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Crowley LM, Wawman DC, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective, Darwin Tree of Life Consortium. The genome sequence of the Red-clover Case-bearer, Coleophora deauratella Zeller, 1846. Wellcome Open Res 2024; 9:370. [PMID: 39469292 PMCID: PMC11513577 DOI: 10.12688/wellcomeopenres.22581.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2024] [Indexed: 10/30/2024] Open
Abstract
We present a genome assembly from an individual female Coleophora deauratella (the Red-clover Case-bearer; Arthropoda; Insecta; Lepidoptera; Coleophoridae). The genome sequence is 518.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.76 kilobases in length.
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Affiliation(s)
- Liam M. Crowley
- Department of Biology, University of Oxford, Oxford, England, UK
| | - Denise C. Wawman
- Department of Biology, University of Oxford, Oxford, England, UK
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Tietjen M, Pérez de León AA, Sagel A, Skoda SR, Phillips PL, Mitchell RD, Caruth J, Durán U, Musai L, Tortosa S, Arp AP. Geographic Population Genetic Structure of the New World Screwworm, Cochliomyia hominivorax (Diptera: Calliphoridae), Using SNPs. JOURNAL OF MEDICAL ENTOMOLOGY 2022; 59:874-882. [PMID: 35323976 DOI: 10.1093/jme/tjac024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 06/14/2023]
Abstract
The New World screwworm, Cochliomyia hominivorax (Coquerel 1858) (Diptera: Calliphoridae), is a serious parasite of livestock, humans, and other warm-blooded animals. It has been eradicated from the northern parts of its historical range down to the Panama-Colombian border where a permanent barrier zone is maintained. This eradication was accomplished through using the sterile insect technique (SIT). In 2016 there was an outbreak of C. hominivorax in the Florida Keys. In only six months, this pest was successfully re-eradicated using SIT, but the geographic origin of the invasion has yet to be resolved. It was previously determined that the Florida flies most likely represented a single invasion, and it was recommended that a finer-scale genetic assessment should be completed. Thus, this current proof-of-concept study aimed to develop a population genetic database using single nucleotide polymorphisms (SNPs) to reference outbreaks and potentially identify the origin of the Florida outbreak. This initial database consists of wild-caught samples from 4 geographic locations as well as laboratory colony samples that originated from 7 additional locations using a genotyping by sequencing (GBS) approach. Geographic population structuring was identified for twelve populations that clustered according to geographic location. The Florida outbreak samples appeared similar to samples from the outer Caribbean cluster which included samples from Dominican Republic and Trinidad and Tobago, however, these results will be further clarified with the replacement of laboratory colony samples with future wild-caught samples.
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Affiliation(s)
- Mackenzie Tietjen
- United States Department of Agriculture, Agricultural Research Service, Knipling-Bushland U.S. Livestock Insects Research Laboratory, 2700 Fredericksburg Road, Kerrville, TX, 78028, USA
| | - Adalberto A Pérez de León
- United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center: Parlier, CA, 93648, USA
| | - Agustin Sagel
- United States Department of Agriculture, Agricultural Research Service, Screwworm Research Unit, Pacora, Panama
| | - Steve R Skoda
- United States Department of Agriculture, Agricultural Research Service, Knipling-Bushland U.S. Livestock Insects Research Laboratory, 2700 Fredericksburg Road, Kerrville, TX, 78028, USA
| | - Pamela L Phillips
- United States Department of Agriculture, Animal and Plant Health Inspection Service, International Services, International Services, Pacora, Panama
| | - Robert D Mitchell
- U.S. Environmental Protection Agency, Office of Pesticide Programs, Washington, DC, 20460, USA
| | - Joanne Caruth
- Animal Health Unit, Division of Food Production Forestry and Fisheries, Tobago House of Assembly. Hope Farm, Trinidad and Tobago
| | - Uziel Durán
