1
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Chen W, Guo J, Liu Y, Champer J. Population suppression by release of insects carrying a dominant sterile homing gene drive targeting doublesex in Drosophila. Nat Commun 2024; 15:8053. [PMID: 39277611 PMCID: PMC11401859 DOI: 10.1038/s41467-024-52473-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 09/09/2024] [Indexed: 09/17/2024] Open
Abstract
CRISPR homing gene drives can suppress pest populations by targeting female fertility genes, converting wild-type alleles into drive alleles in the germline of drive heterozygotes. fsRIDL (female-specific Release of Insects carrying a Dominant Lethal) is a self-limiting population suppression strategy involving continual release of transgenic males carrying female lethal alleles. Here, we propose an improved pest suppression system called "Release of Insects carrying a Dominant-sterile Drive" (RIDD), combining performance characteristics of homing drive and fsRIDL. We construct a split RIDD system in Drosophila melanogaster by creating a 3-gRNA drive disrupting the doublesex female exon. Drive alleles bias their inheritance in males, while drive alleles and resistance alleles formed by end-joining cause dominant female sterility. Weekly releases of RIDD males progressively suppressed and eventually eliminated cage populations. Modeling shows that RIDD is substantially stronger than SIT and fsRIDL. RIDD is also self-limiting, potentially allowing targeted population suppression.
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Affiliation(s)
- Weizhe Chen
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, Beijing, China
- PTN program, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jialiang Guo
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, Beijing, China
- PTN program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yiran Liu
- 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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2
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Hou S, Chen J, Feng R, Xu X, Liang N, Champer J. A homing rescue gene drive with multiplexed gRNAs reaches high frequency in cage populations but generates functional resistance. J Genet Genomics 2024; 51:836-843. [PMID: 38599514 DOI: 10.1016/j.jgg.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
CRISPR homing gene drives have considerable potential for managing populations of medically and agriculturally significant insects. They operate by Cas9 cleavage followed by homology-directed repair, copying the drive allele to the wild-type chromosome and thus increasing in frequency and spreading throughout a population. However, resistance alleles formed by end-joining repair pose a significant obstacle. To address this, we create a homing drive targeting the essential hairy gene in Drosophila melanogaster. Nonfunctional resistance alleles are recessive lethal, while drive carriers have a recoded "rescue" version of hairy. The drive inheritance rate is moderate, and multigenerational cage studies show drive spread to 96%-97% of the population. However, the drive does not reach 100% due to the formation of functional resistance alleles despite using four gRNAs. These alleles have a large deletion but likely utilize an alternate start codon. Thus, revised designs targeting more essential regions of a gene may be necessary to avoid such functional resistance. Replacement of the rescue element's native 3' UTR with a homolog from another species increases drive inheritance by 13%-24%. This was possibly because of reduced homology between the rescue element and surrounding genomic DNA, which could also be an important design consideration for rescue gene drives.
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Affiliation(s)
- Shibo Hou
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jingheng Chen
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ruobing Feng
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xuejiao Xu
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Nan Liang
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jackson Champer
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China.
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3
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Snyder RE, Ellner SP. To Prosper, Live Long: Understanding the Sources of Reproductive Skew and Extreme Reproductive Success in Structured Populations. Am Nat 2024; 204:E11-E27. [PMID: 39008843 DOI: 10.1086/730557] [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] [Indexed: 07/17/2024]
Abstract
AbstractIn many species, a few individuals produce most of the next generation. How much of this reproductive skew is driven by variation among individuals in fixed traits, how much by external factors, and how much by random chance? And what does it take to have truly exceptional lifetime reproductive output (LRO)? In the past, we and others have partitioned the variance of LRO as a proxy for reproductive skew. Here we explain how to partition LRO skewness itself into contributions from fixed trait variation, four forms of "demographic luck" (birth state, fecundity luck, survival trajectory luck, and growth trajectory luck), and two kinds of "environmental luck" (birth environment and environment trajectory). Each of these is further partitioned into contributions at different ages. We also determine what we can infer about individuals with exceptional LRO. We find that reproductive skew is largely driven by random variation in lifespan, and exceptional LRO generally results from exceptional lifespan. Other kinds of luck frequently bring skewness down rather than increasing it. In populations where fecundity varies greatly with environmental conditions, getting a good year at the right time can be an alternate route to exceptional LRO, so that LRO is less predictive of lifespan.
