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Sim SB, Congrains C, Velasco-Cuervo SM, Corpuz RL, Kauwe AN, Scheffler B, Geib SM. Genome report: chromosome-scale genome assembly of the West Indian fruit fly Anastrepha obliqua (Diptera: Tephritidae). G3 (BETHESDA, MD.) 2024; 14:jkae024. [PMID: 38301265 PMCID: PMC10989853 DOI: 10.1093/g3journal/jkae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 09/21/2023] [Accepted: 01/11/2024] [Indexed: 02/03/2024]
Abstract
The West Indian fruit fly, Anastrepha obliqua, is a major pest of mango in Central and South America and attacks more than 60 species of host fruits. To support current genetic and genomic research on A. obliqua, we sequenced the genome using high-fidelity long-read sequencing. This resulted in a highly contiguous contig assembly with 90% of the genome in 10 contigs. The contig assembly was placed in a chromosomal context using synteny with a closely related species, Anastrepha ludens, as both are members of the Anastrepha fraterculus group. The resulting assembly represents the five autosomes and the X chromosome which represents 95.9% of the genome, and 199 unplaced contigs representing the remaining 4.1%. Orthology analysis across the structural annotation sets of high quality tephritid genomes demonstrates the gene annotations are robust, and identified genes unique to Anastrepha species that may help define their pestiferous nature that can be used as a starting point for comparative genomics. This genome assembly represents the first of this species and will serve as a foundation for future genetic and genomic research in support of its management as an agricultural pest.
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Affiliation(s)
- Sheina B Sim
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, HI 96720, USA
| | - Carlos Congrains
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, HI 96720, USA
- Entomology Section, Department of Plant and Environmental Protection Sciences, University of Hawai’i at Mānoa Plant and Environmental Protection Sciences, Honolulu, HI 96822, USA
| | - Sandra M Velasco-Cuervo
- Department of Agricultural, Food, and Nutritional Sciences, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Renee L Corpuz
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, HI 96720, USA
| | - Angela N Kauwe
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, HI 96720, USA
| | - Brian Scheffler
- USDA-ARS Jamie Whitten Delta States Research Center, Genetics and Bioinformatics Research Unit, Stoneville, MS 38776, USA
| | - Scott M Geib
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, HI 96720, USA
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Congrains C, Dupuis JR, Rodriguez EJ, Norrbom AL, Steck G, Sutton B, Nolazco N, de Brito RA, Geib SM. Phylogenomic analysis provides diagnostic tools for the identification of Anastrepha fraterculus (Diptera: Tephritidae) species complex. Evol Appl 2023; 16:1598-1618. [PMID: 37752958 PMCID: PMC10519418 DOI: 10.1111/eva.13589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 07/24/2023] [Accepted: 08/10/2023] [Indexed: 09/28/2023] Open
Abstract
Insect pests cause tremendous impact to agriculture worldwide. Species identification is crucial for implementing appropriate measures of pest control but can be challenging in closely related species. True fruit flies of the genus Anastrepha Schiner (Diptera: Tephritidae) include some of the most serious agricultural pests in the Americas, with the Anastrepha fraterculus (Wiedemann) complex being one of the most important due to its extreme polyphagy and wide distribution across most of the New World tropics and subtropics. The eight morphotypes described for this complex as well as other closely related species are classified in the fraterculus species group, whose evolutionary relationships are unresolved due to incomplete lineage sorting and introgression. We performed multifaceted phylogenomic approaches using thousands of genes to unravel the evolutionary relationships within the A. fraterculus complex to provide a baseline for molecular diagnosis of these pests. We used a methodology that accommodates variable sources of data (transcriptome, genome, and whole-genome shotgun sequencing) and developed a tool to align and filter orthologs, generating reliable datasets for phylogenetic studies. We inferred 3031 gene trees that displayed high levels of discordance. Nevertheless, the topologies of the inferred coalescent species trees were consistent across methods and datasets, except for one lineage in the A. fraterculus complex. Furthermore, network analysis indicated introgression across lineages in the fraterculus group. We present a robust phylogeny of the group that provides insights into the intricate patterns of evolution of the A. fraterculus complex supporting the hypothesis that this complex is an assemblage of closely related cryptic lineages that have evolved under interspecific gene flow. Despite this complex evolutionary scenario, our subsampling analysis revealed that a set of as few as 80 loci has a similar phylogenetic resolution as the genome-scale dataset, offering a foundation to develop more efficient diagnostic tools in this species group.