- Direccion General de Ganaderia (DIGEGA), Ministry of Agriculture of the Dominican Republic, Santo Domingo, Dominican Republic
| | - Lisa Musai
- Animal Production and Health Division, Ministry of Agriculture, Land and Fisheries, Port of Spain, Trinidad and Tobago
| | - Silvia Tortosa
- Direccion General de Ganaderia (DIGEGA), Ministry of Agriculture of the Dominican Republic, Santo Domingo, Dominican Republic
| | - Alex P Arp
- United States Department of Agriculture, Agricultural Research Service, Screwworm Research Unit, Pacora, Panama
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Genetic and Epigenetic Changes during the Upward Expansion of Deyeuxia angustifolia Kom. in the Alpine Tundra of the Changbai Mountains, China. PLANTS 2021; 10:plants10020291. [PMID: 33546517 PMCID: PMC7913720 DOI: 10.3390/plants10020291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 11/17/2022]
Abstract
Ecological adaptation plays an important role in the process of plant expansion, and genetics and epigenetics are important in the process of plant adaptation. In this study, genetic and epigenetic analyses and soil properties were performed on D. angustifolia of 17 populations, which were selected in the tundra zone on the western slope of the Changbai Mountains. Our results showed that the levels of genetic and epigenetic diversity of D. angustifolia were relatively low, and the main variation occurred among different populations (amplified fragment length polymorphism (AFLP): 95%, methylation sensitive amplification polymorphism (MSAP): 87%). In addition, DNA methylation levels varied from 23.36% to 35.70%. Principal component analysis (PCA) results showed that soil properties of different populations were heterogeneous. Correlation analyses showed that soil moisture, pH and total nitrogen were significantly correlated with genetic diversity of D. angustifolia, and soil temperature and pH were closely related to epigenetic diversity. Simple Mantel tests and partial Mantel tests showed that genetic variation significantly correlated with habitat or geographical distance. However, the correlation between epigenetic variation and habitat or geographical distance was not significant. Our results showed that, in the case of low genetic variation and genetic diversity, epigenetic variation and DNA methylation may provide a basis for the adaptation of D. angustifolia.
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Campbell EO, Dupuis JR, Holowachuk J, Hladun S, Vankosky MA, Mori BA. Disjunction between canola distribution and the genetic structure of its recently described pest, the canola flower midge ( Contarinia brassicola). Ecol Evol 2020; 10:13284-13296. [PMID: 33304537 PMCID: PMC7713945 DOI: 10.1002/ece3.6927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/10/2020] [Accepted: 09/07/2020] [Indexed: 12/31/2022] Open
Abstract
Population genomics is a useful tool to support integrated pest management as it can elucidate population dynamics, demography, and histories of invasion. Here, we use a restriction site-associated DNA sequencing approach combined with whole-genome amplification (WGA) to assess genomic population structure of a newly described pest of canola, the diminutive canola flower midge, Contarinia brassicola. Clustering analyses recovered little geographic structure across the main canola production region but differentiated several geographically disparate populations at edges of the agricultural zone. Given a lack of alternative hypotheses for this pattern, we suggest these data support alternative hosts for this species and thus our canola-centric view of this midge as a pest has limited our understanding of its biology. These results speak to the need for increased surveying efforts across multiple habitats and other potential hosts within Brassicaceae to improve both our ecological and evolutionary knowledge of this species and contribute to effective management strategies. We additionally found that use of WGA prior to library preparation was an effective method for increasing DNA quantity of these small insects prior to restriction site-associated DNA sequencing and had no discernible impact on genotyping consistency for population genetic analysis; WGA is therefore likely to be tractable for other similar studies that seek to randomly sample markers across the genome in small organisms.
