1
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Adams S, Pires-daSilva A. Non-Mendelian transmission of X chromosomes: mechanisms and impact on sex ratios and population dynamics in different breeding systems. Biochem Soc Trans 2024; 52:1777-1784. [PMID: 39149984 DOI: 10.1042/bst20231411] [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: 05/10/2024] [Revised: 07/20/2024] [Accepted: 08/05/2024] [Indexed: 08/17/2024]
Abstract
The non-Mendelian transmission of sex chromosomes during gametogenesis carries significant implications, influencing sex ratios and shaping evolutionary dynamics. Here we focus on known mechanisms that drive non-Mendelian inheritance of X chromosomes during spermatogenesis and their impact on population dynamics in species with different breeding systems. In Drosophila and mice, X-linked drivers targeting Y-bearing sperm for elimination or limiting their fitness, tend to confer unfavourable effects, prompting the evolution of suppressors to mitigate their impact. This leads to a complex ongoing evolutionary arms race to maintain an equal balance of males and females. However, in certain insects and nematodes with XX/X0 sex determination, the preferential production of X-bearing sperm through atypical meiosis yields wild-type populations with highly skewed sex ratios, suggesting non-Mendelian transmission of the X may offer selective advantages in these species. Indeed, models suggest X-meiotic drivers could bolster population size and persistence under certain conditions, challenging the conventional view of their detrimental effects. Furthering our understanding of the diverse mechanisms and evolutionary consequences of non-Mendelian transmission of X chromosomes will provide insights into genetic inheritance, sex determination, and population dynamics, with implications for fundamental research and practical applications.
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Affiliation(s)
- Sally Adams
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K
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2
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Liu P, Yu S, Zheng W, Zhang Q, Qiao J, Li Z, Deng Z, Zhang H. Identification and functional verification of Y-chromosome-specific gene typo-gyf in Bactrocera dorsalis. INSECT SCIENCE 2024; 31:1270-1284. [PMID: 38189161 DOI: 10.1111/1744-7917.13311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 01/09/2024]
Abstract
Genes on the Y chromosome play important roles in male sex determination and development. The identification of Y-chromosome-specific genes not only provides a theoretical basis for the study of male reproductive development, but also offers genetic control targets for agricultural pests. However, Y-chromosome genes are rarely characterized due to their high repeatability and high heterochromatinization, especially in the oriental fruit fly. In this study, 1 011 Y-chromosome-specific candidate sequences were screened from 2 to 4 h Bactrocera dorsalis embryo datasets with the chromosome quotient method, 6 of which were identified as Y-chromosome-specific sequences by polymerase chain reaction, including typo-gyf, a 19 126-bp DNA sequence containing a 575-amino acid open reading frame. Testicular deformation and a significant reduction in sperm number were observed after typo-gyf knockdown with RNA interference in embryos. After typo-gyf knockout with clustered regularly interspaced palindromic repeats (CRISPR) / CRISPR-associated protein 9 in the embryonic stage, the sex ratio of the emergent adults was unbalanced, with far more females than males. A genotype analysis of these females with the Y-chromosome gene MoY revealed no sex reversal. Typo-gyf knockout led to the death of XY individuals in the embryonic stage. We conclude that typo-gyf is an essential gene for male survival, and is also involved in testicular development and spermatogenesis. The identification of typo-gyf and its functional verification provide insight into the roles of Y-chromosome genes in male development.
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Affiliation(s)
- Peipei Liu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shuning Yu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wenping Zheng
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qiuyuan Zhang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiao Qiao
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ziniu Li
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhurong Deng
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hongyu Zhang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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3
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Bunting MD, Godahewa GI, McPherson NO, Robertson LJ, Gierus L, Piltz SG, Edwards O, Tizard M, Thomas PQ. Investigating the potential of X chromosome shredding for mouse genetic biocontrol. Sci Rep 2024; 14:13466. [PMID: 38866815 PMCID: PMC11169450 DOI: 10.1038/s41598-024-63706-4] [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: 01/08/2024] [Accepted: 05/31/2024] [Indexed: 06/14/2024] Open
Abstract
CRISPR-Cas9 technology has facilitated development of strategies that can potentially provide more humane and effective methods to control invasive vertebrate species, such as mice. One promising strategy is X chromosome shredding which aims to bias offspring towards males, resulting in a gradual and unsustainable decline of females. This method has been explored in insects with encouraging results. Here, we investigated this strategy in Mus musculus by targeting repeat DNA sequences on the X chromosome with the aim of inducing sufficient DNA damage to specifically eliminate X chromosome-bearing sperm during gametogenesis. We tested three different guide RNAs (gRNAs) targeting different repeats on the X chromosome, together with three male germline-specific promoters for inducing Cas9 expression at different stages of spermatogenesis. A modest bias towards mature Y-bearing sperm was detected in some transgenic males, although this did not translate into significant male-biasing of offspring. Instead, cleavage of the X chromosome during meiosis typically resulted in a spermatogenic block, manifest as small testes volume, empty tubules, low sperm concentration, and sub/infertility. Our study highlights the importance of controlling the timing of CRISPR-Cas9 activity during mammalian spermatogenesis and the sensitivity of spermatocytes to X chromosome disruption.
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Affiliation(s)
- Mark D Bunting
- School of Biomedicine and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Gelshan I Godahewa
- School of Biomedicine and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- CSIRO Environment, Floreat, WA, 6014, Australia
| | - Nicole O McPherson
- School of Biomedicine and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Louise J Robertson
- School of Biomedicine and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Luke Gierus
- School of Biomedicine and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Sandra G Piltz
- School of Biomedicine and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | | | - Mark Tizard
- Australian Centre for Disease Preparedness, CSIRO Health and Biosecurity, Geelong, VIC, 3220, Australia
| | - Paul Q Thomas
- School of Biomedicine and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia.
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia.
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4
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Sanz Juste S, Okamoto EM, Nguyen C, Feng X, López Del Amo V. Next-generation CRISPR gene-drive systems using Cas12a nuclease. Nat Commun 2023; 14:6388. [PMID: 37821497 PMCID: PMC10567717 DOI: 10.1038/s41467-023-42183-9] [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: 02/20/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023] Open
Abstract
One method for reducing the impact of vector-borne diseases is through the use of CRISPR-based gene drives, which manipulate insect populations due to their ability to rapidly propagate desired genetic traits into a target population. However, all current gene drives employ a Cas9 nuclease that is constitutively active, impeding our control over their propagation abilities and limiting the generation of alternative gene drive arrangements. Yet, other nucleases such as the temperature sensitive Cas12a have not been explored for gene drive designs in insects. To address this, we herein present a proof-of-concept gene-drive system driven by Cas12a that can be regulated via temperature modulation. Furthermore, we combined Cas9 and Cas12a to build double gene drives capable of simultaneously spreading two independent engineered alleles. The development of Cas12a-mediated gene drives provides an innovative option for designing next-generation vector control strategies to combat disease vectors and agricultural pests.