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Affiliation(s)
- Carlos Congrains
- U.S. Department of Agriculture‐Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research UnitHiloHawaiiUSA
- Department of Plant and Environmental Protection ServicesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Julian R. Dupuis
- Department of EntomologyUniversity of KentuckyLexingtonKentuckyUSA
| | - Erick J. Rodriguez
- Division of Plant Industry, Florida Department of Agriculture and Consumer ServicesGainesvilleFloridaUSA
| | - Allen L. Norrbom
- Systematic Entomology LabUSDA, ARS c/o Smithsonian InstitutionWashington DCUSA
| | - Gary Steck
- Division of Plant Industry, Florida Department of Agriculture and Consumer ServicesGainesvilleFloridaUSA
| | - Bruce Sutton
- Department of Entomology (Research Associate), National Museum of Natural HistorySmithsonian InstitutionGainesvilleFloridaUSA
| | - Norma Nolazco
- Centro de Diagnóstico de Sanidad Vegetal, Servicio Nacional de Sanidad AgrariaPeru
| | - Reinaldo A. de Brito
- Departamento de Genética e EvoluçãoUniversidade Federal de São CarlosSão CarlosSão PauloBrazil
| | - Scott M. Geib
- U.S. Department of Agriculture‐Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research UnitHiloHawaiiUSA
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da Silva Santana G, Ronchi-Teles B, Dos Santos CM, Soares MA, Souza PGC, Araújo FHV, de Aguiar CVS, da Silva RS. Climate suitability modeling for Anastrepha suspensa (Diptera: Tephritidae): current and future invasion risk analysis. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2023:10.1007/s00484-023-02487-3. [PMID: 37222775 DOI: 10.1007/s00484-023-02487-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 04/09/2023] [Accepted: 05/05/2023] [Indexed: 05/25/2023]
Abstract
The Caribbean fruit fly, Anastrepha suspensa (Lower, 1862) (Diptera: Tephritidae), is a pest of significant economic importance in Central America and Florida (USA). This study was carried out to examine the influence of climate change on the space-time distribution of A. suspensa on temporal and spatial scales. The CLIMEX software was used to model the current distribution and for climate change. The future distribution was performed using two global climate models (GCMs), CSIRO-Mk3.0 (CS) and MIROC-H (MR), under the emission scenarios (SRES) A2 and A1B for the years 2050, 2080, and 2100. The results indicate a low potential for global distribution of A. suspensa in all scenarios studied. However, tropical areas were identified with high climatic suitability for A. suspensa in South America, Central America, Africa, and Oceania until the end of the century. Projections of areas with climatic suitability for A. suspensa can provide helpful information to develop preventive strategies of phytosanitary management avoiding economic impacts with the introduction of the species.
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Affiliation(s)
- Geovani da Silva Santana
- Instituto Nacional de Pesquisa da Amazônia, Av. André Araújo, 2936-Petrópolis, Manaus, AM, 69067-375, Brazil.
| | - Beatriz Ronchi-Teles
- Instituto Nacional de Pesquisa da Amazônia, Av. André Araújo, 2936-Petrópolis, Manaus, AM, 69067-375, Brazil
| | - Cícero Manoel Dos Santos
- Universidade Federal Do Pará R. Cel. José Porfírio, 030-Recreio, Altamiram, PA, 68371-030, Brazil
| | - Marcus Alvarenga Soares
- Universidade Federal Dos Vales de Jequitinhonha E Mucuri, Rodovia MGT 367-Km 583, No. 5000-Alto da Jacuba, Diamantina, MG, 39100-000, Brazil
| | - Philipe Guilherme Corcino Souza
- Universidade Federal Dos Vales de Jequitinhonha E Mucuri, Rodovia MGT 367-Km 583, No. 5000-Alto da Jacuba, Diamantina, MG, 39100-000, Brazil
| | - Fausto Henrique Vieira Araújo
- Universidade Federal Dos Vales de Jequitinhonha E Mucuri, Rodovia MGT 367-Km 583, No. 5000-Alto da Jacuba, Diamantina, MG, 39100-000, Brazil
| | | | - Ricardo Siqueira da Silva
- Universidade Federal Dos Vales de Jequitinhonha E Mucuri, Rodovia MGT 367-Km 583, No. 5000-Alto da Jacuba, Diamantina, MG, 39100-000, Brazil
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Rodriguez EJ, Steck GJ, Moore MR, Norrbom AL, Diaz J, Somma LA, Ruiz-Arce R, Sutton BD, Nolazco N, Muller A, Branham MA. Exceptional larval morphology of nine species of the Anastrephamucronota species group (Diptera, Tephritidae). Zookeys 2022; 1127:155-215. [PMID: 36760355 PMCID: PMC9836592 DOI: 10.3897/zookeys.1127.84628] [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] [Received: 03/31/2022] [Accepted: 07/04/2022] [Indexed: 02/11/2023] Open
Abstract
Anastrepha is the most diverse and economically important genus of Tephritidae in the American tropics and subtropics. The striking morphology of the third instars of Anastrephacaballeroi Norrbom, Anastrephacrebra Stone, Anastrephahaplacantha Norrbom & Korytkowski, Anastrephakorytkowskii Norrbom, Anastrephanolazcoae Norrbom & Korytkowski, and three newly discovered and as yet formally unnamed species (Anastrepha sp. Peru-82, Anastrephasp.nr.protuberans, and Anastrepha sp. Sur-16), and the more typical morphology of Anastrephaaphelocentema Stone, are described using light and scanning electron microscopy. To contribute to a better understanding of the interspecific and intraspecific variation among species in the mucronota species group and facilitate phylogenetic studies, we integrate molecular and morphological techniques to confirm the identity and describe third instars. Larva-adult associations and the identification of described larvae were confirmed using DNA barcodes. We provide diagnostic characters to distinguish larvae among these nine species of the mucronota group and separate them from those of the 29 other Anastrepha species previously described. We introduce the vertical comb-like processes on the oral margin as a novel character, and the unusual character states, including position and shape of the preoral lobe, and dentate or fringed posterior margins of the oral ridges and accessory plates. Our comparative morphology concurs with most previously inferred phylogenetic relationships within the mucronota group.
