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Ghosh A, Tyagi K, Dubey AK, Sweet AD, Singha D, Goswami P, Kumar V. Purifying selection drove the adaptation of mitochondrial genes along with correlation of gene rearrangements and evolutionary rates in two subfamilies of Whitefly (Insecta: Hemiptera). Funct Integr Genomics 2024; 24:121. [PMID: 38976062 DOI: 10.1007/s10142-024-01400-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 05/06/2024] [Accepted: 06/27/2024] [Indexed: 07/09/2024]
Abstract
Insect mitochondrial genomes (mitogenomes) are usually represented by a conserved gene order. Whiteflies exhibit gene rearrangement in their mitogenomes; however, understanding how nucleotide substitution rates shape gene rearrangement in whiteflies is unclear due to the limited number of mitogenomes. Additionally, the mechanisms by which selection pressure drives adaptations in mitochondrial genes in the two subfamilies of whiteflies are not yet known. Here, we analyzed 18 whitefly mitogenomes, including one newly generated mitogenome, to compare nucleotide substitution rates, selection pressure, and gene arrangements. The newly generated mitogenome is reported along with reannotation of Pealius mori and comparisons to other whitefly mitogenomes. Comparative studies on nucleotide composition of 18 whiteflies revealed the positive GC skewness, confirming the reversal of strand asymmetry. We found 11 rearranged gene orders within two subfamilies of whiteflies with 8-18 breakpoints of gene rearrangements. Members of the subfamily Aleyrodinae exhibit more complex pathways in the evolution of gene order as compared to the subfamily Aleurodicinae. Our findings also revealed that the increase or reduction of nucleotide substitution rates does not have an impact on any of the gene rearrangement scenarios depicting neutral correlation. Selection pressure analysis revealed that the mitogenomes from members of both the subfamilies Aleurodicinae and Aleyrodinae are characterized by intense purifying selection pressure.
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Affiliation(s)
- Abhishek Ghosh
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
| | - Anil Kumar Dubey
- Hemiptera Section, Zoological Survey of India, West Bengal, Kolkata, India
| | | | - Devkant Singha
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
| | - Prathana Goswami
- Lepidoptera Section, Zoological Survey of India, Kolkata, West Bengal, India
- Department of Zoology, Gauhati University, Guwahati, Assam, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
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El Hamss H, Maruthi MN, Omongo CA, Wang HL, van Brunschot S, Colvin J, Delatte H. Microbiome diversity and composition in Bemisia tabaci SSA1-SG1 whitefly are influenced by their host's life stage. Microbiol Res 2024; 278:127538. [PMID: 37952351 DOI: 10.1016/j.micres.2023.127538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/19/2023] [Accepted: 10/29/2023] [Indexed: 11/14/2023]
Abstract
Within the Bemisia tabaci group of cryptic whitefly species, many are damaging agricultural pests and plant-virus vectors, conferring upon this group the status of one of the world's top 100 most invasive and destructive species, affecting farmers' income and threatening their livelihoods. Studies on the microbiome of whitefly life stages are scarce, although their composition and diversity greatly influence whitefly fitness and development. We used high-throughput sequencing to understand microbiome diversity in different developmental stages of the B. tabaci sub-Saharan Africa 1 (SSA1-SG1) species of the whitefly from Uganda. Endosymbionts (Portiera, Arsenophonus, Wolbachia, and Hemipteriphilus were detected but excluded from further statistical analysis as they were not influenced by life stage using Permutational Multivariate Analysis of Variance Using Distance Matrices (ADONIS, p = 0.925 and Bray, p = 0.903). Our results showed significant differences in the meta microbiome composition in different life stages of SSA1-SG1. The diversity was significantly higher in eggs (Shannon, p = 0.024; Simpson, p = 0.047) than that in nymphs and pupae, while the number of microbial species observed by the amplicon sequence variant (ASV) was not significant (n(ASV), p = 0.094). At the phylum and genus levels, the dominant constituents in the microbiome changed significantly during various developmental stages, with Halomonas being present in eggs, whereas Bacillus and Caldalkalibacillus were consistently found across all life stages. These findings provide the first description of differing meta microbiome diversity in the life stage of whiteflies, suggesting their putative role in whitefly development.
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Affiliation(s)
- Hajar El Hamss
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, United Kingdom.
| | - M N Maruthi
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, United Kingdom.
| | - Christopher A Omongo
- Root Crops Programme, National Crops Resource Research Institute (RCP-NaCRRI), Kampala, Uganda
| | - Hua-Ling Wang
- College of Forestry, Hebei Agricultural University, Hebei, China
| | - Sharon van Brunschot
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, United Kingdom; School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - John Colvin
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, United Kingdom
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Li H, Jiang Z, Zhou J, Liu X, Zhang Y, Chu D. Ecological Factors Associated with the Distribution of Bemisia tabaci Cryptic Species and Their Facultative Endosymbionts. INSECTS 2023; 14:252. [PMID: 36975937 PMCID: PMC10053707 DOI: 10.3390/insects14030252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/22/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
The sweetpotato whitefly, Bemisia tabaci species complex, comprises at least 44 morphologically indistinguishable cryptic species, whose endosymbiont infection patterns often varied at the spatial and temporal dimension. However, the effects of ecological factors (e.g., climatic or geographical factors) on the distribution of whitefly and the infection frequencies of their endosymbionts have not been fully elucidated. We, here, analyzed the associations between ecological factors and the distribution of whitefly and their three facultative endosymbionts (Candidatus Cardinium hertigii, Candidatus Hamiltonella defensa, and Rickettsia sp.) by screening 665 individuals collected from 29 geographical localities across China. The study identified eight B. tabaci species via mitochondrial cytochrome oxidase I (mtCOI) gene sequence alignment: two invasive species, MED (66.9%) and MEAM1 (12.2%), and six native cryptic species (20.9%), which differed in distribution patterns, ecological niches, and high suitability areas. The infection frequencies of the three endosymbionts in different cryptic species were distinct and multiple infections were relatively common in B. tabaci MED populations. Furthermore, the annual mean temperature positively affected Cardinium sp. and Rickettsia sp. infection frequencies in B. tabaci MED but negatively affected the quantitative distribution of B. tabaci MED, which indicates that Cardinium sp. and Rickettsia sp. maybe play a crucial role in the thermotolerance of B. tabaci MED, although the host whitefly per se exhibits no resistance to high temperature. Our findings revealed the complex effects of ecological factors on the expansion of the invasive whitefly.
