دورية أكاديمية
A genotyping array for the globally invasive vector mosquito, Aedes albopictus.
| العنوان: | A genotyping array for the globally invasive vector mosquito, Aedes albopictus. |
|---|---|
| المؤلفون: | Cosme LV; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520-8105, USA. luciano.cosme@yale.edu., Corley M; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520-8105, USA., Johnson T; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520-8105, USA., Severson DW; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA., Yan G; Department of Population Health and Disease Prevention, University of California, Irvine, CA, USA., Wang X; Department of Population Health and Disease Prevention, University of California, Irvine, CA, USA., Beebe N; School of the Environment, University of Queensland Australia, St Lucia, Australia., Maynard A; School of the Environment, University of Queensland Australia, St Lucia, Australia., Bonizzoni M; Department of Biology and Biotechnology 'Lazzaro Spallanzani', University of Pavia, Pavia, Italy., Khorramnejad A; Department of Biology and Biotechnology 'Lazzaro Spallanzani', University of Pavia, Pavia, Italy., Martins AJ; Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, RJ, Brazil., Lima JBP; Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, RJ, Brazil., Munstermann LE; Yale School of Public Health and Yale Peabody Museum, Yale University, New Haven, CT, USA., Surendran SN; Department of Zoology, Faculty of Science, University of Jaffna, Jaffna, Sri Lanka., Chen CH; National Health Research Institutes, National Mosquito-Borne Disease Control Research Center & National Institute of Infectious Diseases and Vaccinology, Miaoli, Taiwan., Maringer K; Pirbright Institute, Pirbright, England, UK., Wahid I; Center for Zoonotic and Emerging Diseases, Hasanuddin University Medical Research Centre (HUMRC), Makassar, Indonesia., Mukherjee S; Mitrani Department of Desert Ecology, Jacob Blaustein Institutes of Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel.; Biological and Life Sciences Division, School of Arts and Sciences, Ahmedabad University, Ahmedabad, Gujarat, India., Xu J; Department of Biology, New Mexico State University, Las Cruces, NM, USA., Fontaine MC; MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France.; University of Groningen, Groningen Institute for Evolutionary Life Sciences, Groningen, The Netherlands., Estallo EL; Facultad de Ciencias Exactas, Físicas y Naturales, Centro de Investigaciones Entomológicas de Córdoba, Universidad Nacional de Córdoba, Córdoba, Argentina.; Instituto de Investigaciones Biológicas y Tecnológicas, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Córdoba, Córdoba, Argentina., Stein M; Instituto de Medicina Regional, Universidad Nacional del Nordeste, CONICET CCT Nordeste, Resistencia, Argentina., Livdahl T; Clark University, Worcester, MA, USA., Scaraffia PY; School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA., Carter BH; School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA., Mogi M; Division of Parasitology, Faculty of Medicine, Saga University, Nabeshima, Saga, Japan., Tuno N; Laboratory of Ecology, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan., Mains JW; MosquitoMate Inc., Lexington, KY, USA., Medley KA; Tyson Research Center, Washington University in St. Louis, St. Louis, USA., Bowles DE; US National Park Service, Washington, USA., Gill RJ; Department of Life Sciences, Georgina Mace Centre for the Living Planet, Imperial College London, Berkshire, UK., Eritja R; Centre d'Estudis Avançats de Blanes, Consejo Superior de Investigaciones Científicas, Blanes, Spain., González-Obando R; Department of Biology, Universidad del Valle, Calle, Colombia., Trang HTT; Department of Medical Entomology and Zoonotics, Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam., Boyer S; Medical