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4
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Du J, Chen W, Jia X, Xu X, Yang E, Zhou R, Zhang Y, Metzloff M, Messer PW, Champer J. Germline Cas9 promoters with improved performance for homing gene drive. Nat Commun 2024; 15:4560. [PMID: 38811556 PMCID: PMC11137117 DOI: 10.1038/s41467-024-48874-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 05/16/2024] [Indexed: 05/31/2024] Open
Abstract
Gene drive systems could be a viable strategy to prevent pathogen transmission or suppress vector populations by propagating drive alleles with super-Mendelian inheritance. CRISPR-based homing gene drives convert wild type alleles into drive alleles in heterozygotes with Cas9 and gRNA. It is thus desirable to identify Cas9 promoters that yield high drive conversion rates, minimize the formation rate of resistance alleles in both the germline and the early embryo, and limit somatic Cas9 expression. In Drosophila, the nanos promoter avoids leaky somatic expression, but at the cost of high embryo resistance from maternally deposited Cas9. To improve drive efficiency, we test eleven Drosophila melanogaster germline promoters. Some achieve higher drive conversion efficiency with minimal embryo resistance, but none completely avoid somatic expression. However, such somatic expression often does not carry detectable fitness costs for a rescue homing drive targeting a haplolethal gene, suggesting somatic drive conversion. Supporting a 4-gRNA suppression drive, one promoter leads to a low drive equilibrium frequency due to fitness costs from somatic expression, but the other outperforms nanos, resulting in successful suppression of the cage population. Overall, these Cas9 promoters hold advantages for homing drives in Drosophila species and may possess valuable homologs in other organisms.
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Affiliation(s)
- Jie Du
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, 100871, Beijing, China.
| | - Weizhe Chen
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, 100871, Beijing, China
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Xihua Jia
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Xuejiao Xu
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Emily Yang
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Ruizhi Zhou
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Yuqi Zhang
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Matt Metzloff
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Philipp W Messer
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jackson Champer
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, 100871, Beijing, China.
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5
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Ma S, Ni X, Chen S, Qiao X, Xu X, Chen W, Champer J, Huang J. A small-molecule approach to restore female sterility phenotype targeted by a homing suppression gene drive in the fruit pest Drosophila suzukii. PLoS Genet 2024; 20:e1011226. [PMID: 38578788 PMCID: PMC11023630 DOI: 10.1371/journal.pgen.1011226] [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: 09/04/2023] [Revised: 04/17/2024] [Accepted: 03/15/2024] [Indexed: 04/07/2024] Open
Abstract
CRISPR-based gene drives offer promising prospects for controlling disease-transmitting vectors and agricultural pests. A significant challenge for successful suppression-type drive is the rapid evolution of resistance alleles. One approach to mitigate the development of resistance involves targeting functionally constrained regions using multiple gRNAs. In this study, we constructed a 3-gRNA homing gene drive system targeting the recessive female fertility gene Tyrosine decarboxylase 2 (Tdc2) in Drosophila suzukii, a notorious fruit pest. Our investigation revealed only a low level of homing in the germline, but feeding octopamine restored the egg-laying defects in Tdc2 mutant females, allowing easier line maintenance than for other suppression drive targets. We tested the effectiveness of a similar system in Drosophila melanogaster and constructed additional split drive systems by introducing promoter-Cas9 transgenes to improve homing efficiency. Our findings show that genetic polymorphisms in wild populations may limit the spread of gene drive alleles, and the position effect profoundly influences Cas9 activity. Furthermore, this study highlights the potential of conditionally rescuing the female infertility caused by the gene drive, offering a valuable tool for the industrial-scale production of gene drive transgenic insects.
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Affiliation(s)
- Suhan Ma
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xuyang Ni
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shimin Chen
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | | | - Xuejiao Xu
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, Beijing, China
| | - Weizhe Chen
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, Beijing, China
- PTN program, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jackson Champer
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, Beijing, China
| | - Jia Huang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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6
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Yamamichi M, Ellner SP, Hairston NG. Beyond simple adaptation: Incorporating other evolutionary processes and concepts into eco-evolutionary dynamics. Ecol Lett 2023; 26 Suppl 1:S16-S21. [PMID: 37840027 DOI: 10.1111/ele.14197] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/18/2023] [Accepted: 02/20/2023] [Indexed: 10/17/2023]
Abstract
Studies of eco-evolutionary dynamics have integrated evolution with ecological processes at multiple scales (populations, communities and ecosystems) and with multiple interspecific interactions (antagonistic, mutualistic and competitive). However, evolution has often been conceptualised as a simple process: short-term directional adaptation that increases population growth. Here we argue that diverse other evolutionary processes, well studied in population genetics and evolutionary ecology, should also be considered to explore the full spectrum of feedback between ecological and evolutionary processes. Relevant but underappreciated processes include (1) drift and mutation, (2) disruptive selection causing lineage diversification or speciation reversal and (3) evolution driven by relative fitness differences that may decrease population growth. Because eco-evolutionary dynamics have often been studied by population and community ecologists, it will be important to incorporate a variety of concepts in population genetics and evolutionary ecology to better understand and predict eco-evolutionary dynamics in nature.
