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Affiliation(s)
- Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Matthew V Rockman
- Department of Biology and Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
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37
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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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38
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Xie D, Ye P, Ma Y, Li Y, Liu X, Sarkies P, Zhao Z. Genetic exchange with an outcrossing sister species causes severe genome-wide dysregulation in a selfing Caenorhabditis nematode. Genome Res 2022; 32:2015-2027. [PMID: 36351773 PMCID: PMC9808620 DOI: 10.1101/gr.277205.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022]
Abstract
Different modes of reproduction evolve rapidly, with important consequences for genome composition. Selfing species often occupy a similar niche as their outcrossing sister species with which they are able to mate and produce viable hybrid progeny, raising the question of how they maintain genomic identity. Here, we investigate this issue by using the nematode Caenorhabditis briggsae, which reproduces as a hermaphrodite, and its outcrossing sister species Caenorhabditis nigoni We hypothesize that selfing species might develop some barriers to prevent gene intrusions through gene regulation. We therefore examined gene regulation in the hybrid F2 embryos resulting from reciprocal backcrosses between F1 hybrid progeny and C. nigoni or C. briggsae F2 hybrid embryos with ∼75% of their genome derived from C. briggsae (termed as bB2) were inviable, whereas those with ∼75% of their genome derived from C. nigoni (termed as nB2) were viable. Misregulation of transposable elements, coding genes, and small regulatory RNAs was more widespread in the bB2 compared with the nB2 hybrids, which is a plausible explanation for the differential phenotypes between the two hybrids. Our results show that regulation of the C. briggsae genome is strongly affected by genetic exchanges with its outcrossing sister species, C. nigoni, whereas regulation of the C. nigoni genome is more robust on genetic exchange with C. briggsae The results provide new insights into how selfing species might maintain their identity despite genetic exchanges with closely related outcrossing species.
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Affiliation(s)
- Dongying Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Pohao Ye
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yiming Ma
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yongbin Li
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Xiao Liu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Peter Sarkies
- Department of Biochemistry, University of Oxford, Oxford, OX1 4BH, United Kingdom
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, China;,State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
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39
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Onken B, Sedore CA, Coleman‐Hulbert AL, Hall D, Johnson E, Jones EG, Banse SA, Huynh P, Guo S, Xue J, Chen E, Harinath G, Foulger A, Chao EA, Hope J, Bhaumik D, Plummer T, Inman D, Morshead M, Guo M, Lithgow G, Phillips PC, Driscoll M. Metformin treatment of diverse Caenorhabditis species reveals the importance of genetic background in longevity and healthspan extension outcomes. Aging Cell 2022; 21:e13488. [PMID: 34837316 PMCID: PMC8761014 DOI: 10.1111/acel.13488] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 08/31/2021] [Accepted: 09/19/2021] [Indexed: 11/30/2022] Open
Abstract
Metformin, the most commonly prescribed anti‐diabetes medication, has multiple reported health benefits, including lowering the risks of cardiovascular disease and cancer, improving cognitive function with age, extending survival in diabetic patients, and, in several animal models, promoting youthful physiology and lifespan. Due to its longevity and health effects, metformin is now the focus of the first proposed clinical trial of an anti‐aging drug—the Targeting Aging with Metformin (TAME) program. Genetic variation will likely influence outcomes when studying metformin health effects in human populations. To test for metformin impact in diverse genetic backgrounds, we measured lifespan and healthspan effects of metformin treatment in three Caenorhabditis species representing genetic variability greater than that between mice and humans. We show that metformin increases median survival in three C. elegans strains, but not in C. briggsae and C. tropicalis strains. In C. briggsae, metformin either has no impact on survival or decreases lifespan. In C. tropicalis, metformin decreases median survival in a dose‐dependent manner. We show that metformin prolongs the period of youthful vigor in all C. elegans strains and in two C. briggsae strains, but that metformin has a negative impact on the locomotion of C. tropicalis strains. Our data demonstrate that metformin can be a robust promoter of healthy aging across different genetic backgrounds, but that genetic variation can determine whether metformin has positive, neutral, or negative lifespan/healthspan impact. These results underscore the importance of tailoring treatment to individuals when testing for metformin health benefits in diverse human populations.
