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Collier TC, Lee Y, Mathias DK, López Del Amo V. CRISPR-Cas9 and Cas12a target site richness reflects genomic diversity in natural populations of Anopheles gambiae and Aedes aegypti mosquitoes. BMC Genomics 2024; 25:700. [PMID: 39020310 PMCID: PMC11253549 DOI: 10.1186/s12864-024-10597-4] [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: 05/28/2024] [Accepted: 07/04/2024] [Indexed: 07/19/2024] Open
Abstract
Due to limitations in conventional disease vector control strategies including the rise of insecticide resistance in natural populations of mosquitoes, genetic control strategies using CRISPR gene drive systems have been under serious consideration. The identification of CRISPR target sites in mosquito populations is a key aspect for developing efficient genetic vector control strategies. While genome-wide Cas9 target sites have been explored in mosquitoes, a precise evaluation of target sites focused on coding sequence (CDS) is lacking. Additionally, target site polymorphisms have not been characterized for other nucleases such as Cas12a, which require a different DNA recognition site (PAM) and would expand the accessibility of mosquito genomes for genetic engineering. We undertook a comprehensive analysis of potential target sites for both Cas9 and Cas12a nucleases within the genomes of natural populations of Anopheles gambiae and Aedes aegypti from multiple continents. We demonstrate that using two nucleases increases the number of targets per gene. Also, we identified differences in nucleotide diversity between North American and African Aedes populations, impacting the abundance of good target sites with a minimal degree of polymorphisms that can affect the binding of gRNA. Lastly, we screened for gRNAs targeting sex-determination genes that could be widely applicable for developing field genetic control strategies. Overall, this work highlights the utility of employing both Cas9 and Cas12a nucleases and underscores the importance of designing universal genetic strategies adaptable to diverse mosquito populations.
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Affiliation(s)
| | - Yoosook Lee
- Florida Medical Entomology Laboratory, Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, 32962, USA
| | - Derrick K Mathias
- Florida Medical Entomology Laboratory, Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, 32962, USA
| | - Víctor López Del Amo
- Center for Infectious Diseases, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center, Houston, TX, 77030, USA.
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Kelly ET, Mack LK, Attardo GM. Exploring the Wilderness within: An Integrative Metabolomics and Transcriptomics Study on Near-Wild and Colonized Aedes aegypti. INSECTS 2024; 15:507. [PMID: 39057240 PMCID: PMC11277204 DOI: 10.3390/insects15070507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/28/2024]
Abstract
This study examines the phenotypic differences between wild-derived F2 Central Valley mosquitoes and the insecticide-susceptible Rockefeller (Rock) lab strain of Ae. aegypti. Given the rarity of wild pyrethroid-susceptible populations, the focus of this work is to develop an understanding of the resistance physiology in this invasive mosquito population and explore the potential of metabolites as diagnostic biomarkers for metabolic resistance. This study utilizes metabolomic, gene expression, and lifespan data for a comparison between strains. The findings indicate that wild-derived mosquitoes with greater metabolic resistance have a lifespan sensitivity to restricted larval nutrition. In terms of metabolism and gene expression, Central Valley mosquitoes show increased activity in oxidoreductase, glutathione metabolism, and the pentose phosphate pathway. Conversely, Rock mosquitoes display signs of metabolic inefficiency and mitochondrial dysregulation, likely tolerated due to the consistency and nutritional abundance of a controlled lab environment. The study also examines Ae. aegypti P450 and GSTE profiles in relation to other insecticide-resistant groups. While metabolomic data can differentiate our study groups, the challenges in biomarker development arise from few detected markers meeting high fold change thresholds.
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Affiliation(s)
| | | | - Geoffrey M. Attardo
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA; (E.T.K.); (L.K.M.)