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Affiliation(s)
- Erick J. Rodriguez
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USAUniversity of FloridaGainesvilleUnited States of America
| | - Gary J. Steck
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry (FDACS/DPI), Gainesville, FL, USAFlorida Department of Agriculture and Consumer Services, Division of Plant IndustryGainesvilleUnited States of America
| | - Matthew R. Moore
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry (FDACS/DPI), Gainesville, FL, USAFlorida Department of Agriculture and Consumer Services, Division of Plant IndustryGainesvilleUnited States of America
| | - Allen L. Norrbom
- Systematic Entomology Laboratory, USDA, ARS, c/o Smithsonian Institution, Washington, DC, USAc/o Smithsonian InstitutionWashingtonUnited States of America
| | - Jessica Diaz
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USAUniversity of FloridaGainesvilleUnited States of America
| | - Louis A. Somma
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry (FDACS/DPI), Gainesville, FL, USAFlorida Department of Agriculture and Consumer Services, Division of Plant IndustryGainesvilleUnited States of America
| | - Raul Ruiz-Arce
- USDA APHIS PPQ S and T Insect Management and Molecular Diagnostic Laboratory, 22675 N. Moorefield Road, Edinburg, TX 78541, USAUSDA APHIS PPQ S and T Insect Management and Molecular Diagnostic LaboratoryEdinburgUnited States of America
| | - Bruce D. Sutton
- Research Associate, Department of Entomology, Smithsonian Institution, USNM, Gainesville, FL, USASmithsonian InstitutionGainesvilleUnited States of America
| | - Norma Nolazco
- Centro de Diagnostico de Sanidad Vegetal, Servicio Nacional de Sanidad Agraria, Av. La Molina 1915, La Molina, PeruCentro de Diagnostico de Sanidad Vegetal, Servicio Nacional de Sanidad AgrariaLa MolinaPeru
| | - Alies Muller
- (retired) Ministry of Agriculture, Animal Husbandry and Fisheries, Paramaribo, SurinameMinistry of AgricultureParamariboSuriname
| | - Marc A. Branham
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USAUniversity of FloridaGainesvilleUnited States of America
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Souza AV, Miranda EA, Passos JF, Araujo EL, Alvarenga CD, Silva JG. Predicting the Invasion Risk by Anastrepha sororcula (Diptera: Tephritidae) in Distinct Geographic Regions. NEOTROPICAL ENTOMOLOGY 2021; 50:989-998. [PMID: 34410677 DOI: 10.1007/s13744-021-00907-w] [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: 04/05/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
The movement of endemic fruit flies to new habitats represents a major biological and economic threat. Anastrepha sororcula Zucchi, 1979 is widely distributed in Brazil and also in Colombia, Ecuador, and Paraguay. Here, we present the potential distribution of A. sororcula in endemic areas and project this model into other regions such as part of sub-Saharan Africa, Central America, and Asia to show areas around the world that this species can potentially establish. We combined geographic coordinates with climate data. The models were built using the maximum entropy (MaxEnt) algorithm. Many mango- and guava-producing countries exhibited climatic suitability for A. sororcula in the regions studied including the nine largest world producers: India, Brazil, Malawi, Kenya, Haiti, Cuba, Colombia, Madagascar, and the Democratic Republic of the Congo. Many of these countries showed ideal host plant availability and climatic conditions for the entry and establishment of A. sororcula. This study is a pioneer in the identification of representative areas in the world with climatic suitability for A. sororcula, which shows the importance of predicting areas at risk of invasion to monitor the movement and establishment of fruit fly species in new regions, which is fundamental to area-wide integrated pest management programs.