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Affiliation(s)
- Brian Onken
- Nelson Biological Laboratories Department of Molecular Biology and Biochemistry Rutgers University Piscataway New Jersey USA
| | | | | | - David Hall
- The Buck Institute for Research on Aging Novato California USA
| | - Erik Johnson
- Institute of Ecology and Evolution University of Oregon Eugene Oregon USA
| | | | - Stephen A. Banse
- Institute of Ecology and Evolution University of Oregon Eugene Oregon USA
| | - Phu Huynh
- Nelson Biological Laboratories Department of Molecular Biology and Biochemistry Rutgers University Piscataway New Jersey USA
| | - Suzhen Guo
- Nelson Biological Laboratories Department of Molecular Biology and Biochemistry Rutgers University Piscataway New Jersey USA
| | - Jian Xue
- Nelson Biological Laboratories Department of Molecular Biology and Biochemistry Rutgers University Piscataway New Jersey USA
| | - Esteban Chen
- Nelson Biological Laboratories Department of Molecular Biology and Biochemistry Rutgers University Piscataway New Jersey USA
| | - Girish Harinath
- Nelson Biological Laboratories Department of Molecular Biology and Biochemistry Rutgers University Piscataway New Jersey USA
| | - Anna C. Foulger
- The Buck Institute for Research on Aging Novato California USA
| | | | - June Hope
- The Buck Institute for Research on Aging Novato California USA
| | - Dipa Bhaumik
- The Buck Institute for Research on Aging Novato California USA
| | - Todd Plummer
- The Buck Institute for Research on Aging Novato California USA
| | - Delaney Inman
- The Buck Institute for Research on Aging Novato California USA
| | | | - Max Guo
- Division of Aging Biology National Institute on Aging Bethesda Maryland USA
| | | | | | - Monica Driscoll
- Nelson Biological Laboratories Department of Molecular Biology and Biochemistry Rutgers University Piscataway New Jersey USA
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40
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Insights from C. elegans into Microsporidia Biology and Host-Pathogen Relationships. EXPERIENTIA SUPPLEMENTUM 2022; 114:115-136. [PMID: 35544001 PMCID: PMC9208714 DOI: 10.1007/978-3-030-93306-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Microsporidia are poorly understood, ubiquitous eukaryotic parasites that are completely dependent on their hosts for replication. With the discovery of microsporidia species naturally infecting the genetically tractable transparent nematode C. elegans, this host has been used to explore multiple areas of microsporidia biology. Here we review results about microsporidia infections in C. elegans, which began with the discovery of the intestinal-infecting species Nematocida parisii. Recent findings include new species identification in the Nematocida genus, with more intestinal-infecting species, and also a species with broader tissue tropism, the epidermal and muscle-infecting species Nematocida displodere. This species has a longer polar tube infection apparatus, which may enable its wider tissue range. After invasion, multiple Nematocida species appear to fuse host cells, which likely promotes their dissemination within host organs. Localized proteomics identified Nematocida proteins that have direct contact with the C. elegans intestinal cytosol and nucleus, and many of these host-exposed proteins belong to expanded, species-specific gene families. On the host side, forward genetic screens have identified regulators of the Intracellular Pathogen Response (IPR), which is a transcriptional response induced by both microsporidia and the Orsay virus, which is also a natural, obligate intracellular pathogen of the C. elegans intestine. The IPR constitutes a novel immune/stress response that promotes resistance against microsporidia, virus, and heat shock. Overall, the Nematocida/C. elegans system has provided insights about strategies for microsporidia pathogenesis, as well as innate defense pathways against these parasites.
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41
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Wang A, Chen W, Tao S. Genome-wide characterization, evolution, structure, and expression analysis of the F-box genes in Caenorhabditis. BMC Genomics 2021; 22:889. [PMID: 34895149 PMCID: PMC8665587 DOI: 10.1186/s12864-021-08189-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 11/19/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND F-box proteins represent a diverse class of adaptor proteins of the ubiquitin-proteasome system (UPS) that play critical roles in the cell cycle, signal transduction, and immune response by removing or modifying cellular regulators. Among closely related organisms of the Caenorhabditis genus, remarkable divergence in F-box gene copy numbers was caused by sizeable species-specific expansion and contraction. Although F-box gene number expansion plays a vital role in shaping genomic diversity, little is known about molecular evolutionary mechanisms responsible for substantial differences in gene number of F-box genes and their functional diversification in Caenorhabditis. Here, we performed a comprehensive evolution and underlying mechanism analysis of F-box genes in five species of Caenorhabditis genus, including C. brenneri, C. briggsae, C. elegans, C. japonica, and C. remanei. RESULTS Herein, we identified and characterized 594, 192, 377, 39, 1426 F-box homologs encoding putative F-box proteins in the genome of C. brenneri, C. briggsae, C. elegans, C. japonica, and C. remanei, respectively. Our work suggested that extensive species-specific tandem duplication followed by a small amount of gene loss was the primary mechanism responsible for F-box gene number divergence in Caenorhabditis genus. After F-box gene duplication events occurred, multiple mechanisms have contributed to gene structure divergence, including exon/intron gain/loss, exonization/pseudoexonization, exon/intron boundaries alteration, exon splits, and intron elongation by tandem repeats. Based on high-throughput RNA sequencing data analysis, we proposed that F-box gene functions have diversified by sub-functionalization through highly divergent stage-specific expression patterns in Caenorhabditis species. CONCLUSIONS Massive species-specific tandem duplications and occasional gene loss drove the rapid evolution of the F-box gene family in Caenorhabditis, leading to complex gene structural variation and diversified functions affecting growth and development within and among Caenorhabditis species. In summary, our findings outline the evolution of F-box genes in the Caenorhabditis genome and lay the foundation for future functional studies.