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Affiliation(s)
- Masato Yamamichi
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Stephen P Ellner
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Nelson G Hairston
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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7
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Langmüller AM, Champer J, Lapinska S, Xie L, Metzloff M, Champer SE, Liu J, Xu Y, Du J, Clark AG, Messer PW. Fitness effects of CRISPR endonucleases in Drosophila melanogaster populations. eLife 2022; 11:e71809. [PMID: 36135925 PMCID: PMC9545523 DOI: 10.7554/elife.71809] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 provides a highly efficient and flexible genome editing technology with numerous potential applications ranging from gene therapy to population control. Some proposed applications involve the integration of CRISPR/Cas9 endonucleases into an organism's genome, which raises questions about potentially harmful effects to the transgenic individuals. One example for which this is particularly relevant are CRISPR-based gene drives conceived for the genetic alteration of entire populations. The performance of such drives can strongly depend on fitness costs experienced by drive carriers, yet relatively little is known about the magnitude and causes of these costs. Here, we assess the fitness effects of genomic CRISPR/Cas9 expression in Drosophila melanogaster cage populations by tracking allele frequencies of four different transgenic constructs that allow us to disentangle 'direct' fitness costs due to the integration, expression, and target-site activity of Cas9, from fitness costs due to potential off-target cleavage. Using a maximum likelihood framework, we find that a model with no direct fitness costs but moderate costs due to off-target effects fits our cage data best. Consistent with this, we do not observe fitness costs for a construct with Cas9HF1, a high-fidelity version of Cas9. We further demonstrate that using Cas9HF1 instead of standard Cas9 in a homing drive achieves similar drive conversion efficiency. These results suggest that gene drives should be designed with high-fidelity endonucleases and may have implications for other applications that involve genomic integration of CRISPR endonucleases.
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Affiliation(s)
- Anna M Langmüller
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Institut für Populationsgenetik, Vetmeduni ViennaViennaAustria
- Vienna Graduate School of Population Genetics, Vetmeduni ViennaViennaAustria
| | - Jackson Champer
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking UniversityBeijingChina
| | - Sandra Lapinska
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Lin Xie
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Matthew Metzloff
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Samuel E Champer
- Department of Computational Biology, Cornell UniversityIthacaUnited States
| | - Jingxian Liu
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Yineng Xu
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Jie Du
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking UniversityBeijingChina
| | - Andrew G Clark
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Philipp W Messer
- Department of Computational Biology, Cornell UniversityIthacaUnited States
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8
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Yang E, Metzloff M, Langmüller AM, Xu X, Clark AG, Messer PW, Champer J. A homing suppression gene drive with multiplexed gRNAs maintains high drive conversion efficiency and avoids functional resistance alleles. G3 (BETHESDA, MD.) 2022; 12:jkac081. [PMID: 35394026 PMCID: PMC9157102 DOI: 10.1093/g3journal/jkac081] [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] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/30/2022] [Indexed: 11/14/2022]
Abstract
Gene drives are engineered alleles that can bias inheritance in their favor, allowing them to spread throughout a population. They could potentially be used to modify or suppress pest populations, such as mosquitoes that spread diseases. CRISPR/Cas9 homing drives, which copy themselves by homology-directed repair in drive/wild-type heterozygotes, are a powerful form of gene drive, but they are vulnerable to resistance alleles that preserve the function of their target gene. Such resistance alleles can prevent successful population suppression. Here, we constructed a homing suppression drive in Drosophila melanogaster that utilized multiplexed gRNAs to inhibit the formation of functional resistance alleles in its female fertility target gene. The selected gRNA target sites were close together, preventing reduction in drive conversion efficiency. The construct reached a moderate equilibrium frequency in cage populations without apparent formation of resistance alleles. However, a moderate fitness cost prevented elimination of the cage population, showing the importance of using highly efficient drives in a suppression strategy, even if resistance can be addressed. Nevertheless, our results experimentally demonstrate the viability of the multiplexed gRNAs strategy in homing suppression gene drives.
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Affiliation(s)
- Emily Yang
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Matthew Metzloff
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Anna M Langmüller
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Wien, Austria
- Vienna Graduate School of Population Genetics, 1210 Wien, Austria
| | - Xuejiao Xu
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Andrew G Clark
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Philipp W Messer
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jackson Champer
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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9
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Metzloff M, Yang E, Dhole S, Clark AG, Messer PW, Champer J. Experimental demonstration of tethered gene drive systems for confined population modification or suppression. BMC Biol 2022; 20:119. [PMID: 35606745 PMCID: PMC9128227 DOI: 10.1186/s12915-022-01292-5] [Citation(s) in RCA: 12] [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: 08/27/2021] [Accepted: 04/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Homing gene drives hold great promise for the genetic control of natural populations. However, current homing systems are capable of spreading uncontrollably between populations connected by even marginal levels of migration. This could represent a substantial sociopolitical barrier to the testing or deployment of such drives and may generally be undesirable when the objective is only local population control, such as suppression of an invasive species outside of its native range. Tethered drive systems, in which a locally confined gene drive provides the CRISPR nuclease needed for a homing drive, could provide a solution to this problem, offering the power of a homing drive and confinement of the supporting drive. RESULTS Here, we demonstrate the engineering of a tethered drive system in Drosophila, using a regionally confined CRISPR Toxin-Antidote Recessive Embryo (TARE) drive to support modification and suppression homing drives. Each drive was able to bias inheritance in its favor, and the TARE drive was shown to spread only when released above a threshold frequency in experimental cage populations. After the TARE drive had established in the population, it facilitated the spread of a subsequently released split homing modification drive (to all individuals in the cage) and of a homing suppression drive (to its equilibrium frequency). CONCLUSIONS Our results show that the tethered drive strategy is a viable and easily engineered option for providing confinement of homing drives to target populations.