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Affiliation(s)
- Sara Sanz Juste
- Department of Epigenetics & Molecular Carcinogenesis at MD Anderson, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
- Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Emily M Okamoto
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Christina Nguyen
- University of Texas Health Science Center, School of Public Health, Department of Epidemiology, Human Genetics, and Environmental Sciences, Center for Infectious Diseases, Houston, TX, 77030, USA
| | - Xuechun Feng
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA.
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518106, China.
| | - Víctor López Del Amo
- University of Texas Health Science Center, School of Public Health, Department of Epidemiology, Human Genetics, and Environmental Sciences, Center for Infectious Diseases, Houston, TX, 77030, USA.
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5
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Pan M, Champer J. Making waves: Comparative analysis of gene drive spread characteristics in a continuous space model. Mol Ecol 2023; 32:5673-5694. [PMID: 37694511 DOI: 10.1111/mec.17131] [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: 11/11/2022] [Revised: 08/16/2023] [Accepted: 08/31/2023] [Indexed: 09/12/2023]
Abstract
With their ability to rapidly increase in frequency, gene drives can be used to modify or suppress target populations after an initial release of drive individuals. Recent advances have revealed many possibilities for different types of drives, and several of these have been realized in experiments. These drives have advantages and disadvantages related to their ease of construction, confinement and capacity to be used for modification or suppression. Though characteristics of these drives have been explored in modelling studies, assessment in continuous space environments has been limited, often focusing on outcomes rather than fundamental properties. Here, we conduct a comparative analysis of many different gene drive types that have the capacity to form a wave of advance in continuous space using individual-based simulations in continuous space. We evaluate the drive wave speed as a function of drive performance and ecological parameters, which reveals substantial differences between drive performance in panmictic versus spatial environments. In particular, we find that suppression drive waves are uniquely vulnerable to fitness costs and undesired CRISPR cleavage activity in embryos by maternal deposition. Some drives, however, retain robust performance even with widely varying efficiency parameters. To gain a better understanding of drive waves, we compare their panmictic performance and find that the rate of wild-type allele removal is correlated with drive wave speed, though this is also affected by other factors. Overall, our results provide a useful resource for understanding the performance of drives in spatially continuous environments, which may be most representative of potential drive deployment in many relevant scenarios.
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Affiliation(s)
- Mingzuyu Pan
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, Beijing, China
| | - Jackson Champer
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, Beijing, China
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6
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Kim J, Harris KD, Kim IK, Shemesh S, Messer PW, Greenbaum G. Incorporating ecology into gene drive modelling. Ecol Lett 2023; 26 Suppl 1:S62-S80. [PMID: 37840022 DOI: 10.1111/ele.14194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 10/17/2023]
Abstract
Gene drive technology, in which fast-spreading engineered drive alleles are introduced into wild populations, represents a promising new tool in the fight against vector-borne diseases, agricultural pests and invasive species. Due to the risks involved, gene drives have so far only been tested in laboratory settings while their population-level behaviour is mainly studied using mathematical and computational models. The spread of a gene drive is a rapid evolutionary process that occurs over timescales similar to many ecological processes. This can potentially generate strong eco-evolutionary feedback that could profoundly affect the dynamics and outcome of a gene drive release. We, therefore, argue for the importance of incorporating ecological features into gene drive models. We describe the key ecological features that could affect gene drive behaviour, such as population structure, life-history, environmental variation and mode of selection. We review previous gene drive modelling efforts and identify areas where further research is needed. As gene drive technology approaches the level of field experimentation, it is crucial to evaluate gene drive dynamics, potential outcomes, and risks realistically by including ecological processes.
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Affiliation(s)
- Jaehee Kim
- Department of Computational Biology, Cornell University, Ithaca, New York, USA
| | - Keith D Harris
- Department of Ecology, Evolution and Behavior, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isabel K Kim
- Department of Computational Biology, Cornell University, Ithaca, New York, USA
| | - Shahar Shemesh
- Department of Ecology, Evolution and Behavior, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Philipp W Messer
- Department of Computational Biology, Cornell University, Ithaca, New York, USA
| | - Gili Greenbaum
- Department of Ecology, Evolution and Behavior, The Hebrew University of Jerusalem, Jerusalem, Israel
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7
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Djihinto O, Saizonou HD, Djogbenou LS. Single nucleotide polymorphism (SNP) in the doublesex ( dsx) gene splice sites and relevance for its alternative splicing in the malaria vector Anopheles gambiae. Wellcome Open Res 2023; 7:31. [PMID: 37546169 PMCID: PMC10397894 DOI: 10.12688/wellcomeopenres.17572.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2023] [Indexed: 08/08/2023] Open
Abstract
Background: Malaria burden continues to be significant in tropical regions, and conventional vector control methods are faced with challenges such as insecticide resistance. To overcome these challenges, additional vector control interventions are vital and include modern genetic approaches as well as classical methods like the sterile insect technique (SIT). In the major human malaria vector Anopheles gambiae, a candidate gene favourable for sterility induction is the doublesex ( dsx) gene, involved in mosquitos' somatic sexually dimorphic traits determination. However, the pathways that trigger the signal of dsx gene exon skipping alternative splicing mechanism in anopheline mosquitoes are not well characterized. This study aims to screen the An. gambiae dsx gene splice site sequences for single-nucleotide polymorphisms (SNPs) that could be critical to its alternative splicing. Methods: Variant annotation data from Ag1000G project phase 2 was analysed, in order to identify splice-relevant SNPs within acceptor and donor splice sites of the An. gambiae dsx gene ( Agdsx). Results: SNPs were found in both donor and acceptor sites of the Agdsx. No splice-relevant SNPs were identified in the female-specific intron 4 acceptor site and the corresponding region in males. Two SNPs (rs48712947, rs48712962) were found in the female-specific donor site of exon 5. They were not specific to either males or females as the rs48712947 was found in female mosquitoes from Cameroon, and in both males and females from Burkina Faso. In the other splice sites, the intron 3 acceptor site carried the greatest abundance of SNPs. Conclusions: There were no gender association between the identified SNPs and the random distribution of these SNPs in mosquito populations. The SNPs in Agdsx splice sites are not critical for the alternative splicing. Other molecular mechanisms should be considered and investigated.