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Affiliation(s)
- Erin O. Campbell
- Department of Agriculture, Food, and Nutrition Sciences4‐10 Agriculture/Forestry CentreUniversity of AlbertaEdmontonABCanada
| | | | - Jennifer Holowachuk
- Agriculture and Agri‐Food CanadaSaskatoon Research and Development CentreSaskatoonSKCanada
| | - Shane Hladun
- Agriculture and Agri‐Food CanadaSaskatoon Research and Development CentreSaskatoonSKCanada
| | - Meghan A. Vankosky
- Agriculture and Agri‐Food CanadaSaskatoon Research and Development CentreSaskatoonSKCanada
| | - Boyd A. Mori
- Department of Agriculture, Food, and Nutrition Sciences4‐10 Agriculture/Forestry CentreUniversity of AlbertaEdmontonABCanada
- Agriculture and Agri‐Food CanadaSaskatoon Research and Development CentreSaskatoonSKCanada
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Dupuis JR, Ruiz‐Arce R, Barr NB, Thomas DB, Geib SM. Range-wide population genomics of the Mexican fruit fly: Toward development of pathway analysis tools. Evol Appl 2019; 12:1641-1660. [PMID: 31462920 PMCID: PMC6708432 DOI: 10.1111/eva.12824] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/17/2019] [Accepted: 05/23/2019] [Indexed: 11/30/2022] Open
Abstract
Recurrently invading pests provide unique challenges for pest management, but also present opportunities to utilize genomics to understand invasion dynamics and inform regulatory management through pathway analysis. In the southern United States, the Mexican fruit fly Anastrepha ludens is such a pest, and its incursions into Texas and California represent major threats to the agricultural systems of those regions. We developed a draft genome assembly for A. ludens, conducted range-wide population genomics using restriction site-associated DNA sequencing, and then developed and demonstrated a panel of highly differentiated diagnostic SNPs for source determination of intercepted flies in this system. Using 2,081 genomewide SNPs, we identified four populations across the range of A. ludens, corresponding to western Mexico, eastern Mexico/Texas, Guatemala/Belize/Honduras, and Costa Rica/Panama, with some intergradation present between clusters, particularly in Central America. From this population genomics framework, we developed a diagnostic panel of 28 highly differentiated SNPs that were able to recreate the genomewide population structure in this species. We demonstrated this panel on a set of test specimens, including specimens intercepted as part of regular trapping surveillance in Texas and California, and we were able to predict populations of origin for these specimens. This methodology presents a highly applied use of genomic techniques and can be implemented in any group of recurrently invading pests.
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Affiliation(s)
- Julian R. Dupuis
- U.S. Department of Agriculture‐Agricultural Research ServiceDaniel K. Inouye U.S. Pacific Basin Agricultural Research CenterHiloHawaii
- Department of Plant and Environmental Protection SciencesUniversity of Hawai’i at MānoaHonoluluHawaii
| | - Raul Ruiz‐Arce
- U.S. Department of Agriculture‐Animal and Plant Health Inspection Service, Plant Protection & Quarantine, Science and TechnologyMission LaboratoryEdinburgTexas
| | - Norman B. Barr
- U.S. Department of Agriculture‐Animal and Plant Health Inspection Service, Plant Protection & Quarantine, Science and TechnologyMission LaboratoryEdinburgTexas
| | - Donald B. Thomas
- U.S. Department of Agriculture‐Agricultural Research ServiceCattle Fever Tick Research LaboratoryEdinburgTexas
| | - Scott M. Geib
- U.S. Department of Agriculture‐Agricultural Research ServiceDaniel K. Inouye U.S. Pacific Basin Agricultural Research CenterHiloHawaii
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Dupuis JR, Guerrero FD, Skoda SR, Phillips PL, Welch JB, Schlater JL, Azeredo-Espin AML, Pérez de León AA, Geib SM. Molecular Characterization of the 2016 New World Screwworm (Diptera: Calliphoridae) Outbreak in the Florida Keys. JOURNAL OF MEDICAL ENTOMOLOGY 2018; 55:938-946. [PMID: 29788142 DOI: 10.1093/jme/tjy078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Indexed: 06/08/2023]
Abstract
New World screwworm (NWS), Cochliomyia hominivorax (Coquerel 1858) (Diptera: Calliphoridae), is a myiasis-causing fly that can be a serious threat to the health of livestock, wildlife, and humans. Its progressive eradication from the southern United States, Mexico, and Central America from the 1950s to 2000s is an excellent example of successful pest management using sterile insect technique (SIT). In late 2016, autochthonous NWS were detected in the Florida Keys, representing this species' first invasion in the United States in >30 yr. Rapid use of quarantine and SIT was successful in eliminating the infestation by early 2017; however, the geographic source of this infestation remains unknown. Here, we use amplicon sequencing to generate mitochondrial and nuclear sequence data representing all confirmed cases of NWS from this infestation, and compare these sequences to preexisting data sets sampling the native distribution of NWS. We ask two questions regarding the FL Keys outbreak. First, is this infestation the result of a single invasion from one source, or multiple invasions from different sources? And second, what is the geographic origin of this invasion? We found virtually no sequence variation between specimens collected from the FL Keys outbreak, which is consistent with a single source of introduction. However, we also found very little geographic resolution in any of the data sets, which precludes identification of the source of this outbreak. Our lack of success in answering our second question speaks to the need for finer-scale genetic or genomic assessments of NWS population structure, which would facilitate source determination of potential future outbreaks.