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Affiliation(s)
- Matthew Metzloff
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Emily Yang
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Sumit Dhole
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Andrew G Clark
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Philipp W Messer
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jackson Champer
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA.
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.
- Present Address: Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
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10
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Shen R, Messer PW. Predicting the genomic resolution of bulk segregant analysis. G3 (BETHESDA, MD.) 2022; 12:6523970. [PMID: 35137024 PMCID: PMC8895995 DOI: 10.1093/g3journal/jkac012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/03/2022] [Indexed: 11/18/2022]
Abstract
Bulk segregant analysis is a technique for identifying the genetic loci that underlie phenotypic trait differences. The basic approach is to compare two pools of individuals from the opposing tails of the phenotypic distribution, sampled from an interbred population. Each pool is sequenced and scanned for alleles that show divergent frequencies between the pools, indicating potential association with the observed trait differences. Bulk segregant analysis has already been successfully applied to the mapping of various quantitative trait loci in organisms ranging from yeast to maize. However, these studies have typically suffered from rather low mapping resolution, and we still lack a detailed understanding of how this resolution is affected by experimental parameters. Here, we use coalescence theory to calculate the expected genomic resolution of bulk segregant analysis for a simple monogenic trait. We first show that in an idealized interbreeding population of infinite size, the expected length of the mapped region is inversely proportional to the recombination rate, the number of generations of interbreeding, and the number of genomes sampled, as intuitively expected. In a finite population, coalescence events in the genealogy of the sample reduce the number of potentially informative recombination events during interbreeding, thereby increasing the length of the mapped region. This is incorporated into our model by an effective population size parameter that specifies the pairwise coalescence rate of the interbreeding population. The mapping resolution predicted by our calculations closely matches numerical simulations and is surprisingly robust to moderate levels of contamination of the segregant pools with alternative alleles. Furthermore, we show that the approach can easily be extended to modifications of the crossing scheme. Our framework will allow researchers to predict the expected power of their mapping experiments, and to evaluate how their experimental design could be tuned to optimize mapping resolution.
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Affiliation(s)
- Runxi Shen
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Philipp W Messer
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
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11
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Chong X, Zhang F, Li Y, Wang C, Zhou Y, Zhou T, Wang Y, Lu X, Chen H. Complete chloroplast genome sequence and phylogenetic analysis of Ilex × attenuata 'Fosteri' (Aquifoliaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2799-2800. [PMID: 34514131 PMCID: PMC8425775 DOI: 10.1080/23802359.2021.1970637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Ilex × attenuata ‘Fosteri’ is an important ornamental plant widely distributed in mid-southern China and south-eastern United States. In this study, we assembled the complete chloroplast (cp) genome of I. attenuata by high-throughput sequencing and bioinformatics. The full length of cp genome was 157,833 bp with 37.63% overall GC content, which contained two inverted repeats (IR) of 26,093 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 87,188 bp and 18,459 bp, respectively. The cp genome contained 135 genes, including 88 protein-coding genes, 8 rRNA genes and 39 tRNA genes. Phylogenetic tree showed that the close relationship of three species of Ilex (I. attenuata, I. viridis and I. szechwanensis) in the Aquifoliaceae family.
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Affiliation(s)
- Xinran Chong
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Fan Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yunlong Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Chuanyong Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yanwei Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Ting Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yinjie Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Xiaoqing Lu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Hong Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
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Chong X, Chen H, Wang C, Zhou T, Li Y, Zhou Y, Zhang T, Lu X, Zhang F. Characterization of the complete chloroplast genome of Ilex crenata Thunb. (Aquifoliaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2599-2600. [PMID: 34395890 PMCID: PMC8354146 DOI: 10.1080/23802359.2021.1961626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ilex crenata Thunb. is a species of Aquifoliaceae with high ornamental and ecological values. In this study, the complete chloroplast (cp) genome of I. crenata was assembled and characterized through Illumina sequencing data. The entire cp genome of I. crenata was 157,988 bp in length with 37.64% overall GC content, containing a large single-copy (LSC) region of 87,414 bp and a small single-copy (SSC) region of 18,422 bp, which were separated by a pair of 26,076 bp inverted repeat (IR) regions. A total of 135 genes were annotated, including 88 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 78 conserved protein-coding genes demonstrated that I. crenata is closely related to I. viridis and I. szechwanensis.