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Spadar A, Collins E, Messenger LA, Clark TG, Campino S. Uncovering the genetic diversity in Aedes aegypti insecticide resistance genes through global comparative genomics. Sci Rep 2024; 14:13447. [PMID: 38862628 PMCID: PMC11166649 DOI: 10.1038/s41598-024-64007-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/04/2024] [Indexed: 06/13/2024] Open
Abstract
Aedes aegypti is vector of many arboviruses including Zika, dengue, yellow fever, West Nile, and Chikungunya. Its control efforts are hampered by widespread insecticide resistance reported in the Americas and Asia, while data from Africa is more limited. Here we use publicly available 729 Ae. aegypti whole-genome sequencing samples from 15 countries, including nine in Africa, to investigate the genetic diversity in four insecticide resistance linked genes: ace-1, GSTe2, rdl and vgsc. Apart from vgsc, the other genes have been less investigated in Ae. aegypti, and almost no genetic diversity information is available. Among the four genes, we identified 1,829 genetic variants including 474 non-synonymous substitutions, some of which have been previously documented, as well as putative copy number variations in GSTe2 and vgsc. Global insecticide resistance phenotypic data demonstrated variable resistance in geographic areas with resistant genotypes. Overall, our work provides the first global catalogue and geographic distribution of known and new amino-acid mutations and duplications that can be used to guide the identification of resistance drivers in Ae. aegypti and thereby support monitoring efforts and strategies for vector control.
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Affiliation(s)
- Anton Spadar
- Faculty of Infectious and Tropical Diseases, Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Emma Collins
- Faculty of Infectious and Tropical Diseases, Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Louisa A Messenger
- Department of Environmental and Occupational Health, School of Public Health, University of Nevada, Las Vegas, Las Vegas, NV, USA
- Parasitology and Vector Biology Laboratory (UNLV PARAVEC Lab), School of Public Health, University of Nevada, Las Vegas, NV, USA
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK.
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Love RR, Sikder JR, Vivero RJ, Matute DR, Schrider DR. Strong Positive Selection in Aedes aegypti and the Rapid Evolution of Insecticide Resistance. Mol Biol Evol 2023; 40:msad072. [PMID: 36971242 PMCID: PMC10118305 DOI: 10.1093/molbev/msad072] [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: 07/27/2022] [Revised: 02/13/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Aedes aegypti vectors the pathogens that cause dengue, yellow fever, Zika virus, and chikungunya and is a serious threat to public health in tropical regions. Decades of work has illuminated many aspects of Ae. aegypti's biology and global population structure and has identified insecticide resistance genes; however, the size and repetitive nature of the Ae. aegypti genome have limited our ability to detect positive selection in this mosquito. Combining new whole genome sequences from Colombia with publicly available data from Africa and the Americas, we identify multiple strong candidate selective sweeps in Ae. aegypti, many of which overlap genes linked to or implicated in insecticide resistance. We examine the voltage-gated sodium channel gene in three American cohorts and find evidence for successive selective sweeps in Colombia. The most recent sweep encompasses an intermediate-frequency haplotype containing four candidate insecticide resistance mutations that are in near-perfect linkage disequilibrium with one another in the Colombian sample. We hypothesize that this haplotype may continue to rapidly increase in frequency and perhaps spread geographically in the coming years. These results extend our knowledge of how insecticide resistance has evolved in this species and add to a growing body of evidence suggesting that Ae. aegypti has an extensive genomic capacity to rapidly adapt to insecticide-based vector control.