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Affiliation(s)
- Adriane Vieira Souza
- Programa de Pós-Graduação em Genética e Biologia Molecular, Depto de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil.
| | - Elder Assis Miranda
- Programa de Pós-Graduação em Genética e Biologia Molecular, Depto de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
- Instituto Federal do Tocantins - IFTO - Porto Nacional, Tocantins, Brazil
| | - Joseane Fernanda Passos
- Programa de Pós-Graduação em Genética e Biologia Molecular, Depto de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - Elton Lucio Araujo
- Depto de Ciências Agronômicas e Florestais, Universidade Federal Rural do Semi-Árido, Mossoró, Rio Grande do Norte, Brazil
| | | | - Janisete Gomes Silva
- Programa de Pós-Graduação em Genética e Biologia Molecular, Depto de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
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Wang J, Chen Y, Hou X, Wang Y, Zhou L, Chen X. An intelligent identification system combining image and DNA sequence methods for fruit flies with economic importance (Diptera: Tephritidae). PEST MANAGEMENT SCIENCE 2021; 77:3382-3395. [PMID: 33786962 DOI: 10.1002/ps.6383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Images and DNA sequences are two important methods for identifying fruit fly species. In addition, the identification of insect species complexes is highly problematic when attempting to utilize automatic identification methods in an actual environment. We integrated the image and DNA sequence identification methods into a single system for the first time and explored an open interactive multi-image comparison function for solving the problem of species complexes. The Automated Fruit Fly Identification System 1.0 (AFIS1.0) was updated to AFIS2.0 by employing different models and developing the system under a novel framework. RESULTS AFIS2.0 was developed using 83 species belonging to eight genera in the Tephritidae, which includes most pests of this family. The system applies the Mask Region Convolutional Neural Network (Mask R-CNN) and discriminative deep metric learning (AlexNet based) methods for image identification, integrates Blast+ for DNA sequence comparison and specific weighting for the fusion result. At the species level, the best classification success rate for wing images (as the Top 1 species in the species list of outcomes) reached 90%, and the average classification success rate for wing, thorax, and abdomen images (as the Top 5 species in the species list of outcomes) was 94%. CONCLUSION AFIS2.0 is more accurate and convenient than AFIS1.0 and can be beneficial for users with or without specific expertise regarding Tephritidae. It also provides a more compact and fluent computer system for fruit fly identification, and can be easily applied in practice. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Jiangning Wang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yingying Chen
- Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Xinwen Hou
- Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Yong Wang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Libing Zhou
- Yunnan Entry-Exit Inspections and Quarantine Bureau, Kunming, China
| | - Xiaolin Chen
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Giardini MC, Nieves M, Scannapieco AC, Conte CA, Milla FH, Schapovaloff ME, Frissolo MS, Remis MI, Cladera JL, Lanzavecchia SB. Geographic distribution of sex chromosome polymorphism in Anastrepha fraterculus sp. 1 from Argentina. BMC Genet 2020; 21:149. [PMID: 33339514 PMCID: PMC7747450 DOI: 10.1186/s12863-020-00944-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Anastrepha fraterculus is recognized as a quarantine pest in several American countries. This fruit fly species is native to the American continent and distributed throughout tropical and subtropical regions. It has been reported as a complex of cryptic species, and at least eight morphotypes have been described. Only one entity of this complex, formerly named Anastrepha fraterculus sp. 1, is present in Argentina. Previous cytogenetic studies on this morphotype described the presence of sex chromosome variation identified by chromosomal size and staining patterns. In this work, we expanded the cytological study of this morphotype by analyzing laboratory strains and wild populations to provide information about the frequency and geographic distribution of these sex chromosome variants. We analyzed the mitotic metaphases of individuals from four laboratory strains and five wild populations from the main fruit-producing areas of Argentina, including the northwest (Tucumán and La Rioja), northeast (Entre Ríos and Misiones), and center (Buenos Aires) of the country. RESULTS In wild samples, we observed a high frequency of X1X1 (0.94) and X1Y5 (0.93) karyomorphs, whereas X1X2 and X1Y6 were exclusively found at a low frequency in Buenos Aires (0.07 and 0.13, respectively), Entre Ríos (0.16 and 0.14, respectively) and Tucumán (0.03 and 0.04, respectively). X2X2 and X2Y5 karyomorphs were not found in wild populations but were detected at a low frequency in laboratory strains. In fact, karyomorph frequencies differed between wild populations and laboratory strains. No significant differences among A. fraterculus wild populations were evidenced in either karyotypic or chromosomal frequencies. However, a significant correlation was observed between Y5 chromosomal frequency and latitude. CONCLUSIONS We discuss the importance of cytogenetics to understand the possible route of invasion and dispersion of this pest in Argentina and the evolutionary forces acting under laboratory conditions, possibly driving changes in the chromosomal frequencies. Our findings provide deep and integral genetic knowledge of this species, which has become of relevance to the characterization and selection of valuable A. fraterculus sp. 1 strains for mass rearing production and SIT implementation.