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Affiliation(s)
- Xinran Chong
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Hong Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Chuanyong Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Ting Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yunlong Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yanwei Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Ting Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Xiaoqin Lu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Fan Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
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13
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Gene-drive suppression of mosquito populations in large cages as a bridge between lab and field. Nat Commun 2021; 12:4589. [PMID: 34321476 PMCID: PMC8319305 DOI: 10.1038/s41467-021-24790-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/05/2021] [Indexed: 12/03/2022] Open
Abstract
CRISPR-based gene-drives targeting the gene doublesex in the malaria vector Anopheles gambiae effectively suppressed the reproductive capability of mosquito populations reared in small laboratory cages. To bridge the gap between laboratory and the field, this gene-drive technology must be challenged with vector ecology. Here we report the suppressive activity of the gene-drive in age-structured An. gambiae populations in large indoor cages that permit complex feeding and reproductive behaviours. The gene-drive element spreads rapidly through the populations, fully supresses the population within one year and without selecting for resistance to the gene drive. Approximate Bayesian computation allowed retrospective inference of life-history parameters from the large cages and a more accurate prediction of gene-drive behaviour under more ecologically-relevant settings. Generating data to bridge laboratory and field studies for invasive technologies is challenging. Our study represents a paradigm for the stepwise and sound development of vector control tools based on gene-drive. Experimental analysis of gene drive population dynamics has mostly been limited to small cage trials. Here the authors, to fill the gap between lab based studies and field studies, use large indoor cages and see population suppression without the emergence of resistant alleles
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14
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Wilson AE, Siddiqui A, Dworkin I. Spatial heterogeneity in resources alters selective dynamics in Drosophila melanogaster. Evolution 2021; 75:1792-1804. [PMID: 33963761 DOI: 10.1111/evo.14262] [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] [Received: 09/07/2020] [Revised: 04/13/2021] [Accepted: 04/23/2021] [Indexed: 11/26/2022]
Abstract
Environmental features can alter the behaviors and phenotypes of organisms, influencing the dynamics of natural and sexual selection. Experimental environmental manipulation, particularly when conducted in experiments where the dynamics of the purging of deleterious alleles are compared, has demonstrated both direct and indirect effects on the strength and direction of selection. However, many of these studies are conducted with fairly simplistic environments, where it is not always clear how or why particular forms of spatial heterogeneity influence behavior or selection. Using Drosophila melanogaster, we tested three different spatial environments designed to determine if spatial constraint of critical resources influences the efficiency of natural and sexual selection. We conducted two allele purging experiments to (1) assess effects of these spatial treatments on selective dynamics of six recessive mutations, and (2) determine how these dynamics changed when sexual selection was relaxed and spatial area reduced for two of the mutants. Allele purging dynamics depended on spatial environment, however the patterns of purging rates between the environments differed across distinct deleterious mutations. We also tested two of the mutant alleles, and demonstrate sexual selection increased the purging rate.
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Affiliation(s)
- Audrey E Wilson
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Ali Siddiqui
- Department of Health Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Ian Dworkin
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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15
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Zhou Y, Li N, Chen H, Chong X, Li Y, Lu X, Zhou T, Zhang F. The complete chloroplast genome sequence of Ilex chinensis Sims. (Aquifoliaceae), a folk herbal medicine plant in China. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1241-1242. [PMID: 33829094 PMCID: PMC8008935 DOI: 10.1080/23802359.2021.1904800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The complete chloroplast (cp) genome of Ilex chinensis, an important economic plant with ornamental and ecological values, was sequenced to investigate its phylogenetic relationship. The entire cp genome of I. chinensis was 157,885 bp in length with 37.61% overall GC content, including a large single-copy (LSC) region of 87,289 bp, and a small single-copy (SSC) region of 18,388 bp, which were separated by a pair of inverted repeats (IRs) of 52,208 bp. The cp genome contained 135 genes, including 90 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on whole cp genome sequences showed that I. chinensis was closely related to I. szechwanensis and I. viridis species.
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Affiliation(s)
- Yanwei Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, PR China
| | - Naiwei Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, PR China
| | - Hong Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, PR China
| | - Xinran Chong
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, PR China
| | - Yunlong Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, PR China
| | - Xiaoqing Lu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, PR China
| | - Ting Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, PR China
| | - Fan Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, PR China
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16
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Chong X, Li Y, Zhou Y, Chen H, Li X, Li N, Lu X, Zhang F. The complete chloroplast genome sequence and phylogenetic analysis of Ilex × Koehneana 'Wirt L. Winn' (Aquifoliaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:796-797. [PMID: 33763582 PMCID: PMC7954430 DOI: 10.1080/23802359.2021.1882904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Ilex × Koehneana ‘Wirt L. Winn’, an important ornamental tree, has been widely distributed in southeastern China. In this study, we assembled and characterized the complete chloroplast (cp) genome of I. Koehneana to investigate its phylogenetic relationship. The whole cp genome of I. Koehneana is 157,538 bp, which contained a large single-copy (LSC) region of 87,055 bp and a small single-copy (SSC) region of 18,429 bp, and a pair of inverted repeats (IR) of 52,054 bp. A total of 137 genes, including 90 protein-coding genes, eight rRNAs, and 39 tRNAs, were identified. Phylogenetic analysis based on 74 conserved protein-coding genes revealed that I. Koehneana is closely related to I. ‘tall boy’.
