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Feltman NR, Burkness EC, Ebbenga D, Hutchison WD, Smanski MJ. HUGE pipeline to measure temporal genetic variation in Drosophila suzukii populations for genetic biocontrol applications. FRONTIERS IN INSECT SCIENCE 2022; 2:981974. [PMID: 38468784 PMCID: PMC10926429 DOI: 10.3389/finsc.2022.981974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/22/2022] [Indexed: 03/13/2024]
Abstract
Understanding the fine-scale genome sequence diversity that exists within natural populations is important for developing models of species migration, temporal stability, and range expansion. For invasive species, agricultural pests, and disease vectors, sequence diversity at specific loci in the genome can impact the efficacy of next-generation genetic biocontrol strategies. Here we describe a pipeline for haplotype-resolution genetic variant discovery and quantification from thousands of Spotted Wing Drosophila (Drosophila suzukii, SWD) isolated at two field sites in the North-Central United States (Minnesota) across two seasons. We observed highly similar single nucleotide polymorphism (SNP) frequencies at each genomic location at each field site and year. This supports the hypotheses that SWD overwinters in Minnesota, is annually populated by the same source populations or a combination of both theories. Also, the stable genetic structure of SWD populations allows for the rational design of genetic biocontrol technologies for population suppression.
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Affiliation(s)
- Nathan R. Feltman
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Saint Paul, MN, United States
- Biotechnology Institute, University of Minnesota, Saint Paul, MN, United States
| | - Eric C. Burkness
- Department of Entomology, University of Minnesota, Saint Paul, MN, United States
| | - Dominique N. Ebbenga
- Department of Entomology, University of Minnesota, Saint Paul, MN, United States
| | - William D. Hutchison
- Department of Entomology, University of Minnesota, Saint Paul, MN, United States
| | - Michael J. Smanski
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Saint Paul, MN, United States
- Biotechnology Institute, University of Minnesota, Saint Paul, MN, United States
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Milton A, Muhanguzi D, Male A, Kajubi A, Buah S, Kubiriba J, Tumuhimbise R. Analysis of Genetic Diversity of Banana Weevils (Cosmopolites sordidus) (Coleoptera: Curculionidae) Using Transcriptome-Derived Simple Sequence Repeat Markers. JOURNAL OF ECONOMIC ENTOMOLOGY 2022; 115:637-646. [PMID: 35021224 DOI: 10.1093/jee/toab213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Indexed: 06/14/2023]
Abstract
The banana weevil, Cosmopolites sordidus (Germar) (Coleoptera: Curculionidae) is an economically important insect pest of bananas. It causes up to 100% yield losses and substantial lifespan reduction in bananas. Advances in genomics, proteomics, and sequencing technologies have provided powerful pathways to genotyping disastrous pests such as C. sordidus. However, such technologies are often not available to the majority of rural subtropical African banana growers and pest control managers. This study was therefore motivated by the need to create cheap and easily accessible C. sordidus genotyping methods that could be deployed by banana pest control managers to the benefit of C. sordidus control programs in the tropics where such advanced technologies are not readily accessible. We used an in-house C. sordidus transcriptome from the an-ongoing study from which we mined an array of simple sequence repeat (SSR) markers. Of these, six highly polymorphic transcriptome-derived SSR markers were used to successfully genotype within and among banana weevil population genetic diversity of 12 C. sordidus populations collected from four banana-growing agro-ecological zones (AEZs) in Uganda. The developed transcriptome-derived SSR markers can be used by researchers in population genetics for characterization of the C. sordidus and identification of new genes that are linked to traits of particular interest. The significant genetic diversity revealed in C. sordidus provides pertinent information for integrated pest management strategies.