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Affiliation(s)
- María Cecilia Giardini
- Laboratorio de Insectos de Importancia Agronómica, Instituto de Genética (IGEAF), Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA- CONICET, Hurlingham, Buenos Aires, Argentina
| | - Mariela Nieves
- Grupo de Investigación en Biología Evolutiva, Departamento de Ecología, Genética y Evolución, IEGEBA (CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alejandra Carla Scannapieco
- Laboratorio de Insectos de Importancia Agronómica, Instituto de Genética (IGEAF), Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA- CONICET, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Claudia Alejandra Conte
- Laboratorio de Insectos de Importancia Agronómica, Instituto de Genética (IGEAF), Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA- CONICET, Hurlingham, Buenos Aires, Argentina
| | - Fabián Horacio Milla
- Laboratorio de Insectos de Importancia Agronómica, Instituto de Genética (IGEAF), Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA- CONICET, Hurlingham, Buenos Aires, Argentina
| | - María Elena Schapovaloff
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Estación Experimental Agropecuaria Montecarlo, Instituto Nacional de Tecnología Agropecuaria (INTA), Misiones, Argentina
| | - Maria Soledad Frissolo
- Subprograma La Rioja, Programa Nacional de Control y Erradicación de Moscas de los Frutos (PROCEM), La Rioja, Argentina
| | - María Isabel Remis
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Genética de la Estructura Poblacional, Departamento de Ecología, Genética y Evolución,IEGEBA (CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jorge Luis Cladera
- Laboratorio de Insectos de Importancia Agronómica, Instituto de Genética (IGEAF), Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA- CONICET, Hurlingham, Buenos Aires, Argentina
| | - Silvia Beatriz Lanzavecchia
- Laboratorio de Insectos de Importancia Agronómica, Instituto de Genética (IGEAF), Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA- CONICET, Hurlingham, Buenos Aires, Argentina
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Bartolini I, Rivera J, Nolazco N, Olórtegui A. Towards the implementation of a DNA barcode library for the identification of Peruvian species of Anastrepha (Diptera: Tephritidae). PLoS One 2020; 15:e0228136. [PMID: 32004351 PMCID: PMC6994132 DOI: 10.1371/journal.pone.0228136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 01/08/2020] [Indexed: 11/18/2022] Open
Abstract
The genus Anastrepha is a diverse lineage of fruit-damaging tephritid flies widespread across the Neotropical Region. Accurate taxonomic identification of these flies is therefore of paramount importance in agricultural contexts. DNA barcoding libraries are molecular-based tools based on a short sequence of the mitochondrial COI gene enabling rapid taxonomic identification of biological species. In this study, we evaluate the utility of this method for species identification of Peruvian species of Anastrepha and assemble a preliminary barcode profile for the group. We obtained 73 individual sequences representing the 15 most common species, 13 of which were either assigned to previously recognized or newly established BINs. Intraspecific genetic divergence between sampled species averaged 1.01% (range 0-3.3%), whereas maximum interspecific values averaged 8.67 (range 8.26-17.12%). DNA barcoding was found to be an effective method to discriminate between many Peruvian species of Anastrepha that were tested, except for most species of the fraterculus species group, which were all assigned to the same BIN as they shared similar and, in some cases, identical barcodes. We complemented this newly produced dataset with 86 published sequences to build a DNA barcoding library of 159 sequences representing 56 Peruvian species of Anastrepha (approx. 58% of species reported from that country). We conclude that DNA barcoding is an effective method to distinguish among Peruvian species of Anastrepha outside the fraterculus group, and that complementary methods (e.g., morphometrics, additional genetic markers) would be desirable to assist sensu stricto species identification for phytosanitary surveillance and management practices of this important group of pestiferous flies.