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Affiliation(s)
- Xinran Chong
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, PR China
| | - Yunlong Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, PR China
| | - Yanwei Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, PR China
| | - Hong Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, PR China
| | - Xinzhi Li
- Jiangsu Forestry Bureau, Nanjing, Jiangsu, PR China
| | - Naiwei Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, PR China
| | - Xiaoqing Lu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, PR China
| | - Fan Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, PR China
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17
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Snyder RE, Ellner SP, Hooker G. Time and Chance: Using Age Partitioning to Understand How Luck Drives Variation in Reproductive Success. Am Nat 2021; 197:E110-E128. [PMID: 33755543 DOI: 10.1086/712874] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractOver the course of individual lifetimes, luck usually explains a large fraction of the between-individual variation in life span or lifetime reproductive output (LRO) within a population, while variation in individual traits or "quality" explains much less. To understand how, where in the life cycle, and through which demographic processes luck trumps trait variation, we show how to partition by age the contributions of luck and trait variation to LRO variance and how to quantify three distinct components of luck. We apply these tools to several empirical case studies. We find that luck swamps effects of trait variation at all ages, primarily because of randomness in individual state dynamics ("state trajectory luck"). Luck early in life is most important. Very early state trajectory luck generally determines whether an individual ever breeds, likely by ensuring that they are not dead or doomed quickly. Less early luck drives variation in success among those breeding at least once. Consequently, the importance of luck often has a sharp peak early in life or it has two peaks. We suggest that ages or stages where the importance of luck peaks are potential targets for interventions to benefit a population of concern, different from those identified by eigenvalue elasticity analysis.
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18
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Zhang F, Chen H, Zhou Y, Li N, Chong X, Li Y, Lu X, Wang C. The complete chloroplast genome sequence and phylogenetic analysis of Ilex 'Beryl', a hybrid of Ilex cornuta × Ilex latifolia (Aquifoliaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:227-228. [PMID: 33537450 PMCID: PMC7832488 DOI: 10.1080/23802359.2020.1861569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Ilex ‘Beryl’ is an ornamental and ecological tree widespread in southeastern China. In this study, the complete chloroplast (cp) genome of Ilex ‘Beryl’ was assembled and characterized to investigate its phylogenetic relationship. The entire cp genome of ‘Beryl’ was a typical quadripartite structure with 157,575 bp in length, including a large single-copy (LSC) region of 87,080 bp and a small single-copy (SSC) region of 18,427 bp, which were separated by a pair of inverted repeats (IRs) of 52,068 bp. There are 135 genes annotated, including 90 protein-coding genes, eight rRNA genes and 37 tRNA genes. Phylogenetic analysis based on whole cp genome sequences showed that ‘Beryl’ is closest to I. ‘Emily Bruner’ and I. ‘tall boy’.
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Affiliation(s)
- Fan Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu, China
| | - Hong Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu, China
| | - Yanwei Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu, China
| | - Naiwei Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu, China
| | - Xinran Chong
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu, China
| | - Yunlong Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu, China
| | - Xiaoqing Lu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu, China
| | - Chuanyong Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu, China
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19
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Zhang F, Zhou Y, Chen H, Li N, Wang C, Lu X, Li Y. The complete chloroplast genome of Ilex 'Tall Boy', Ilex aquifolium × Ilex latifolia (Aquifoliaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:229-230. [PMID: 33537451 PMCID: PMC7832594 DOI: 10.1080/23802359.2020.1852898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Thecomplete chloroplast (cp) genome of Ilex ‘Tall Boy’, an important economic plant with ornamental and ecological values, was sequenced to investigate its phylogenetic relationship. The entire cp genome of ‘Tall Boy’ was 157,527 bp in length with 37.65% overall GC content, including a large single-copy (LSC) region of 87,044 bp and a small single-copy (SSC) region of 18,429 bp, which were separated by a pair of inverted repeats (IRs) of 52,054 bp. The cp genome contained 135 genes, including 90 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on whole cp genome sequences showed that ‘Tall Boy’ is closest to I. latifolia Thunb. species.