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Affiliation(s)
- Oswald Djihinto
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Abomey-Calavi, 01BP526 Cotonou, Benin
| | - Helga D.M. Saizonou
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Abomey-Calavi, 01BP526 Cotonou, Benin
| | - Luc S. Djogbenou
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Abomey-Calavi, 01BP526 Cotonou, Benin
- Institut Régional de Santé Publique, University of Abomey-Calavi, Ouidah, BP 384 Ouidah, Benin
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
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8
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Djihinto O, Saizonou HD, Djogbenou LS. Single nucleotide polymorphism (SNP) in the doublesex (dsx) gene splice sites and relevance for its alternative splicing in the malaria vector Anopheles gambiae. Wellcome Open Res 2022. [DOI: 10.12688/wellcomeopenres.17572.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background: Malaria burden continues to be significant in tropical regions, and conventional vector control methods are faced with challenges such as insecticide resistance. To overcome these challenges, additional vector control interventions are vital and include modern genetic approaches as well as classical methods like the sterile insect technique (SIT). In the major human malaria vector Anopheles gambiae, a candidate gene favourable for sterility induction is the doublesex (dsx) gene, involved in mosquitos’ somatic sexually dimorphic traits determination. However, the pathways that trigger the signal of dsx gene exon skipping alternative splicing mechanism in anopheline mosquitoes are not well characterized. This study aims to screen the An. gambiae dsx gene splice site sequences for single-nucleotide polymorphisms (SNPs) that could be critical to its alternative splicing. Methods: Variant annotation data from Ag1000G project phase 2 was analysed, in order to identify splice-relevant SNPs within acceptor and donor splice sites of the An. gambiae dsx gene (Agdsx). Results: SNPs were found in both donor and acceptor sites of the Agdsx. No splice-relevant SNPs were identified in the female-specific intron 4 acceptor site and the corresponding region in males. Two SNPs (rs48712947, rs48712962) were found in the female-specific donor site of exon 5. They were not specific to either males or females as the rs48712947 was found in female mosquitoes from Cameroon, and in both males and females from Burkina Faso. In the other splice sites, the intron 3 acceptor site carried the greatest abundance of SNPs. Conclusions: There were no gender association between the identified SNPs and the random distribution of these SNPs in mosquito populations. The SNPs in Agdsx splice sites are not critical for the alternative splicing. Other molecular mechanisms should be considered and investigated.
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9
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Abstract
Invasive rodents are a major cause of environmental damage and biodiversity loss, particularly on islands. Unlike insects, genetic biocontrol strategies including population-suppressing gene drives with biased inheritance have not been developed in mice. Here, we demonstrate a gene drive strategy (tCRISPR) that leverages super-Mendelian transmission of the t haplotype to spread inactivating mutations in a haplosufficient female fertility gene (Prl). Using spatially explicit individual-based in silico modeling, we show that tCRISPR can eradicate island populations under a range of realistic field-based parameter values. We also engineer transgenic tCRISPR mice that, crucially, exhibit biased transmission of the modified t haplotype and Prl mutations at levels our modeling predicts would be sufficient for eradication. This is an example of a feasible gene drive system for invasive alien rodent population control.
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10
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Birand A, Cassey P, Ross JV, Thomas PQ, Prowse TAA. Scalability of genetic biocontrols for eradicating invasive alien mammals. NEOBIOTA 2022. [DOI: 10.3897/neobiota.74.82394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
CRISPR-based gene drives offer novel solutions for controlling invasive alien species, which could ultimately extend eradication efforts to continental scales. Gene drives for suppressing invasive alien vertebrates are now under development. Using a landscape-scale individual-based model, we present the first estimates of times to eradication for long-lived alien mammals. We show that demography and life-history traits interact to determine the scalability of gene drives for vertebrate pest eradication. Notably, optimism around eradicating smaller-bodied pests (rodents and rabbits) with gene-drive technologies does not easily translate into eradication of larger-bodied alien species (cats and foxes).
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11
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Pacheco ID, Walling LL, Atkinson PW. Gene Editing and Genetic Control of Hemipteran Pests: Progress, Challenges and Perspectives. Front Bioeng Biotechnol 2022; 10:900785. [PMID: 35747496 PMCID: PMC9209771 DOI: 10.3389/fbioe.2022.900785] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/09/2022] [Indexed: 12/16/2022] Open
Abstract
The origin of the order Hemiptera can be traced to the late Permian Period more than 230 MYA, well before the origin of flowering plants 100 MY later in during the Cretaceous period. Hemipteran species consume their liquid diets using a sucking proboscis; for phytophagous hemipterans their mouthparts (stylets) are elegant structures that enable voracious feeding from plant xylem or phloem. This adaptation has resulted in some hemipteran species becoming globally significant pests of agriculture resulting in significant annual crop losses. Due to the reliance on chemical insecticides for the control of insect pests in agricultural settings, many hemipteran pests have evolved resistance to insecticides resulting in an urgent need to develop new, species-specific and environmentally friendly methods of pest control. The rapid advances in CRISPR/Cas9 technologies in model insects such as Drosophila melanogaster, Tribolium castaneum, Bombyx mori, and Aedes aegypti has spurred a new round of innovative genetic control strategies in the Diptera and Lepidoptera and an increased interest in assessing genetic control technologies for the Hemiptera. Genetic control approaches in the Hemiptera have, to date, been largely overlooked due to the problems of introducing genetic material into the germline of these insects. The high frequency of CRISPR-mediated mutagenesis in model insect species suggest that, if the delivery problem for Hemiptera could be solved, then gene editing in the Hemiptera might be quickly achieved. Significant advances in CRISPR/Cas9 editing have been realized in nine species of Hemiptera over the past 4 years. Here we review progress in the Hemiptera and discuss the challenges and opportunities for extending contemporary genetic control strategies into species in this agriculturally important insect orderr.
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Affiliation(s)
- Inaiara D. Pacheco
- Department of Entomology, University of California, Riverside, Riverside, CA, United States
| | - Linda L. Walling
- Department of Botany & Plant Sciences, University of California, Riverside, Riverside, CA, United States
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | - Peter W. Atkinson
- Department of Entomology, University of California, Riverside, Riverside, CA, United States
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
- *Correspondence: Peter W. Atkinson,
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12
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Wang GH, Du J, Chu CY, Madhav M, Hughes GL, Champer J. Symbionts and gene drive: two strategies to combat vector-borne disease. Trends Genet 2022; 38:708-723. [PMID: 35314082 DOI: 10.1016/j.tig.2022.02.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/24/2022] [Accepted: 02/24/2022] [Indexed: 01/26/2023]
Abstract
Mosquitoes bring global health problems by transmitting parasites and viruses such as malaria and dengue. Unfortunately, current insecticide-based control strategies are only moderately effective because of high cost and resistance. Thus, scalable, sustainable, and cost-effective strategies are needed for mosquito-borne disease control. Symbiont-based and genome engineering-based approaches provide new tools that show promise for meeting these criteria, enabling modification or suppression approaches. Symbiotic bacteria like Wolbachia are maternally inherited and manipulate mosquito host reproduction to enhance their vertical transmission. Genome engineering-based gene drive methods, in which mosquitoes are genetically altered to spread drive alleles throughout wild populations, are also proving to be a potentially powerful approach in the laboratory. Here, we review the latest developments in both symbionts and gene drive-based methods. We describe some notable similarities, as well as distinctions and obstacles, relating to these promising technologies.