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Affiliation(s)
- R Rebecca Love
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NCUSA
| | - Josh R Sikder
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NCUSA
| | - Rafael J Vivero
- Programa de Estudio y Control de Enfermedades Tropicales, PECET, Universidad de Antioquia, Chapel Hill, NCColombia
| | - Daniel R Matute
- Department of Biology, College of Arts and Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Daniel R Schrider
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NCUSA
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Nguyen VT, Collier TC, Seok S, Wang X, Mburu MM, Simubali L, Gebhardt ME, Norris DE, Lee Y. The first genome sequence of Anopheles squamous from Macha, Zambia. F1000Res 2023; 12:330. [PMID: 37842340 PMCID: PMC10568211 DOI: 10.12688/f1000research.130734.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/10/2023] [Indexed: 10/17/2023] Open
Abstract
Despite efforts to minimize the impacts of malaria and reduce the number of primary vectors, malaria has yet to be eliminated in Zambia. Understudied vector species may perpetuate malaria transmission in pre-elimination settings. Anopheles squamosus is one of the most abundantly caught mosquito species in southern Zambia and has previously been found with Plasmodium falciparum sporozoites, a causal agent of human malaria. This species may be a critical vector of malaria transmission, however, there is a lack of genetic information available for An. squamosus. We report the first genome data and the first complete mitogenome (Mt) sequence of An. squamosus. The sequence was extracted from one individual mosquito from the Chidakwa area in Macha, Zambia. The raw reads were obtained using Illumina Novaseq 6000 and assembled through NOVOplasty alignment with related species. The length of the An. squamosus Mt was 15,351 bp, with 77.9 % AT content. The closest match to the whole mitochondrial genome in the phylogenetic tree is the African malaria mosquito, Anopheles gambiae. Its genome data is available through National Center for Biotechnology Information (NCBI) Sequencing Reads Archive (SRA) with accession number SRR22114392. The mitochondrial genome was deposited in NCBI GenBank with the accession number OP776919. The ITS2 containing contig sequence was deposited in GenBank with the accession number OQ241725. Mitogenome annotation and a phylogenetic tree with related Anopheles mosquito species are provided.
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Affiliation(s)
- Valerie T. Nguyen
- Florida Medical Entomology Laboratory, Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, 32962, USA
| | | | - Sangwoo Seok
- Florida Medical Entomology Laboratory, Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, 32962, USA
| | - Xiaodi Wang
- Florida Medical Entomology Laboratory, Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, 32962, USA
| | | | | | - Mary E. Gebhardt
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, 21205, USA
| | - Douglas E. Norris
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, 21205, USA
| | - Yoosook Lee
- Florida Medical Entomology Laboratory, Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, 32962, USA
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Seok S, Jacobsen CM, Romero-Weaver AL, Wang X, Nguyen VT, Collier TC, Riles MT, Akbari OS, Lee Y. Complete mitogenome sequence of Aedes (Hulecoeteomyia) japonicus japonicus from Hawai'i Island. Mitochondrial DNA B Resour 2023; 8:64-68. [PMID: 36685646 PMCID: PMC9848326 DOI: 10.1080/23802359.2022.2161328] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/18/2022] [Indexed: 01/18/2023] Open
Abstract
We report the first complete mitogenome (Mt) sequence of Aedes japonicus japonicus (Diptera: Culicidae). The sequence was extracted from one adult from the Big Island of Hawai'i Island. The length of the Ae. japonicus japonicus Mt was 16,528bp with 78.1% AT content. Its sequence is most similar to the Mt sequence of Aedes koreicus with 90.81% sequence identity. This is the first full Mt sequence available for this species and provides important genetic resource for studying population genetics and dynamics of this important invasive mosquito species.
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Affiliation(s)
- Sangwoo Seok
- Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, Florida Medical Entomology Laboratory, University of Florida, Vero Beach, FL, USA
| | | | - Ana L. Romero-Weaver
- Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, Florida Medical Entomology Laboratory, University of Florida, Vero Beach, FL, USA
| | - Xiaodi Wang
- Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, Florida Medical Entomology Laboratory, University of Florida, Vero Beach, FL, USA
| | - Valerie T. Nguyen
- Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, Florida Medical Entomology Laboratory, University of Florida, Vero Beach, FL, USA
| | | | | | - Omar S. Akbari
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | - Yoosook Lee
- Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, Florida Medical Entomology Laboratory, University of Florida, Vero Beach, FL, USA
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