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Affiliation(s)
- Ali Milton
- National Agricultural Research Laboratories-Kawanda, Kampala, Uganda
- College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Dennis Muhanguzi
- College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Allan Male
- International Center for Tropical Agriculture, Kampala, Uganda
| | - Ali Kajubi
- National Agricultural Research Laboratories-Kawanda, Kampala, Uganda
| | - Stephen Buah
- National Agricultural Research Laboratories-Kawanda, Kampala, Uganda
| | - Jerome Kubiriba
- National Agricultural Research Laboratories-Kawanda, Kampala, Uganda
| | - Robooni Tumuhimbise
- Rwebitaba Zonal Agricultural Research and Development Institute, Fort-Portal, Uganda
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Bergamo LW, Silva-Brandão KL, Vicentini R, Fresia P, Azeredo-Espin AML. Genetic Differentiation of a New World Screwworm Fly Population from Uruguay Detected by SNPs, Mitochondrial DNA and Microsatellites in Two Consecutive Years. INSECTS 2020; 11:E539. [PMID: 32824385 PMCID: PMC7469150 DOI: 10.3390/insects11080539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/02/2020] [Accepted: 08/09/2020] [Indexed: 06/11/2023]
Abstract
The New World screwworm (NWS) fly, Cochliomyia hominivorax (Diptera: Calliphoridae), is an economically important ectoparasite currently distributed in South America and in the Caribbean basin. The successful eradication of this species in USA, Mexico and continental Central America was achieved by a control program based on the sterile insect technique (SIT). In order to implement a genetic control strategy over the NWS fly's current area of occurrence, first, it is necessary to understand the species dynamics and population structure. In order to address this objective, the spatial genetic structure of the NWS fly was previously reported in South America based on different genetic markers; however, to date, no study has investigated temporal changes in the genetic composition of its populations. In the current study, the temporal genetic structure of a NWS fly population from Uruguay was investigated through two consecutive samplings from the same locality over an interval of approximately 18 generations. The genetic structure was accessed with neutral and under selection SNPs obtained with genotyping-by-sequencing. The results gathered with these data were compared to estimates achieved with mitochondrial DNA sequences and eight microsatellite markers. Temporal changes in the genetic composition were revealed by all three molecular markers, which may be attributed to seasonal changes in the NWS fly's southern distribution. SNPs were employed for the first time for estimating the genetic structure in a NWS fly population; these results provide new clues and perspectives on its population genetic structure. This approach could have significant implications for the planning and implementation of management programs.
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Affiliation(s)
- Luana Walravens Bergamo
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas SP 13083-970, Brazil;
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas (UNICAMP), Campinas SP 13083-862, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (CBMEG-UNICAMP), Campinas SP 13083-875, Brazil;
| | - Karina Lucas Silva-Brandão
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (CBMEG-UNICAMP), Campinas SP 13083-875, Brazil;
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (CCNH-UFABC), Santo André SP 09210-580, Brazil
| | - Renato Vicentini
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas SP 13083-970, Brazil;
| | - Pablo Fresia
- Unidad Mixta Pasteur + INIA (UMPI), Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Ana Maria Lima Azeredo-Espin
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas SP 13083-970, Brazil;
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (CBMEG-UNICAMP), Campinas SP 13083-875, Brazil;
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Development and characterization of 15 novel polymorphic microsatellite loci for two important bot flies (Diptera, Oestridae) by next-generation sequencing. Parasitol Res 2020; 119:2829-2835. [PMID: 32705375 DOI: 10.1007/s00436-020-06824-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/19/2020] [Indexed: 12/12/2022]
Abstract
Cephenemyia stimulator and Oestrus ovis are two important parasitic bot flies (Oestridae) species causing myiasis, with a potential negative impact on the welfare of the host. Using next-generation sequencing approach and bioinformatics tools, a large panel of possible microsatellites loci was obtained in both species. Primer pairs were designed for 15 selected microsatellite loci in C. stimulator and other 15 loci in O. ovis for PCR amplification. Loci amplification and analysis were performed in four populations of each species. The results demonstrated that all selected loci were polymorphic, with the number of alleles ranging from 2 to 6 per locus in C. stimulator and 3 to 13 per locus in O. ovis. This is the first time to describe these microsatellite loci for C. stimulator and O. ovis. These two sets of microsatellite markers could be further used for biogeographic and population genetics studies.