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Affiliation(s)
- Guan-Hong Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jie Du
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Chen Yi Chu
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Mukund Madhav
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Disease, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Grant L Hughes
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Disease, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Jackson Champer
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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13
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Djihinto O, Saizonou HD, Djogbenou LS. Single nucleotide polymorphism (SNP) in the doublesex (dsx) gene splice sites and relevance for its alternative splicing in the malaria vector Anopheles gambiae. Wellcome Open Res 2022. [DOI: 10.12688/wellcomeopenres.17572.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: The malaria burden continues to be significant in tropical regions, and conventional vector control methods are faced with challenges such as insecticide resistance. To overcome these challenges, additional vector control interventions are vital and include modern genetic approaches as well as classical methods like the sterile insect technique (SIT). In the major human malaria vector Anopheles gambiae, a candidate gene favourable for sterility induction is the doublesex (dsx) gene, encoding somatic sexually dimorphic traits in mosquitoes. However, the mechanism that regulates the expression of this gene in anopheline mosquitoes is poorly understood. This study aimed to screen the An. gambiae dsx gene splice site sequences for single nucleotide polymorphisms (SNPs) that could be critical to its alternative splicing. Methods: Variant annotation data from Ag1000G project phase 2 was analysed, in order to identify splice-relevant SNPs within acceptor and donor splice sites of the An. gambiae dsx gene (Agdsx). Results: SNPs were found in both donor and acceptor sites of the Agdsx. No splice-relevant SNPs were identified in the female-specific intron 4 acceptor site and the corresponding region in males. Two SNPs (rs48712947, rs48712962) were found in the female-specific donor site of exon 5. They were not specific to either males or females as the rs48712947 was found in female mosquitoes from Cameroon, and in both males and females from Burkina Faso. In the other splice sites, the intron 3 acceptor site carried the greatest abundance of SNPs. Conclusions: There were no gender association between the identified SNPs and the random distribution of these SNPs in mosquito populations. The SNPs in Agdsx splice sites are not critical for the alternative splicing. Other molecular mechanisms should be considered and investigated.
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14
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Birand A, Cassey P, Ross JV, Russell JC, Thomas P, Prowse TAA. Gene drives for vertebrate pest control: realistic spatial modelling of eradication probabilities and times for island mouse populations. Mol Ecol 2022; 31:1907-1923. [PMID: 35073448 PMCID: PMC9303646 DOI: 10.1111/mec.16361] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 01/07/2022] [Accepted: 01/12/2022] [Indexed: 11/29/2022]
Abstract
Invasive alien species continue to threaten global biodiversity. CRISPR‐based gene drives, which can theoretically spread through populations despite imparting a fitness cost, could be used to suppress or eradicate pest populations. We develop an individual‐based, spatially explicit, stochastic model to simulate the ability of CRISPR‐based homing and X chromosome shredding drives to eradicate populations of invasive house mice (Mus muculus) from islands. Using the model, we explore the interactive effect of the efficiency of the drive constructs and the spatial ecology of the target population on the outcome of a gene‐drive release. We also consider the impact of polyandrous mating and sperm competition, which could compromise the efficacy of some gene‐drive strategies. Our results show that both drive strategies could be used to eradicate large populations of mice. Whereas parameters related to drive efficiency and demography strongly influence drive performance, we find that sperm competition following polyandrous mating is unlikely to impact the outcome of an eradication effort substantially. Assumptions regarding the spatial ecology of mice influenced the probability of and time required for eradication, with short‐range dispersal capacities and limited mate‐search areas producing ‘chase’ dynamics across the island characterized by cycles of local extinction and recolonization by mice. We also show that highly efficient drives are not always optimal, when dispersal and mate‐search capabilities are low. Rapid local population suppression around the introduction sites can cause loss of the gene drive before it can spread to the entire island. We conclude that, although the design of efficient gene drives is undoubtedly critical, accurate data on the spatial ecology of target species are critical for predicting the result of a gene‐drive release.
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Affiliation(s)
- Aysegul Birand
- Invasion Science and Wildlife Ecology Lab, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Phillip Cassey
- Invasion Science and Wildlife Ecology Lab, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Joshua V Ross
- School of Mathematical Sciences, The University of Adelaide, Adelaide, Australia
| | - James C Russell
- School of Biological Sciences, Department of Statistics, University of Auckland, Auckland, New Zealand
| | - Paul Thomas
- School of Medicine, Robinson Research Institute, The University of Adelaide, Adelaide, Australia.,South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Thomas A A Prowse
- Invasion Science and Wildlife Ecology Lab, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
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15
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Bunting MD, Pfitzner C, Gierus L, White M, Piltz S, Thomas PQ. Generation of Gene Drive Mice for Invasive Pest Population Suppression. Methods Mol Biol 2022; 2495:203-230. [PMID: 35696035 DOI: 10.1007/978-1-0716-2301-5_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Gene drives are genetic elements that are transmitted to greater than 50% of offspring and have potential for population modification or suppression. While gene drives are known to occur naturally, the recent emergence of CRISPR-Cas9 genome-editing technology has enabled generation of synthetic gene drives in a range of organisms including mosquitos, flies, and yeast. For example, studies in Anopheles mosquitos have demonstrated >95% transmission of CRISPR-engineered gene drive constructs, providing a possible strategy for malaria control. Recently published studies have also indicated that it may be possible to develop gene drive technology in invasive rodents such as mice. Here, we discuss the prospects for gene drive development in mice, including synthetic "homing drive" and X-shredder strategies as well as modifications of the naturally occurring t haplotype. We also provide detailed protocols for generation of gene drive mice through incorporation of plasmid-based transgenes in a targeted and non-targeted manner. Importantly, these protocols can be used for generating transgenic mice for any project that requires insertion of kilobase-scale transgenes such as knock-in of fluorescent reporters, gene swaps, overexpression/ectopic expression studies, and conditional "floxed" alleles.
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Affiliation(s)
- Mark D Bunting
- School of Medicine, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Chandran Pfitzner
- School of Medicine, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Luke Gierus
- School of Medicine, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Melissa White
- School of Medicine, University of Adelaide, North Terrace, Adelaide, SA, Australia
- South Australian Genome Editing Facility, North Terrace, Adelaide, SA, Australia
| | - Sandra Piltz
- School of Medicine, University of Adelaide, North Terrace, Adelaide, SA, Australia
- South Australian Genome Editing Facility, North Terrace, Adelaide, SA, Australia
| | - Paul Q Thomas
- School of Medicine, University of Adelaide, North Terrace, Adelaide, SA, Australia.
- South Australian Genome Editing Facility, North Terrace, Adelaide, SA, Australia.
- South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia.