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Affiliation(s)
- Fan Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
| | - Yanwei Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
| | - Hong Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
| | - Naiwei Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
| | - Chuanyong Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
| | - Xiaoqing Lu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
| | - Yunlong Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
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20
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Champer J, Yang E, Lee E, Liu J, Clark AG, Messer PW. A CRISPR homing gene drive targeting a haplolethal gene removes resistance alleles and successfully spreads through a cage population. Proc Natl Acad Sci U S A 2020; 117:24377-24383. [PMID: 32929034 PMCID: PMC7533649 DOI: 10.1073/pnas.2004373117] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Engineered gene drives are being explored as a new strategy in the fight against vector-borne diseases due to their potential for rapidly spreading genetic modifications through a population. However, CRISPR-based homing gene drives proposed for this purpose have faced a major obstacle in the formation of resistance alleles that prevent Cas9 cleavage. Here, we present a homing drive in Drosophila melanogaster that reduces the prevalence of resistance alleles below detectable levels by targeting a haplolethal gene with two guide RNAs (gRNAs) while also providing a rescue allele. Resistance alleles that form by end-joining repair typically disrupt the haplolethal target gene and are thus removed from the population because individuals that carry them are nonviable. We demonstrate that our drive is highly efficient, with 91% of the progeny of drive heterozygotes inheriting the drive allele and with no functional resistance alleles observed in the remainder. In a large cage experiment, the drive allele successfully spread to all individuals within a few generations. These results show that a haplolethal homing drive can provide an effective tool for targeted genetic modification of entire populations.
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Affiliation(s)
- Jackson Champer
- Department of Computational Biology, Cornell University, Ithaca, NY 14853;
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Emily Yang
- Department of Computational Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Esther Lee
- Department of Computational Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Jingxian Liu
- Department of Computational Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Andrew G Clark
- Department of Computational Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Philipp W Messer
- Department of Computational Biology, Cornell University, Ithaca, NY 14853;
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21
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Abstract
Gene drive systems that propagate transgenes via super-Mendelian inheritance can potentially control insect-borne diseases and agricultural pests. However, concerns have been raised regarding unforeseen ecological consequences, and methods that prevent undesirable gene drive effects have been proposed. Here, we report a chemical-induced control of gene drive. We prepared a CRISPR-based gene drive system that can be removed by a site-specific recombinase, Rippase, the expression of which is induced by the chemical RU486 in fruit flies. Exposure of fruit flies to RU486 resulted in 7-12% removal of gene drive elements at each generation, leading to a significant reduction in gene drive-fly propagation. Mathematical modeling and simulation suggest that our system offers several advantages over a previously reported gene drive control system. Our chemical control system can provide a proof-of-principle for the reversible control of gene drive effects depending on ecological status and human needs.
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Affiliation(s)
- Dongwoo Chae
- Department of Pharmacology, BK21 PLUS Project for Medical Science, Yonsei University College of Medicine, 50-1Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Junwon Lee
- Department of Ophthalmology, Institute of Vision Research, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Nayoung Lee
- Department of Oral Biology, BK21 PLUS Project, Yonsei University College of Dentistry, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Kyungsoo Park
- Department of Pharmacology, BK21 PLUS Project for Medical Science, Yonsei University College of Medicine, 50-1Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Seok Jun Moon
- Department of Oral Biology, BK21 PLUS Project, Yonsei University College of Dentistry, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Hyongbum H Kim
- Department of Pharmacology, BK21 PLUS Project for Medical Science, Yonsei University College of Medicine, 50-1Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
- Center for Nanomedicine, Institute for Basic Science (IBS), 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
- Graduate Program of Nano Biomedical Engineering, Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
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22
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Zhang F, Li Y, Sun L, Zhou Y, Chen H, Lu X, Li N, Wang C. The complete chloroplast genome of Ilex 'Emily Bruner', Ilex cornuta 'Burfordii' × Ilex latifolia (Aquifoliaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3227-3228. [PMID: 33458120 PMCID: PMC7782960 DOI: 10.1080/23802359.2020.1810146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ilex ‘Emily Bruner’ is an important economic plant with ornamental and ecological functions in southeastern China. In this study, we characterized the complete chloroplast (cp) genome sequence of ‘Emily Bruner’ to investigate its phylogenetic relationship. The entire cp genome of ‘Emily Bruner’ was 157,216 bp in length with 37.68% overall GC content, including a large single-copy (LSC) region of 86,721 bp and a small single-copy (SSC) region of 18,427 bp, which were separated by a pair of inverted repeats (IRs) of 52,068 bp. The cp genome contained 135 genes, including 90 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on whole cp genome sequences showed that ‘Emily Bruner’ is closest to I. cornuta species.