Entomology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia., Abunyewa AM; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520-8105, USA., Hackett K; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520-8105, USA., Wu T; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520-8105, USA., Nguyễn J; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520-8105, USA., Shen J; Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06510, USA., Zhao H; Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06510, USA.; Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA., Crawford JE; Verily Life Sciences, San Francisco, CA, USA., Armbruster P; Department of Biology, Georgetown University, Washington, DC, USA., Caccone A; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520-8105, USA. |
| المصدر: | Parasites & vectors [Parasit Vectors] 2024 Mar 04; Vol. 17 (1), pp. 106. Date of Electronic Publication: 2024 Mar 04. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: BioMed Central Country of Publication: England NLM ID: 101462774 Publication Model: Electronic Cited Medium: Internet ISSN: 1756-3305 (Electronic) Linking ISSN: 17563305 NLM ISO Abbreviation: Parasit Vectors Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: London : BioMed Central |
| مواضيع طبية MeSH: | Mosquito Vectors*/genetics , Aedes*/genetics, Humans ; Animals ; Genotype ; Heterozygote |
| مستخلص: | Background: Although whole-genome sequencing (WGS) is the preferred genotyping method for most genomic analyses, limitations are often experienced when studying genomes characterized by a high percentage of repetitive elements, high linkage, and recombination deserts. The Asian tiger mosquito (Aedes albopictus), for example, has a genome comprising up to 72% repetitive elements, and therefore we set out to develop a single-nucleotide polymorphism (SNP) chip to be more cost-effective. Aedes albopictus is an invasive species originating from Southeast Asia that has recently spread around the world and is a vector for many human diseases. Developing an accessible genotyping platform is essential in advancing biological control methods and understanding the population dynamics of this pest species, with significant implications for public health. Methods: We designed a SNP chip for Ae. albopictus (Aealbo chip) based on approximately 2.7 million SNPs identified using WGS data from 819 worldwide samples. We validated the chip using laboratory single-pair crosses, comparing technical replicates, and comparing genotypes of samples genotyped by WGS and the SNP chip. We then used the chip for a population genomic analysis of 237 samples from 28 sites in the native range to evaluate its usefulness in describing patterns of genomic variation and tracing the origins of invasions. Results: Probes on the Aealbo chip targeted 175,396 SNPs in coding and non-coding regions across all three chromosomes, with a density of 102 SNPs per 1 Mb window, and at least one SNP in each of the 17,461 protein-coding genes. Overall, 70% of the probes captured the genetic variation. Segregation analysis found that 98% of the SNPs followed expectations of single-copy Mendelian genes. Comparisons with WGS indicated that sites with genotype disagreements were mostly heterozygotes at loci with WGS read depth < 20, while there was near complete agreement with WGS read depths > 20, indicating that the chip more accurately detects heterozygotes than low-coverage WGS. Sample sizes did not affect the accuracy of the SNP chip genotype calls. Ancestry analyses identified four to five genetic clusters in the native range with various levels of admixture. Conclusions: The Aealbo chip is highly accurate, is concordant with genotypes from WGS with high sequence coverage, and may be more accurate than low-coverage WGS. (© 2024. The Author(s).) |