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16
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Abstract
Gene drives are selfish genetic elements that are transmitted to progeny at super-Mendelian (>50%) frequencies. Recently developed CRISPR-Cas9-based gene-drive systems are highly efficient in laboratory settings, offering the potential to reduce the prevalence of vector-borne diseases, crop pests and non-native invasive species. However, concerns have been raised regarding the potential unintended impacts of gene-drive systems. This Review summarizes the phenomenal progress in this field, focusing on optimal design features for full-drive elements (drives with linked Cas9 and guide RNA components) that either suppress target mosquito populations or modify them to prevent pathogen transmission, allelic drives for updating genetic elements, mitigating strategies including trans-complementing split-drives and genetic neutralizing elements, and the adaptation of drive technology to other organisms. These scientific advances, combined with ethical and social considerations, will facilitate the transparent and responsible advancement of these technologies towards field implementation.
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Affiliation(s)
- Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA.
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17
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Champer SE, Oakes N, Sharma R, García-Díaz P, Champer J, Messer PW. Modeling CRISPR gene drives for suppression of invasive rodents using a supervised machine learning framework. PLoS Comput Biol 2021; 17:e1009660. [PMID: 34965253 PMCID: PMC8716047 DOI: 10.1371/journal.pcbi.1009660] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 11/18/2021] [Indexed: 02/07/2023] Open
Abstract
Invasive rodent populations pose a threat to biodiversity across the globe. When confronted with these invaders, native species that evolved independently are often defenseless. CRISPR gene drive systems could provide a solution to this problem by spreading transgenes among invaders that induce population collapse, and could be deployed even where traditional control methods are impractical or prohibitively expensive. Here, we develop a high-fidelity model of an island population of invasive rodents that includes three types of suppression gene drive systems. The individual-based model is spatially explicit, allows for overlapping generations and a fluctuating population size, and includes variables for drive fitness, efficiency, resistance allele formation rate, as well as a variety of ecological parameters. The computational burden of evaluating a model with such a high number of parameters presents a substantial barrier to a comprehensive understanding of its outcome space. We therefore accompany our population model with a meta-model that utilizes supervised machine learning to approximate the outcome space of the underlying model with a high degree of accuracy. This enables us to conduct an exhaustive inquiry of the population model, including variance-based sensitivity analyses using tens of millions of evaluations. Our results suggest that sufficiently capable gene drive systems have the potential to eliminate island populations of rodents under a wide range of demographic assumptions, though only if resistance can be kept to a minimal level. This study highlights the power of supervised machine learning to identify the key parameters and processes that determine the population dynamics of a complex evolutionary system.
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Affiliation(s)
- Samuel E. Champer
- Department of Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Nathan Oakes
- Department of Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Ronin Sharma
- Department of Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Pablo García-Díaz
- Manaaki Whenua–Landcare Research, Lincoln, New Zealand and School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Jackson Champer
- Department of Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Philipp W. Messer
- Department of Computational Biology, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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18
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Barnhill-Dilling SK, Kokotovich A, Delborne JA. The Decision Phases Framework for Public Engagement: Engaging Stakeholders about Gene Editing in the Wild. Hastings Cent Rep 2021; 51 Suppl 2:S48-S61. [PMID: 34905240 DOI: 10.1002/hast.1320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Some experts and advocates propose environmental biotechnologies such as genetic engineering, gene drive systems, and synthetic biology as potential solutions to accelerating rates of species loss. While these tools may offer hope for a seemingly intractable problem, they also present potential governance challenges for which innovative decision-making systems are required. Two of the perennial governance challenges include, when are broader stakeholder groups involved in these decisions and who exactly should be involved? We propose the decision phases framework-which includes research and development, regulatory review, and deployment, management, and monitoring-as a framework for identifying which stakeholders might be best suited for different phases throughout the innovation and deployment of emerging environmental biotechnologies for species protection.
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19
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Warburton B, Eason C, Fisher P, Hancox N, Hopkins B, Nugent G, Ogilvie S, Prowse TAA, Ross J, Cowan PE. Alternatives for mammal pest control in New Zealand in the context of concerns about 1080 toxicant (sodium fluoroacetate). NEW ZEALAND JOURNAL OF ZOOLOGY 2021. [DOI: 10.1080/03014223.2021.1977345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | - Charles Eason
- Lincoln University, Department of Pest Management and Conservation, Lincoln, New Zealand
| | - Penny Fisher
- Manaaki Whenua – Landcare Research, Lincoln, New Zealand
| | | | - Brian Hopkins
- Manaaki Whenua – Landcare Research, Lincoln, New Zealand
| | - Graham Nugent
- Manaaki Whenua – Landcare Research, Lincoln, New Zealand
| | - Shaun Ogilvie
- Eco Research Associates Ltd, Christchurch, New Zealand
| | | | - James Ross
- Lincoln University, Department of Pest Management and Conservation, Lincoln, New Zealand
| | - Phil E. Cowan
- Manaaki Whenua – Landcare Research, Lincoln, New Zealand
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20
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Mackintosh C, Pomiankowski A, Scott MF. X-linked meiotic drive can boost population size and persistence. Genetics 2021; 217:1-11. [PMID: 33683360 DOI: 10.1093/genetics/iyaa018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 11/16/2020] [Indexed: 11/14/2022] Open
Abstract
X-linked meiotic drivers cause X-bearing sperm to be produced in excess by male carriers, leading to female-biased sex ratios. Here, we find general conditions for the spread and fixation of X-linked alleles. Our conditions show that the spread of X-linked alleles depends on sex-specific selection and transmission rather than the time spent in each sex. Applying this logic to meiotic drive, we show that polymorphism is heavily dependent on sperm competition induced both by female and male mating behavior and the degree of compensation to gamete loss in the ejaculate size of drive males. We extend these evolutionary models to investigate the demographic consequences of biased sex ratios. Our results suggest driving X-alleles that invade and reach polymorphism (or fix and do not bias segregation excessively) will boost population size and persistence time by increasing population productivity, demonstrating the potential for selfish genetic elements to move sex ratios closer to the population-level optimum. However, when the spread of drive causes strong sex-ratio bias, it can lead to populations with so few males that females remain unmated, cannot produce offspring, and go extinct. This outcome is exacerbated when the male mating rate is low. We suggest that researchers should consider the potential for ecologically beneficial side effects of selfish genetic elements, especially in light of proposals to use meiotic drive for biological control.