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Affiliation(s)
- Ida Bartolini
- Laboratorio de Biología Molecular, Servicio Nacional de Sanidad Agrícola, La Molina, Lima, Perú
| | - Julio Rivera
- Unidad de Investigación en Entomología y Medio Ambiente, Universidad San Ignacio de Loyola, La Molina, Lima, Perú
| | - Norma Nolazco
- Laboratorio de Entomología del Centro de Diagnóstico de Sanidad Vegetal, Servicio Nacional de Sanidad Agrícola, La Molina, Lima, Perú
| | - Arturo Olórtegui
- Laboratorio de Biología Molecular, Servicio Nacional de Sanidad Agrícola, La Molina, Lima, Perú
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Han HY, Ro KE. DNA barcoding reveals a species group of the genus Campiglossa (Diptera, Tephritidae, Tephritinae) with recognition of a new species from East Asia and previously unknown females of Campiglossa coei (Hardy). Zookeys 2019; 899:1-36. [PMID: 31871399 PMCID: PMC6923282 DOI: 10.3897/zookeys.899.46779] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 11/14/2019] [Indexed: 11/12/2022] Open
Abstract
While analyzing DNA barcodes of all the Korean and some East Asian tephritid species in conjunction with the barcode sequences available from BOLD Systems (www.boldsystems.org), the large and taxonomically enigmatic genus Campiglossa was recovered as a monophyletic clade, together with the genera Dioxyna and Homoeotricha, which are here synonymized for that reason. Ten major lineages are also recognized within the Campiglossa clade: producta group, loewiana group, sororcula group, irrorata group, achyrophori group, difficilis group, luxorientis group, magniceps group, arisanica group, and misella group. Here, more detailed taxonomic accounts are provided for the misella group, including four DNA analysis-recovered members: C. coei, C. misella, C. paramelaena sp. nov., and C. melaena. A single morphological synapomorphy is proposed for this species group: the presence of a large mid-anterior dark wing marking in males with associated structural modification (more apically positioned crossvein R-M than in females). Based on the morphological characteristics, two presumptive members that are only known from male specimens are further recognized: C. pishanica and C. propria from China. A full description of C. paramelaena sp. nov., and a redescription of C. coei, for which only males were previously known, are provided. For all the included species, a taxonomic key, diagnoses, and photographs to aid their accurate identification are given. Finally, C. favillacea is synonymized with C. coei and C. roscida with C. misella, and C. coei and C. pishanica resurrected from the synonymy of C. misella.
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Affiliation(s)
- Ho-Yeon Han
- Division of Biological Science and Technology, College of Science and Technology, Yonsei University, 1 Yonseidae-gil, Wonju-si, Gangwon-do 26493, South Korea Yonsei University Wonju-si South Korea
| | - Kyung-Eui Ro
- Division of Biological Science and Technology, College of Science and Technology, Yonsei University, 1 Yonseidae-gil, Wonju-si, Gangwon-do 26493, South Korea Yonsei University Wonju-si South Korea
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10
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Zheng L, Zhang Y, Yang W, Zeng Y, Jiang F, Qin Y, Zhang J, Jiang Z, Hu W, Guo D, Wan J, Zhao Z, Liu L, Li Z. New Species-Specific Primers for Molecular Diagnosis of Bactrocera minax and Bactrocera tsuneonis (Diptera: Tephritidae) in China Based on DNA Barcodes. INSECTS 2019; 10:E447. [PMID: 31842348 PMCID: PMC6956326 DOI: 10.3390/insects10120447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/06/2019] [Accepted: 12/09/2019] [Indexed: 12/17/2022]
Abstract
Tephritidae fruit flies (Diptera: Tephritidae) are regarded as important damage-causing species due to their ability to cause great economic losses in fruit and vegetable crops. Bactrocera minax and Bactrocera tsuneonis are two sibling species of the subgenus Tetradacus of Bactrocera that are distributed across a limited area of China, but have caused serious impacts. They share similar morphological characteristics. These characteristics can only be observed in the female adult individuals. The differences between them cannot be observed in preimaginal stages. Thus, it is difficult to distinguish them in preimaginal stages morphologically. In this study, we used molecular diagnostic methods based on cytochrome c oxidase subunit I and species-specific markers to identify these two species and improve upon the false-positive results of previous species-detection primers. DNA barcode sequences were obtained from 900 individuals of B. minax and 63 individuals of B. tsuneonis. Based on these 658 bp DNA barcode sequences of the cytochrome c oxidase subunit I gene, we successfully designed the species-specific primers for B. minax and B. tsuneonis. The size of the B. minax specific fragment was 422 bp and the size of the B. tsuneonis specific fragment was 456 bp. A series of PCR trials ensured the specificity of these two pairs of primers. Sensitivity assay results demonstrated that the detection limit for the DNA template concentration was 0.1~1 ng/μL for these two species. In this study, we established a more reliable, rapid, and low-cost molecular identification method for all life stages of B. minax and B. tsuneonis. Species-specific PCR can be applied in plant quarantine, monitoring and control of B. minax and B. tsuneonis.