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Affiliation(s)
- Julian R Dupuis
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, HI
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, HI
| | - Felix D Guerrero
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Kerrville, TX
| | - Steven R Skoda
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Kerrville, TX
| | - Pamela L Phillips
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Kerrville, TX
| | - John B Welch
- USDA-APHIS, International Services, Action Programs, College Station, TX
| | - Jack L Schlater
- USDA-APHIS, National Veterinary Services Laboratory, Ames, IA
| | - Ana Maria L Azeredo-Espin
- Centro de Biologia Molecular e Engenharia Genética and Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas Instituto de Biologia, São Paulo, Brazil
| | - Adalberto A Pérez de León
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Kerrville, TX
| | - Scott M Geib
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, HI
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Population genomics and comparisons of selective signatures in two invasions of melon fly, Bactrocera cucurbitae (Diptera: Tephritidae). Biol Invasions 2017. [DOI: 10.1007/s10530-017-1621-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Dupuis JR, Bremer FT, Jombart T, Sim SB, Geib SM. mvmapper: Interactive spatial mapping of genetic structures. Mol Ecol Resour 2017; 18:362-367. [PMID: 28987008 DOI: 10.1111/1755-0998.12724] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/02/2017] [Accepted: 10/03/2017] [Indexed: 11/28/2022]
Abstract
Characterizing genetic structure across geographic space is a fundamental challenge in population genetics. Multivariate statistical analyses are powerful tools for summarizing genetic variability, but geographic information and accompanying metadata are not always easily integrated into these methods in a user-friendly fashion. Here, we present a deployable Python-based web-tool, mvmapper, for visualizing and exploring results of multivariate analyses in geographic space. This tool can be used to map results of virtually any multivariate analysis of georeferenced data, and routines for exporting results from a number of standard methods have been integrated in the R package adegenet, including principal components analysis (PCA), spatial PCA, discriminant analysis of principal components, principal coordinates analysis, nonmetric dimensional scaling and correspondence analysis. mvmapper's greatest strength is facilitating dynamic and interactive exploration of the statistical and geographic frameworks side by side, a task that is difficult and time-consuming with currently available tools. Source code and deployment instructions, as well as a link to a hosted instance of mvmapper, can be found at https://popphylotools.github.io/mvMapper/.
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Affiliation(s)
- Julian R Dupuis
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, U.S. Department of Agriculture-Agricultural Research Service, Hilo, HI, USA.,Department of Plant and Environmental Protection Services, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Forest T Bremer
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, U.S. Department of Agriculture-Agricultural Research Service, Hilo, HI, USA.,Department of Plant and Environmental Protection Services, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Thibaut Jombart
- Department of Infectious Disease Epidemiology, MRC Centre for Outbreak Analysis and Modelling, School of Public Health, Imperial College, London, UK
| | - Sheina B Sim
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, U.S. Department of Agriculture-Agricultural Research Service, Hilo, HI, USA
| | - Scott M Geib
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, U.S. Department of Agriculture-Agricultural Research Service, Hilo, HI, USA
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