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Affiliation(s)
- Carl Mackintosh
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.,CoMPLEX, University College London, London WC1E 6BT, UK
| | - Andrew Pomiankowski
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.,CoMPLEX, University College London, London WC1E 6BT, UK
| | - Michael F Scott
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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21
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Verma P, Reeves RG, Gokhale CS. A common gene drive language eases regulatory process and eco-evolutionary extensions. BMC Ecol Evol 2021; 21:156. [PMID: 34372763 PMCID: PMC8351217 DOI: 10.1186/s12862-021-01881-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 07/12/2021] [Indexed: 02/08/2023] Open
Abstract
Background Synthetic gene drive technologies aim to spread transgenic constructs into wild populations even when they impose organismal fitness disadvantages. The extraordinary diversity of plausible drive mechanisms and the range of selective parameters they may encounter makes it very difficult to convey their relative predicted properties, particularly where multiple approaches are combined. The sheer number of published manuscripts in this field, experimental and theoretical, the numerous techniques resulting in an explosion in the gene drive vocabulary hinder the regulators’ point of view. We address this concern by defining a simplified parameter based language of synthetic drives. Results Employing the classical population dynamics approach, we show that different drive construct (replacement) mechanisms can be condensed and evaluated on an equal footing even where they incorporate multiple replacement drives approaches. Using a common language, it is then possible to compare various model properties, a task desired by regulators and policymakers. The generalization allows us to extend the study of the invasion dynamics of replacement drives analytically and, in a spatial setting, the resilience of the released drive constructs. The derived framework is available as a standalone tool. Conclusion Besides comparing available drive constructs, our tool is also useful for educational purpose. Users can also explore the evolutionary dynamics of future hypothetical combination drive scenarios. Thus, our results appraise the properties and robustness of drives and provide an intuitive and objective way for risk assessment, informing policies, and enhancing public engagement with proposed and future gene drive approaches.
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Affiliation(s)
- Prateek Verma
- Research Group for Theoretical Models of Eco-evolutionary Dynamics, Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany.
| | - R Guy Reeves
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Chaitanya S Gokhale
- Research Group for Theoretical Models of Eco-evolutionary Dynamics, Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
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22
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Chakraborty M, Ramaiah A, Adolfi A, Halas P, Kaduskar B, Ngo LT, Jayaprasad S, Paul K, Whadgar S, Srinivasan S, Subramani S, Bier E, James AA, Emerson JJ. Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly. BMC Biol 2021; 19:28. [PMID: 33568145 PMCID: PMC7876825 DOI: 10.1186/s12915-021-00963-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/19/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The mosquito Anopheles stephensi is a vector of urban malaria in Asia that recently invaded Africa. Studying the genetic basis of vectorial capacity and engineering genetic interventions are both impeded by limitations of a vector's genome assembly. The existing assemblies of An. stephensi are draft-quality and contain thousands of sequence gaps, potentially missing genetic elements important for its biology and evolution. RESULTS To access previously intractable genomic regions, we generated a reference-grade genome assembly and full transcript annotations that achieve a new standard for reference genomes of disease vectors. Here, we report novel species-specific transposable element (TE) families and insertions in functional genetic elements, demonstrating the widespread role of TEs in genome evolution and phenotypic variation. We discovered 29 previously hidden members of insecticide resistance genes, uncovering new candidate genetic elements for the widespread insecticide resistance observed in An. stephensi. We identified 2.4 Mb of the Y chromosome and seven new male-linked gene candidates, representing the most extensive coverage of the Y chromosome in any mosquito. By tracking full-length mRNA for > 15 days following blood feeding, we discover distinct roles of previously uncharacterized genes in blood metabolism and female reproduction. The Y-linked heterochromatin landscape reveals extensive accumulation of long-terminal repeat retrotransposons throughout the evolution and degeneration of this chromosome. Finally, we identify a novel Y-linked putative transcription factor that is expressed constitutively throughout male development and adulthood, suggesting an important role. CONCLUSION Collectively, these results and resources underscore the significance of previously hidden genomic elements in the biology of malaria mosquitoes and will accelerate the development of genetic control strategies of malaria transmission.
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Affiliation(s)
- Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| | - Arunachalam Ramaiah
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093-0335, USA
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India
| | - Adriana Adolfi
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, 92697, USA
| | - Paige Halas
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, 92697, USA
| | - Bhagyashree Kaduskar
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093-0335, USA
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India
| | - Luna Thanh Ngo
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| | - Suvratha Jayaprasad
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, KA, 560100, India
| | - Kiran Paul
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, KA, 560100, India
| | - Saurabh Whadgar
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, KA, 560100, India
| | - Subhashini Srinivasan
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, KA, 560100, India
| | - Suresh Subramani
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India
- Section of Molecular Biology, University of California, San Diego, La Jolla, CA, 92093-0322, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093-0335, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093-0335, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093-0335, USA
| | - Anthony A James
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, 92697, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093-0335, USA
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697, USA
| | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA.
- Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA.
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23
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Manser A, König B, Lindholm AK. Polyandry blocks gene drive in a wild house mouse population. Nat Commun 2020; 11:5590. [PMID: 33149121 PMCID: PMC7643059 DOI: 10.1038/s41467-020-18967-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 09/21/2020] [Indexed: 12/18/2022] Open
Abstract
Gene drives are genetic elements that manipulate Mendelian inheritance ratios in their favour. Understanding the forces that explain drive frequency in natural populations is a long-standing focus of evolutionary research. Recently, the possibility to create artificial drive constructs to modify pest populations has exacerbated our need to understand how drive spreads in natural populations. Here, we study the impact of polyandry on a well-known gene drive, called t haplotype, in an intensively monitored population of wild house mice. First, we show that house mice are highly polyandrous: 47% of 682 litters were sired by more than one male. Second, we find that drive-carrying males are particularly compromised in sperm competition, resulting in reduced reproductive success. As a result, drive frequency decreased during the 4.5 year observation period. Overall, we provide the first direct evidence that the spread of a gene drive is hampered by reproductive behaviour in a natural population. This study resolves a long-standing mystery of why t haplotypes, an example of selfish genes, have persisted at unexpectedly low frequencies in wild mouse populations. It shows that multiple mating by females, which is more common at higher mouse population densities, decreases the frequency of driving t haplotypes.
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Affiliation(s)
- Andri Manser
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland. .,Department of Evolution, Ecology and Behaviour, University of Liverpool, Biosciences Building, Crown Street, Liverpool, UK.
| | - Barbara König
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland
| | - Anna K Lindholm
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland
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24
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Dhole S, Lloyd AL, Gould F. Gene Drive Dynamics in Natural Populations: The Importance of Density Dependence, Space, and Sex. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2020; 51:505-531. [PMID: 34366722 PMCID: PMC8340601 DOI: 10.1146/annurev-ecolsys-031120-101013] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The spread of synthetic gene drives is often discussed in the context of panmictic populations connected by gene flow and described with simple deterministic models. Under such assumptions, an entire species could be altered by releasing a single individual carrying an invasive gene drive, such as a standard homing drive. While this remains a theoretical possibility, gene drive spread in natural populations is more complex and merits a more realistic assessment. The fate of any gene drive released in a population would be inextricably linked to the population's ecology. Given the uncertainty often involved in ecological assessment of natural populations, understanding the sensitivity of gene drive spread to important ecological factors is critical. Here we review how different forms of density dependence, spatial heterogeneity, and mating behaviors can impact the spread of self-sustaining gene drives. We highlight specific aspects of gene drive dynamics and the target populations that need further research.