| References: | Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):E5907-15. (PMID: 26483478) PLoS Comput Biol. 2013;9(8):e1003118. (PMID: 23950696) Heredity (Edinb). 1987 Oct;59 ( Pt 2):253-8. (PMID: 3679880) Heredity (Edinb). 1991 Aug;67 ( Pt 1):85-93. (PMID: 1917554) PLoS Negl Trop Dis. 2019 Aug 22;13(8):e0007554. (PMID: 31437154) Pest Manag Sci. 2020 Dec;76(12):4202-4209. (PMID: 32592440) Bioinformatics. 2019 May 15;35(10):1786-1788. (PMID: 30321304) Gigascience. 2018 Mar 1;7(3):1-13. (PMID: 29329394) Bioinformatics. 2011 Nov 1;27(21):3070-1. (PMID: 21926124) Bioinformatics. 2008 Jun 1;24(11):1403-5. (PMID: 18397895) Pathog Glob Health. 2015 Jul;109(5):207-20. (PMID: 26369436) Parasit Vectors. 2020 Aug 13;13(1):417. (PMID: 32791977) Bioinformatics. 2012 Jul 15;28(14):1919-20. (PMID: 22576172) Front Genet. 2022 Apr 11;13:867231. (PMID: 35480313) Gigascience. 2015 Feb 25;4:7. (PMID: 25722852) Theor Appl Genet. 1990 Jun;79(6):748-52. (PMID: 24226734) Heredity (Edinb). 2000 Mar;84 ( Pt 3):331-7. (PMID: 10762403) Front Plant Sci. 2018 Feb 06;9:104. (PMID: 29467780) PLoS Negl Trop Dis. 2017 Jul 25;11(7):e0005653. (PMID: 28742801) BMC Bioinformatics. 2011 Jun 18;12:246. (PMID: 21682921) Mol Ecol Resour. 2016 Mar;16(2):540-8. (PMID: 26417651) Nat Microbiol. 2019 May;4(5):854-863. (PMID: 30833735) Trends Parasitol. 2013 Sep;29(9):460-8. (PMID: 23916878) Mol Ecol. 2020 Oct;29(19):3593-3606. (PMID: 33463828) Mol Ecol. 2015 Jan;24(2):284-95. (PMID: 25230113) G3 (Bethesda). 2023 Jun 1;13(6):. (PMID: 36966413) Proc Natl Acad Sci U S A. 2021 Mar 2;118(9):. (PMID: 33619083) Nature. 2018 Nov;563(7732):501-507. (PMID: 30429615) Mol Ecol. 2016 Nov;25(21):5377-5395. (PMID: 27671732) Int J Infect Dis. 2018 Feb;67:25-35. (PMID: 29196275) Genetics. 2014 Apr;196(4):973-83. (PMID: 24496008) Nat Comput Sci. 2023 Jul;3(7):621-629. (PMID: 37600116) Fly (Austin). 2012 Apr-Jun;6(2):80-92. (PMID: 22728672) G3 (Bethesda). 2015 Feb 26;5(5):711-8. (PMID: 25721127) Bioscience. 2018 Nov 1;68(11):854-860. (PMID: 30464351) Mitochondrial DNA. 2011 Oct;22(5-6):155-8. (PMID: 22165826) Insects. 2021 Feb 16;12(2):. (PMID: 33669192) Bioinformatics. 2016 Sep 15;32(18):2817-23. (PMID: 27283948) Mol Ecol. 2019 May;28(9):2360-2377. (PMID: 30849200) Mol Ecol. 2021 Mar;30(5):1174-1189. (PMID: 33421231) BMC Bioinformatics. 2014 Nov 25;15:356. (PMID: 25420514) Methods Mol Biol. 2019;1858:75-87. (PMID: 30414112) Genetics. 2014 Jun;197(2):573-89. (PMID: 24700103) Genome Biol. 2016 Mar 23;17:53. (PMID: 27009100) Nucleic Acids Res. 2009 Jul;37(13):4181-93. (PMID: 19570852) Genome Biol. 2020 Aug 26;21(1):215. (PMID: 32847630) Evolution. 1984 Nov;38(6):1358-1370. (PMID: 28563791) Bioinformatics. 2009 Aug 15;25(16):2078-9. (PMID: 19505943) Heredity (Edinb). 1988 Apr;60 ( Pt 2):173-81. (PMID: 3366625) PLoS Negl Trop Dis. 2020 Jul 17;14(7):e0008463. (PMID: 32678817) Ecol Evol. 2017 Oct 24;7(23):10143-10157. (PMID: 29238544) J Med Entomol. 2016 Sep;53(5):1013-23. (PMID: 27354438) Genes (Basel). 2021 Oct 06;12(10):. (PMID: 34680974) Evol Appl. 2017 Sep 03;10(10):1031-1039. (PMID: 29151858) PLoS Negl Trop Dis. 2017 Oct 18;11(10):e0006009. (PMID: 29045401) PLoS One. 2017 Oct 5;12(10):e0185220. (PMID: 28981529) Mol Ecol Resour. 2013 Sep;13(5):946-52. (PMID: 23738873) Heredity (Edinb). 2016 Sep;117(3):125-34. (PMID: 27273325) Ecol Evol. 2018 Jul 13;8(16):7835-7848. (PMID: 30250667) |
| معلومات مُعتمدة: | UL1 TR001863 United States TR NCATS NIH HHS; RO1A13409 United States NH NIH HHS |
| فهرسة مساهمة: | Keywords: Aedes albopictus; Population genomics; SNP chip; Validation |
| SCR Organism: | Aedes albopictus |
| تواريخ الأحداث: | Date Created: 20240304 Date Completed: 20240306 Latest Revision: 20240312 |
| رمز التحديث: | 20240312 |
| مُعرف محوري في PubMed: | PMC10910840 |
| DOI: | 10.1186/s13071-024-06158-z |
| PMID: | 38439081 |
| قاعدة البيانات: | MEDLINE |
Find this article in full text from Springer Verlag. 
Full Text Finder | تدمد: | 1756-3305 |
|---|---|
| DOI: | 10.1186/s13071-024-06158-z |