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Affiliation(s)
- Fan Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing, China
| | - Yunlong Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing, China
| | - Linhe Sun
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing, China
| | - Yanwei Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing, China
| | - Hong Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing, China
| | - Xiaoqing Lu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing, China
| | - Naiwei Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing, China
| | - Chuanyong Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing, China
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23
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Tudor MS, Lopez-Anido RN, Yocius CA, Conlin SM, Hamlin HJ. Ecologically relevant arsenic exposure alters female mate preference and anxiety-like behavior in Betta splendens. Heliyon 2019; 5:e02646. [PMID: 31687501 PMCID: PMC6820098 DOI: 10.1016/j.heliyon.2019.e02646] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/12/2019] [Accepted: 10/09/2019] [Indexed: 11/17/2022] Open
Abstract
Arsenic is a metalloid pollutant that is commonly found in surface and groundwater worldwide. Toxicological effects of arsenic are relatively well-known, but much less studied are its effects on behavioral endpoints, which may have considerable evolutionary and population-level consequences. Here we investigated the effects of exposure to environmentally relevant concentrations of arsenic (0, 10 and 100 μg/L) for 96-hours on female preference for male color (i.e. red versus blue) in Betta splendens, an increasingly popular fish model for contaminant-induced behavioral dysfunction. Further, we examined whether arsenic exposure altered anxiety-like behaviors using a standard scototaxis test (preference for light or dark), as well as measured tissue cortisol concentrations to increase our understanding of possible mechanisms driving behavioral responses. We found exposure to 100 μg/L arsenic results in a loss of female preference for red males, and arsenic exposed females showed increased anxiety-like behavior. The loss in preference for male coloration may have been driven by anxiety, as preference for red was negatively correlated with anxiety-like behavior for all fish. Interestingly, increase in anxiety-like behavior occurred without a parallel increase in cortisol. Female preference for red colored males may confer fitness benefits, and this study highlights important arsenic-induced behavioral changes that could have population level consequences.
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Affiliation(s)
- M Scarlett Tudor
- University of Maine Cooperative Extension Aquatic Animal Health Laboratory, 17 Godfrey Drive, University of Maine, Orono, ME 04473 USA.,Aquaculture Research Institute, Margaret Chase Smith Policy Center, York Complex #4, Orono, ME 04469, USA
| | - Rebecca N Lopez-Anido
- School of Marine Sciences, 5751 Murray Hall, University of Maine, Orono, ME 04469 USA
| | - Charly A Yocius
- School of Marine Sciences, 5751 Murray Hall, University of Maine, Orono, ME 04469 USA
| | - Sarah M Conlin
- School of Marine Sciences, 5751 Murray Hall, University of Maine, Orono, ME 04469 USA
| | - Heather J Hamlin
- School of Marine Sciences, 5751 Murray Hall, University of Maine, Orono, ME 04469 USA.,Aquaculture Research Institute, Margaret Chase Smith Policy Center, York Complex #4, Orono, ME 04469, USA
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24
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Massey JH, Chung D, Siwanowicz I, Stern DL, Wittkopp PJ. The yellow gene influences Drosophila male mating success through sex comb melanization. eLife 2019; 8:e49388. [PMID: 31612860 PMCID: PMC6794089 DOI: 10.7554/elife.49388] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/06/2019] [Indexed: 12/28/2022] Open
Abstract
Drosophila melanogaster males perform a series of courtship behaviors that, when successful, result in copulation with a female. For over a century, mutations in the yellow gene, named for its effects on pigmentation, have been known to reduce male mating success. Prior work has suggested that yellow influences mating behavior through effects on wing extension, song, and/or courtship vigor. Here, we rule out these explanations, as well as effects on the nervous system more generally, and find instead that the effects of yellow on male mating success are mediated by its effects on pigmentation of male-specific leg structures called sex combs. Loss of yellow expression in these modified bristles reduces their melanization, which changes their structure and causes difficulty grasping females prior to copulation. These data illustrate why the mechanical properties of anatomy, not just neural circuitry, must be considered to fully understand the development and evolution of behavior.
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Affiliation(s)
- Jonathan H Massey
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborUnited States
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Daayun Chung
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborUnited States
| | - Igor Siwanowicz
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - David L Stern
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Patricia J Wittkopp
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborUnited States
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborUnited States
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Sun X, Shu M, Shang P, Cui R. The complete mitogenome of Fusarium equiseti. Mitochondrial DNA B Resour 2019; 4:2918-2919. [PMID: 33365791 PMCID: PMC7706831 DOI: 10.1080/23802359.2019.1661298] [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] [Indexed: 11/29/2022] Open
Abstract
The complete mitochondrial genome of plant pathogenic fungus, Fusarium equiseti, was sequenced. The circular molecule is 53,411 bp long with a GC content of 32.81%. It contains 22 protein-coding genes, 4 ribosomal RNA (rRNA), and 24 transfer RNA (tRNA) genes. Phylogenetic reconstructions confirmed that it has the closest relationship with Fusarium equiseti. The mitogenome analysis of Fusarium equiseti provides a molecular basis for further studies on molecular systematics and evolutionary dynamics.
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Affiliation(s)
- Xiaotang Sun
- College of Agronomy/Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Mengshuang Shu
- College of Agronomy/Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Pengmei Shang
- College of Agronomy/Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Ruqiang Cui
- College of Agronomy/Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
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