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Affiliation(s)
- Sumit Dhole
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Alun L Lloyd
- Biomathematics Graduate Program and Department of Mathematics, North Carolina State University, Raleigh, North Carolina 27695-8213, USA
- Genetic Engineering and Society Center, North Carolina State University, Raleigh, North Carolina 27695-7565, USA
| | - Fred Gould
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695, USA
- Genetic Engineering and Society Center, North Carolina State University, Raleigh, North Carolina 27695-7565, USA
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25
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Price TAR, Windbichler N, Unckless RL, Sutter A, Runge JN, Ross PA, Pomiankowski A, Nuckolls NL, Montchamp-Moreau C, Mideo N, Martin OY, Manser A, Legros M, Larracuente AM, Holman L, Godwin J, Gemmell N, Courret C, Buchman A, Barrett LG, Lindholm AK. Resistance to natural and synthetic gene drive systems. J Evol Biol 2020; 33:1345-1360. [PMID: 32969551 PMCID: PMC7796552 DOI: 10.1111/jeb.13693] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/10/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023]
Abstract
Scientists are rapidly developing synthetic gene drive elements intended for release into natural populations. These are intended to control or eradicate disease vectors and pests, or to spread useful traits through wild populations for disease control or conservation purposes. However, a crucial problem for gene drives is the evolution of resistance against them, preventing their spread. Understanding the mechanisms by which populations might evolve resistance is essential for engineering effective gene drive systems. This review summarizes our current knowledge of drive resistance in both natural and synthetic gene drives. We explore how insights from naturally occurring and synthetic drive systems can be integrated to improve the design of gene drives, better predict the outcome of releases and understand genomic conflict in general.
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Affiliation(s)
- Tom A. R. Price
- Department of Ecology, Evolution and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
| | - Nikolai Windbichler
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | | | - Andreas Sutter
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK
| | - Jan-Niklas Runge
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
| | - Perran A. Ross
- Bio21 and the School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Andrew Pomiankowski
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | | | - Catherine Montchamp-Moreau
- Evolution Génome Comportement et Ecologie, CNRS, IRD, Université Paris-Saclay, Gif sur Yvette 91190, France
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2 Canada
| | - Oliver Y. Martin
- Department of Biology (D-BIOL) & Institute of Integrative Biology (IBZ), ETH Zurich, Universitätsstrasse 16, CH 8092 Zurich, Switzerland
| | - Andri Manser
- Department of Ecology, Evolution and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
| | - Matthieu Legros
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | | | - Luke Holman
- School of Biosciences, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - John Godwin
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Neil Gemmell
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - Cécile Courret
- Evolution Génome Comportement et Ecologie, CNRS, IRD, Université Paris-Saclay, Gif sur Yvette 91190, France
- Department of Biology, University of Rochester, Rochester, New York, USA
| | - Anna Buchman
- University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
- Verily Life Sciences, 269 E Grand Ave, South San Francisco, CA 94080
| | - Luke G. Barrett
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Anna K. Lindholm
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
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26
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Lester PJ, Bulgarella M, Baty JW, Dearden PK, Guhlin J, Kean JM. The potential for a CRISPR gene drive to eradicate or suppress globally invasive social wasps. Sci Rep 2020; 10:12398. [PMID: 32709966 PMCID: PMC7382497 DOI: 10.1038/s41598-020-69259-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/09/2020] [Indexed: 12/14/2022] Open
Abstract
CRISPR gene drives have potential for widespread and cost-efficient pest control, but are highly controversial. We examined a potential gene drive targeting spermatogenesis to control the invasive common wasp (Vespula vulgaris) in New Zealand. Vespula wasps are haplodiploid. Their life cycle makes gene drive production challenging, as nests are initiated by single fertilized queens in spring followed by several cohorts of sterile female workers and the production of reproductives in autumn. We show that different spermatogenesis genes have different levels of variation between introduced and native ranges, enabling a potential 'precision drive' that could target the reduced genetic diversity and genotypes within the invaded range. In vitro testing showed guide-RNA target specificity and efficacy that was dependent on the gene target within Vespula, but no cross-reactivity in other Hymenoptera. Mathematical modelling incorporating the genetic and life history traits of Vespula wasps identified characteristics for a male sterility drive to achieve population control. There was a trade-off between drive infiltration and impact: a drive causing complete male sterility would not spread, while partial sterility could be effective in limiting population size if the homing rate is high. Our results indicate that gene drives may offer viable suppression for wasps and other haplodiploid pests.
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Affiliation(s)
- Philip J Lester
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand.
| | - Mariana Bulgarella
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - James W Baty
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Peter K Dearden
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Joseph Guhlin
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - John M Kean
- AgResearch Limited, Hamilton, 3240, New Zealand
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27
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Teem JL, Alphey L, Descamps S, Edgington MP, Edwards O, Gemmell N, Harvey-Samuel T, Melnick RL, Oh KP, Piaggio AJ, Saah JR, Schill D, Thomas P, Smith T, Roberts A. Genetic Biocontrol for Invasive Species. Front Bioeng Biotechnol 2020; 8:452. [PMID: 32523938 PMCID: PMC7261935 DOI: 10.3389/fbioe.2020.00452] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/20/2020] [Indexed: 12/11/2022] Open
Abstract
Invasive species are increasingly affecting agriculture, food, fisheries, and forestry resources throughout the world. As a result of global trade, invasive species are often introduced into new environments where they become established and cause harm to human health, agriculture, and the environment. Prevention of new introductions is a high priority for addressing the harm caused by invasive species, but unfortunately efforts to prevent new introductions do not address the economic harm that is presently manifested where invasive species have already become established. Genetic biocontrol can be defined as the release of organisms with genetic methods designed to disrupt the reproduction of invasive populations. While these methods offer the potential to control or even eradicate invasive species, there is a need to ensure that genetic biocontrol methods can be deployed in a way that minimizes potential harm to the environment. This review provides an overview of the state of genetic biocontrol, focusing on several approaches that were the subject of presentations at the Genetic Biocontrol for Invasive Species Workshop in Tarragona, Spain, March 31st, 2019, a workshop sponsored by the OECD’s Co-operative Research Program on Biological Resource Management for Sustainable Agricultural Systems. The review considers four different approaches to genetic biocontrol for invasive species; sterile-release, YY Males, Trojan Female Technique, and gene drive. The different approaches will be compared with respect to the efficiency each affords as a genetic biocontrol tool, the practical utility and cost/benefits associated with implementation of the approach, and the regulatory considerations that will need to be addressed for each. The opinions expressed and arguments employed in this publication are the sole responsibility of the authors and do not necessarily reflect those of the OECD or of the governments of its Member countries.