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Affiliation(s)
- Ailan Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A & F University, Yangling, 712100, Shaanxi, China.,Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China.,Geneis (Beijing) Co., Beijing, China
| | - Wei Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A & F University, Yangling, 712100, Shaanxi, China.,Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Shiheng Tao
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A & F University, Yangling, 712100, Shaanxi, China. .,Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China.
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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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43
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Gems D, Kern CC, Nour J, Ezcurra M. Reproductive Suicide: Similar Mechanisms of Aging in C. elegans and Pacific Salmon. Front Cell Dev Biol 2021; 9:688788. [PMID: 34513830 PMCID: PMC8430333 DOI: 10.3389/fcell.2021.688788] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/21/2021] [Indexed: 12/17/2022] Open
Abstract
In some species of salmon, reproductive maturity triggers the development of massive pathology resulting from reproductive effort, leading to rapid post-reproductive death. Such reproductive death, which occurs in many semelparous organisms (with a single bout of reproduction), can be prevented by blocking reproductive maturation, and this can increase lifespan dramatically. Reproductive death is often viewed as distinct from senescence in iteroparous organisms (with multiple bouts of reproduction) such as humans. Here we review the evidence that reproductive death occurs in C. elegans and discuss what this means for its use as a model organism to study aging. Inhibiting insulin/IGF-1 signaling and germline removal suppresses reproductive death and greatly extends lifespan in C. elegans, but can also extend lifespan to a small extent in iteroparous organisms. We argue that mechanisms of senescence operative in reproductive death exist in a less catastrophic form in iteroparous organisms, particularly those that involve costly resource reallocation, and exhibit endocrine-regulated plasticity. Thus, mechanisms of senescence in semelparous organisms (including plants) and iteroparous ones form an etiological continuum. Therefore understanding mechanisms of reproductive death in C. elegans can teach us about some mechanisms of senescence that are operative in iteroparous organisms.
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Affiliation(s)
- David Gems
- Institute of Healthy Ageing, Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Carina C. Kern
- Institute of Healthy Ageing, Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Joseph Nour
- Institute of Healthy Ageing, Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Marina Ezcurra
- School of Biosciences, University of Kent, Canterbury, United Kingdom
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44
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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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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: 57] [Impact Index Per Article: 19.0] [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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46
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Nelson C, Ambros V. A cohort of Caenorhabditis species lacking the highly conserved let-7 microRNA. G3 (BETHESDA, MD.) 2021; 11:jkab022. [PMID: 33890616 PMCID: PMC8063082 DOI: 10.1093/g3journal/jkab022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/12/2021] [Indexed: 01/13/2023]
Abstract
The let-7 gene encodes a highly conserved microRNA with critical functions integral to cell fate specification and developmental progression in diverse animals. In Caenorhabditis elegans, let-7 is a component of the heterochronic (developmental timing) gene regulatory network, and loss-of-function mutations of let-7 result in lethality during the larval to adult transition due to misregulation of the conserved let-7 target, lin-41. To date, no bilaterian animal lacking let-7 has been characterized. In this study, we identify a cohort of nematode species within the genus Caenorhabditis, closely related to C. elegans, that lack the let-7 microRNA, owing to absence of the let-7 gene. Using Caenorhabditis sulstoni as a representative let-7-lacking species to characterize normal larval development in the absence of let-7, we demonstrate that, except for the lack of let-7, the heterochronic gene network is otherwise functionally conserved. We also report that species lacking let-7 contain a group of divergent let-7 paralogs-also known as the let-7-family of microRNAs-that have apparently assumed the role of targeting the LIN-41 mRNA.