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Affiliation(s)
- Linyu Zheng
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (L.Z.); (Y.Z.); (W.Y.); (Y.Z.); (Z.Z.); (L.L.)
| | - Yue Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (L.Z.); (Y.Z.); (W.Y.); (Y.Z.); (Z.Z.); (L.L.)
| | - Wenzhao Yang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (L.Z.); (Y.Z.); (W.Y.); (Y.Z.); (Z.Z.); (L.L.)
| | - Yiying Zeng
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (L.Z.); (Y.Z.); (W.Y.); (Y.Z.); (Z.Z.); (L.L.)
| | - Fan Jiang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China; (F.J.); (Y.Q.)
| | - Yujia Qin
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China; (F.J.); (Y.Q.)
| | - Jiafeng Zhang
- Hunan Plant Protection and Plant Quarantine Station, Changsha 410006, China;
| | - Zhaochun Jiang
- Guizhou Plant Protection and Plant Quarantine Station, Guiyang 550001, China;
| | - Wenzhao Hu
- Chongqing Plant Protection and Plant Quarantine Station, Yubei 401123, China;
| | - Dijin Guo
- Sichuan Plant Protection and Plant Quarantine Station, Chengdu 610041, China; (D.G.); (J.W.)
| | - Jia Wan
- Sichuan Plant Protection and Plant Quarantine Station, Chengdu 610041, China; (D.G.); (J.W.)
| | - Zihua Zhao
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (L.Z.); (Y.Z.); (W.Y.); (Y.Z.); (Z.Z.); (L.L.)
| | - Lijun Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (L.Z.); (Y.Z.); (W.Y.); (Y.Z.); (Z.Z.); (L.L.)
| | - Zhihong Li
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (L.Z.); (Y.Z.); (W.Y.); (Y.Z.); (Z.Z.); (L.L.)
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11
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Ruiz-Arce R, Islam MS, Aluja M, McPheron BA. Genetic Variation in Anastrepha obliqua (Diptera: Tephritidae) in a Highly Diverse Tropical Environment in the Mexican State of Veracruz. JOURNAL OF ECONOMIC ENTOMOLOGY 2019; 112:2952-2965. [PMID: 31504627 DOI: 10.1093/jee/toz223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Indexed: 06/10/2023]
Abstract
There has been considerable interest in understanding biological, ecological, historical, and evolutionary processes that contribute to the diversification of species and populations among tephritid fruit flies. Only a limited number of studies have examined the genetic diversity and population biology of species belonging to the genus Anastrepha considering fine-scale differentiations associated to locality as well as hosts over an entire fruiting season. To expand our understanding of population structure and genetic diversity in one of the critical Anastrepha fruit flies populations in a highly diverse tropical environment we analyzed Anastrepha obliqua (Macquart) (Diptera: Tephritidae) in the Mexican state of Veracruz from five host fruit species and 52 geographic collections using sequence data from mtDNA and microsatellite markers from nuclear DNA. Indeed, we examined the population structure of this pest in a micro-geographic region and report on relationships and historical processes for individuals collected within a small portion of the geographic range of its distribution. Analyses of 1055 bp mtDNA sequences from CO1and ND1genes across 400 individuals detected 34 haplotypes. Haplotype and nucleotide diversity was low, with 53% of the individuals exhibiting a single haplotype (OBV1). Host association and fine-scale differentiation at 17 microsatellite markers across 719 individuals from 32 of the 52 geographic collections reveal fragmented A. obliqua populations. These findings have important implications for the implementation of the Sterile Insect Technique (SIT) and other pest management programs used to control this pestiferous fruit fly.
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Affiliation(s)
- Raul Ruiz-Arce
- USDA-APHIS-PPQ-Science & Technology, Edinburg, TX
- Department of Entomology, The Pennsylvania State University, University Park, PA
| | - Md-Sajedul Islam
- Department of Entomology, The Pennsylvania State University, University Park, PA
- USDA-APHIS-PPQ-Science & Technology, Plant Epidemiology and Risk Laboratory, Raleigh, NC
| | - Martin Aluja
- Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología, A.C., Xalapa, Veracruz, México
| | - Bruce A McPheron
- Department of Entomology, The Pennsylvania State University, University Park, PA
- The Ohio State University, Columbus, OH
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12
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Velasco-Cuervo SM, Aguirre-Ramirez E, Gallo-Franco JJ, González Obando R, Carrejo N, Toro-Perea N. Saving DNA from museum specimens: The success of DNA mini-barcodes in haplotype reconstruction in the genus Anastrepha (Diptera: Tephritidae). J Adv Res 2019; 16:123-134. [PMID: 30899595 PMCID: PMC6412167 DOI: 10.1016/j.jare.2018.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/01/2018] [Accepted: 11/04/2018] [Indexed: 11/15/2022] Open
Abstract
The fragmentation of DNA in historical specimens is very common, so obtaining sequences that allow molecular identification and the study of diversity is quite challenging. In this study, we used preserved and fresh specimens of the fruit fly genus Anastrepha, a genus of economic impact of fruit crops of the Neotropic. From these specimens, we evaluated: (1) the success PCR amplification rates of mini-barcodes fragments of the cytochrome c oxidase subunit I (COI) gene, and (2) the usefulness of mini-barcodes in the reconstruction of haplotypes for the identification of species and the diversity analysis. We used 93 specimens from 12 species, which had been preserved in 70% ethanol for more than 20 years. Internal primers were designed in the COI region and primers available in the literature were also evaluated. We obtained amplifications for 62.36% of the samples processed, and reconstructed haplotypes between 171 bp and 632 bp. Variable amplification rates between combinations of primers and between species were obtained, and molecular identification of some museum specimens was achieved. It was also possible to compare the haplotypes obtained in four species from which both fresh and museum samples were available. Our results also show the importance of the adjustment of the primers for the amplification, allowing to amplify fragments of up to 400 bp. The use available resources in biological collections is key to increasing knowledge of species of interest, and by means of the amplification of mini-barcodes, short sequences can be obtained that allow the molecular identification of specimens and the reconstruction of haplotypes with multiple purposes.