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Affiliation(s)
- John L Teem
- ILSI Research Foundation, Washington, DC, United States
| | - Luke Alphey
- The Pirbright Institute, Woking, United Kingdom
| | - Sarah Descamps
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | | | - Owain Edwards
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Wembley, WA, Australia
| | - Neil Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | | | | | - Kevin P Oh
- National Wildlife Research Center, USDA/APHIS-Wildlife Services, Fort Collins, CO, United States
| | - Antoinette J Piaggio
- National Wildlife Research Center, USDA/APHIS-Wildlife Services, Fort Collins, CO, United States
| | | | - Dan Schill
- Fisheries Management Solutions, Inc., Boise, ID, United States
| | - Paul Thomas
- School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Trevor Smith
- Florida Department of Agriculture and Consumer Services, Gainesville, FL, United States
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28
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Browett SS, O'Meara DB, McDevitt AD. Genetic tools in the management of invasive mammals: recent trends and future perspectives. Mamm Rev 2020. [DOI: 10.1111/mam.12189] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Samuel S. Browett
- Ecosystems and Environment Research Centre School of Science, Engineering and Environment University of Salford Salford M5 4WTUK
| | - Denise B. O'Meara
- Molecular Ecology Research Group Eco‐Innovation Research Centre School of Science and Computing Waterford Institute of Technology Waterford Ireland
| | - Allan D. McDevitt
- Ecosystems and Environment Research Centre School of Science, Engineering and Environment University of Salford Salford M5 4WTUK
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29
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Heffel MG, Finnigan GC. Mathematical modeling of self-contained CRISPR gene drive reversal systems. Sci Rep 2019; 9:20050. [PMID: 31882576 PMCID: PMC6934693 DOI: 10.1038/s41598-019-54805-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 11/19/2019] [Indexed: 12/15/2022] Open
Abstract
There is a critical need for further research into methods to control biological populations. Numerous challenges to agriculture, ecological systems, and human health could be mitigated by the targeted reduction and management of key species (e.g. pests, parasites, and vectors for pathogens). The discovery and adaptation of the CRISPR/Cas editing platform co-opted from bacteria has provided a mechanism for a means to alter an entire population. A CRISPR-based gene drive system can allow for the forced propagation of a genetic element that bypasses Mendelian inheritance which can be used to bias sex determination, install exogenous information, or remove endogenous DNA within an entire species. Laboratory studies have demonstrated the potency by which gene drives can operate within insects and other organisms. However, continued research and eventual application face serious opposition regarding issues of policy, biosafety, effectiveness, and reversal. Previous mathematical work has suggested the use of modified gene drive designs that are limited in spread such as daisy chain or underdominance drives. However, no system has yet been proposed that allows for an inducible reversal mechanism without requiring the introduction of additional individuals. Here, we study gene drive effectiveness, fitness, and inducible drive systems that could respond to external stimuli expanding from a previous frequency-based population model. We find that programmed modification during gene drive propagation could serve as a potent safeguard to either slow or completely reverse drive systems and allow for a return to the original wild-type population.
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Affiliation(s)
- Matthew G Heffel
- Division of Biology, 116 Ackert Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Gregory C Finnigan
- Department of Biochemistry and Molecular Biophysics, 141 Chalmers Hall, Kansas State University, Manhattan, KS 66506, USA.
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30
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Godwin J, Serr M, Barnhill-Dilling SK, Blondel DV, Brown PR, Campbell K, Delborne J, Lloyd AL, Oh KP, Prowse TAA, Saah R, Thomas P. Rodent gene drives for conservation: opportunities and data needs. Proc Biol Sci 2019; 286:20191606. [PMID: 31690240 PMCID: PMC6842857 DOI: 10.1098/rspb.2019.1606] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 10/11/2019] [Indexed: 12/18/2022] Open
Abstract
Invasive rodents impact biodiversity, human health and food security worldwide. The biodiversity impacts are particularly significant on islands, which are the primary sites of vertebrate extinctions and where we are reaching the limits of current control technologies. Gene drives may represent an effective approach to this challenge, but knowledge gaps remain in a number of areas. This paper is focused on what is currently known about natural and developing synthetic gene drive systems in mice, some key areas where key knowledge gaps exist, findings in a variety of disciplines relevant to those gaps and a brief consideration of how engagement at the regulatory, stakeholder and community levels can accompany and contribute to this effort. Our primary species focus is the house mouse, Mus musculus, as a genetic model system that is also an important invasive pest. Our primary application focus is the development of gene drive systems intended to reduce reproduction and potentially eliminate invasive rodents from islands. Gene drive technologies in rodents have the potential to produce significant benefits for biodiversity conservation, human health and food security. A broad-based, multidisciplinary approach is necessary to assess this potential in a transparent, effective and responsible manner.
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Affiliation(s)
- John Godwin
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Genetic Engineering and Society Center, North Carolina State University, Raleigh, NC 27695, USA
- W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Megan Serr
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Dimitri V. Blondel
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Peter R. Brown
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia
| | - Karl Campbell
- Island Conservation, Charles Darwin Avenue, Puerto Ayora, Galapagos Islands, Ecuador
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, Queensland, Australia
| | - Jason Delborne
- Genetic Engineering and Society Center, North Carolina State University, Raleigh, NC 27695, USA
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Alun L. Lloyd
- Department of Mathematics, North Carolina State University, Raleigh, NC 27695, USA
| | - Kevin P. Oh
- National Wildlife Research Center, US Department of Agriculture, Fort Collins, CO 80521, USA
| | - Thomas A. A. Prowse
- School of Mathematical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Royden Saah
- Genetic Engineering and Society Center, North Carolina State University, Raleigh, NC 27695, USA
- Island Conservation, Charles Darwin Avenue, Puerto Ayora, Galapagos Islands, Ecuador
| | - Paul Thomas
- School of Medicine, The University of Adelaide, Adelaide, South Australia, Australia
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
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31
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Abstract
Synthetic gene drives may soon be used to suppress or eliminate populations of disease vectors, pathogens, invasive species, and agricultural pests. Recent proposals have focused on using Z-linked gene drives to control species with ZW sex determination, which include Lepidopteran pests, parasitic trematodes, and cane toads. These proposals include Z-linked 'W-shredders', which would suppress populations by cleaving the W chromosome and causing females to produce only sons, as well as Z-linked female-sterilizing gene drives. Here, I use eco-evolutionary simulations to evaluate the potential of some proposed Z-linked gene drives, and to produce recommendations regarding their design and use. The simulations show that W-shredders are likely to be highly effective at eradicating populations provided that resistance to W-shredding cannot evolve. However, W-shredder alleles can invade populations from very low frequencies, making it difficult to eliminate specific populations while leaving nearby populations untouched; this issue may restrict their possible uses.
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Affiliation(s)
- Luke Holman
- School of BioSciences, The University of Melbourne, Melbourne, Victoria 3010, Australia
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