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Affiliation(s)
- Charles Nelson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Victor Ambros
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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47
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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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48
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Dayi M, Kanzaki N, Sun S, Ide T, Tanaka R, Masuya H, Okabe K, Kajimura H, Kikuchi T. Additional description and genome analyses of Caenorhabditis auriculariae representing the basal lineage of genus Caenorhabditis. Sci Rep 2021; 11:6720. [PMID: 33762598 PMCID: PMC7991662 DOI: 10.1038/s41598-021-85967-z] [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: 10/21/2020] [Accepted: 03/08/2021] [Indexed: 01/31/2023] Open
Abstract
Caenorhabditis auriculariae, which was morphologically described in 1999, was re-isolated from a Platydema mushroom-associated beetle. Based on the re-isolated materials, some morphological characteristics were re-examined and ascribed to the species. In addition, to clarify phylogenetic relationships with other Caenorhabditis species and biological features of the nematode, the whole genome was sequenced and assembled into 109.5 Mb with 16,279 predicted protein-coding genes. Molecular phylogenetic analyses based on ribosomal RNA and 269 single-copy genes revealed the species is closely related to C. sonorae and C. monodelphis placing them at the most basal clade of the genus. C. auriculariae has morphological characteristics clearly differed from those two species and harbours a number of species-specific gene families, indicating its usefulness as a new outgroup species for Caenorhabditis evolutionary studies. A comparison of carbohydrate-active enzyme (CAZy) repertoires in genomes, which we found useful to speculate about the lifestyle of Caenorhabditis nematodes, suggested that C. auriculariae likely has a life-cycle with tight-association with insects.
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Affiliation(s)
- Mehmet Dayi
- grid.410849.00000 0001 0657 3887Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, 5200 Kiyotakecho Kihara, Miyazaki-City, Miyazaki 889-1692 Japan ,grid.412121.50000 0001 1710 3792Forestry Vocational School, Duzce University, 81620 Duzce, Turkey
| | - Natsumi Kanzaki
- grid.417935.d0000 0000 9150 188XKansai Research Center, Forestry and Forest Products Research Institute, 68 Nagaikyutaroh, Momoyama, Fushimi, Kyoto 612-0855 Japan
| | - Simo Sun
- grid.410849.00000 0001 0657 3887Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, 5200 Kiyotakecho Kihara, Miyazaki-City, Miyazaki 889-1692 Japan
| | - Tatsuya Ide
- grid.410801.cDepartment of Zoology, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005 Japan
| | - Ryusei Tanaka
- grid.410849.00000 0001 0657 3887Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, 5200 Kiyotakecho Kihara, Miyazaki-City, Miyazaki 889-1692 Japan
| | - Hayato Masuya
- grid.417935.d0000 0000 9150 188XForestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki 305-8687 Japan
| | - Kimiko Okabe
- grid.417935.d0000 0000 9150 188XForestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki 305-8687 Japan
| | - Hisashi Kajimura
- grid.27476.300000 0001 0943 978XGraduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601 Japan
| | - Taisei Kikuchi
- grid.410849.00000 0001 0657 3887Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, 5200 Kiyotakecho Kihara, Miyazaki-City, Miyazaki 889-1692 Japan
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49
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Félix MA. Evolution: Drivers in a Traffic Jam. Curr Biol 2021; 31:R257-R260. [PMID: 33689727 DOI: 10.1016/j.cub.2021.01.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Genetic loci coding for a toxin and its antidote behave like selfish elements. Two new studies find an accumulation of such elements in one species.
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Affiliation(s)
- Marie-Anne Félix
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France.
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50
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Jankele R, Jelier R, Gönczy P. Physically asymmetric division of the C. elegans zygote ensures invariably successful embryogenesis. eLife 2021; 10:e61714. [PMID: 33620314 PMCID: PMC7972452 DOI: 10.7554/elife.61714] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 02/22/2021] [Indexed: 12/17/2022] Open
Abstract
Asymmetric divisions that yield daughter cells of different sizes are frequent during early embryogenesis, but the importance of such a physical difference for successful development remains poorly understood. Here, we investigated this question using the first division of Caenorhabditis elegans embryos, which yields a large AB cell and a small P1 cell. We equalized AB and P1 sizes using acute genetic inactivation or optogenetic manipulation of the spindle positioning protein LIN-5. We uncovered that only some embryos tolerated equalization, and that there was a size asymmetry threshold for viability. Cell lineage analysis of equalized embryos revealed an array of defects, including faster cell cycle progression in P1 descendants, as well as defects in cell positioning, division orientation, and cell fate. Moreover, equalized embryos were more susceptible to external compression. Overall, we conclude that unequal first cleavage is essential for invariably successful embryonic development of C. elegans.
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Affiliation(s)
- Radek Jankele
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL)LausanneSwitzerland
| | - Rob Jelier
- Centre of Microbial and Plant Genetics, Katholieke Universiteit LeuvenLeuvenBelgium
| | - Pierre Gönczy
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL)LausanneSwitzerland
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