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Deguenon JM, Travanty N, Zhu J, Carr A, Denning S, Reiskind MH, Watson DW, Michael Roe R, Ponnusamy L. Exogenous and endogenous microbiomes of wild-caught Phormia regina (Diptera: Calliphoridae) flies from a suburban farm by 16S rRNA gene sequencing. Sci Rep 2019; 9:20365. [PMID: 31889104 PMCID: PMC6937299 DOI: 10.1038/s41598-019-56733-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/17/2019] [Indexed: 01/12/2023] Open
Abstract
The black blow fly, Phormia regina (Meigen) (Diptera: Calliphoridae) is one of the most abundant carrion flies in North America. Calliphorids are important in agriculture and animal production, veterinary sciences, forensics and medical entomology. While the role of flies in the epidemiology of human and animal diseases is an active area of research, little is known about the microorganisms associated with these insects. We examined the diversity of wild-caught black blow fly endogenous (internal body) and exogenous (external body) microbial communities using 16S rRNA gene sequencing. Overall, 27 phyla, 171 families and 533 genera were detected, and diversity was significantly higher (P < 0.05) on external body surfaces. At the genus level, Dysgonomonas, Ignatzschineria, Acinetobacter, Vagococcus, Myroides, and Wohlfahrtiimonas were predominant. Cloning and sequencing of nearly full-length fragments of the 16S rRNA gene showed that some of the species identified are known to be pathogenic to humans, animals, and plants. Myroides odoratimimus and Acinetobacter radioresistens are well-known, multi-drug resistant bacteria. These results provide a snapshot of the microbial communities harbored by adult black blow flies and call for more comprehensive studies to better characterize the role these flies may play in the transmission of pathogenic microorganisms.
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Affiliation(s)
- Jean M Deguenon
- Department of Entomology and Plant Pathology, 3230 Ligon Street, Campus Box 7647, North Carolina State University, Raleigh, NC, 27695-7647, USA
| | - Nicholas Travanty
- Department of Entomology and Plant Pathology, 3230 Ligon Street, Campus Box 7647, North Carolina State University, Raleigh, NC, 27695-7647, USA
| | - Jiwei Zhu
- Department of Entomology and Plant Pathology, 3230 Ligon Street, Campus Box 7647, North Carolina State University, Raleigh, NC, 27695-7647, USA
| | - Ann Carr
- Department of Entomology and Plant Pathology, 3230 Ligon Street, Campus Box 7647, North Carolina State University, Raleigh, NC, 27695-7647, USA
| | - Steven Denning
- Department of Entomology and Plant Pathology, 3230 Ligon Street, Campus Box 7647, North Carolina State University, Raleigh, NC, 27695-7647, USA
| | - Michael H Reiskind
- Department of Entomology and Plant Pathology, 3230 Ligon Street, Campus Box 7647, North Carolina State University, Raleigh, NC, 27695-7647, USA
| | - David W Watson
- Department of Entomology and Plant Pathology, 3230 Ligon Street, Campus Box 7647, North Carolina State University, Raleigh, NC, 27695-7647, USA
| | - R Michael Roe
- Department of Entomology and Plant Pathology, 3230 Ligon Street, Campus Box 7647, North Carolina State University, Raleigh, NC, 27695-7647, USA.,Comparative Medicine Institute, North Carolina State University, Raleigh, NC, 27695, USA
| | - Loganathan Ponnusamy
- Department of Entomology and Plant Pathology, 3230 Ligon Street, Campus Box 7647, North Carolina State University, Raleigh, NC, 27695-7647, USA. .,Comparative Medicine Institute, North Carolina State University, Raleigh, NC, 27695, USA.
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