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Affiliation(s)
- Sandra M. Velasco-Cuervo
- Departamento de Biología, Sección de Genética, Universidad del Valle, Calle 13 # 100-00, Cali, Colombia
| | - Elkin Aguirre-Ramirez
- Departamento de Biología, Sección de Genética, Universidad del Valle, Calle 13 # 100-00, Cali, Colombia
| | - Jenny Johana Gallo-Franco
- Departamento de Biología, Sección de Genética, Universidad del Valle, Calle 13 # 100-00, Cali, Colombia
| | - Ranulfo González Obando
- Departamento de Biología, Sección de Entomología, Universidad del Valle, Calle 13 # 100-00, Cali, Colombia
| | - Nancy Carrejo
- Departamento de Biología, Sección de Entomología, Universidad del Valle, Calle 13 # 100-00, Cali, Colombia
| | - Nelson Toro-Perea
- Departamento de Biología, Sección de Genética, Universidad del Valle, Calle 13 # 100-00, Cali, Colombia
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13
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Santos RP, Mariano CSF, Delabie JHC, Costa MA, Lima KM, Pompolo SG, Fernandes IO, Miranda EA, Carvalho AF, Silva JG. Genetic Characterization of Some Neoponera (Hymenoptera: Formicidae) Populations Within the foetida Species Complex. JOURNAL OF INSECT SCIENCE (ONLINE) 2018; 18:5077415. [PMID: 30137374 PMCID: PMC6105101 DOI: 10.1093/jisesa/iey079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/19/2018] [Indexed: 06/08/2023]
Abstract
The foetida species complex comprises 13 Neotropical species in the ant genus Neoponera. Neoponera villosa Fabricius (1804) , Neoponera inversa Smith (1858), Neoponera bactronica Fernandes, Oliveira & Delabie (2013), and Neoponera curvinodis (Forel, 1899) have had an ambiguous taxonomic status for more than two decades. In southern Bahia, Brazil, these four species are frequently found in sympatry. Here we used Bayesian Inference and maximum likelihood analyses of COI and 16S mtDNA sequence data and conventional cytogenetic data together with observations on morphology to characterize sympatric populations of N. villosa, N. inversa, N. bactronica, and N. curvinodis. Our results showed marked differences in the karyotype of these ants. Both N. curvinodis and N. inversa have chromosome number of 2n = 30. Their chromosome composition, however, is distinct, which indicates that N. curvinodis is more closely related to N. bactronica. These four species clustered into three distinct groups. The close relationship between N. bactronica and N. curvinodis deserves further investigation since it has not been fully resolved here. Our results confirm that N. inversa, N. villosa, N. bactronica + N. curvinodis indeed represent four distinct taxa within the foetida species complex.
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Affiliation(s)
- Rebeca P Santos
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, 45662-900 Ilhéus, Bahia, Brazil
| | - Cléa S F Mariano
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, 45662-900 Ilhéus, Bahia, Brazil
- Laboratório de Mirmecologia, Centro de Pesquisa do Cacau, Caixa Postal, Itabuna, Bahia, Brazil
| | - Jacques H C Delabie
- Laboratório de Mirmecologia, Centro de Pesquisa do Cacau, Caixa Postal, Itabuna, Bahia, Brazil
- Departamento de Ciências Agrárias e Ambientais, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, Ilhéus, Bahia, Brazil
| | - Marco A Costa
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, 45662-900 Ilhéus, Bahia, Brazil
| | - Kátia M Lima
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, 45662-900 Ilhéus, Bahia, Brazil
| | - Silvia G Pompolo
- Laboratório de Citogenética de Insetos, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Itanna O Fernandes
- Instituto Nacional de Pesquisas da Amazônia, Av. André Araujo, Petrópolis, Cx. Postal, Manaus, Amazonas, Brazil
| | - Elder A Miranda
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, 45662-900 Ilhéus, Bahia, Brazil
| | - Antonio F Carvalho
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, 45662-900 Ilhéus, Bahia, Brazil
| | - Janisete G Silva
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, 45662-900 Ilhéus, Bahia, Brazil
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