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Affiliation(s)
- Hongran Li
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 515100, China
| | - Zhihui Jiang
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Jincheng Zhou
- Department of Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Xin Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, College of Agriculture, Henan University, Kaifeng 475004, China
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dong Chu
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
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El Hamss H, Maruthi MN, Ally HM, Omongo CA, Wang HL, van Brunschot S, Colvin J, Delatte H. Spatio-temporal changes in endosymbiont diversity and composition in the African cassava whitefly, Bemisia tabaci SSA1. Front Microbiol 2022; 13:986226. [DOI: 10.3389/fmicb.2022.986226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/29/2022] [Indexed: 11/20/2022] Open
Abstract
Sap-sucking insects, including whiteflies, are amongst the most devastating and widely distributed organisms on the planet. They are often highly invasive and endosymbiont communities within these insects help them adapt to new or changing environments. Bemisia tabaci (Gennadius; Hemiptera: Aleyrodidae) whitefly species are vectors of more than 500 known plant-viruses and harbour highly diverse endosymbionts communities. To date, however, whitefly–endosymbiont interactions, community structure and their spatio-temporal changes are still poorly understood. In this study, we investigated the spatio-temporal changes in the composition and diversity of bacterial endosymbionts in the agricultural crop pest whitefly species, Bemisia tabaci sub-Saharan Africa 1-subgroup 1 and 2 (SSA1-SG1 and SSA1-SG2). 16S rRNA amplicon sequencing analysis was carried out to characterise endosymbiont compositionsin field-collected SSA1 (SSA1-SG1 and SSA1-SG2) populations infesting cassava in Uganda in 1997 and 2017. We detected Portiera, Arsenophonus, Wolbachia, Hamiltonella and Hemipteriphilus, with Arsenophonus and Wolbachia infections being predominant. Hemipteriphilus and Hamiltonella frequencies were very low and were detected in seven and two samples, respectively. Bacterial diversity based on three independent parameters including Simpson index, number of haplotypes and Bray–Curtis dissimilarity matrix was significantly higher in 1997 than in 2017. This period also coincided with the advent of super-abundant cassava-whitefly populations on cassava crops in Uganda. We discuss how endosymbionts may influence the biology and behaviour of whiteflies leading to population explosions.
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Tay WT, Court LN, Hoffmann BD, Polaszek A. Draft mitogenomes of the invasive ant Lepisiota frauenfeldi (Mayr 1855) (Hymenoptera: Formicidae). Mitochondrial DNA B Resour 2022; 7:1183-1185. [PMID: 35783040 PMCID: PMC9245994 DOI: 10.1080/23802359.2022.2089602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We present the draft mitochondrial genomes (mitogenomes) of two Lepisiota frauenfeldi (Mayr 1855) workers from two separate invasive populations detected in Western Australia (Perth OK569858) and Queensland (Brisbane OK5569859), Australia. The draft mitogenomes ranged between 16,657 and 17,090 bp and contained 37 genes (13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and two ribosomal RNA (rRNA) genes). As with other arthropod mitogenomes, we observed high A + T content (A: 39.4–39.8%, T: 40.55–41.5%). We confirmed the species identity by molecular diagnostics based on the partial mtCOI gene that showed >99% similarity between the Australian populations and other L. frauenfeldi sequences reported to date, and in the process identified putative origins of the invasive populations as Pakistan and India for the WA and Qld incursions respectively that suggested separate introductions.
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Affiliation(s)
- W. T. Tay
- CSIRO Black Mountain Laboratories, Canberra, Australia
| | - L. N. Court
- CSIRO Black Mountain Laboratories, Canberra, Australia
| | - B. D. Hoffmann
- CSIRO Tropical Ecosystems Research Centre, Canberra, Australia
| | - A. Polaszek
- Department of Life Sciences, Natural History Museum, London, UK
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Global population genomic signature of Spodoptera frugiperda (fall armyworm) supports complex introduction events across the Old World. Commun Biol 2022; 5:297. [PMID: 35393491 PMCID: PMC8989990 DOI: 10.1038/s42003-022-03230-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/02/2022] [Indexed: 11/23/2022] Open
Abstract
Native to the Americas, the invasive Spodoptera frugiperda (fall armyworm; FAW) was reported in West Africa in 2016, followed by its chronological detection across the Old World and the hypothesis of an eastward Asia expansion. We explored population genomic signatures of American and Old World FAW and identified 12 maternal mitochondrial DNA genome lineages across the invasive range. 870 high-quality nuclear single nucleotide polymorphic DNA markers identified five distinct New World population clusters, broadly reflecting FAW native geographical ranges and the absence of host-plant preferences. We identified unique admixed Old World populations, and admixed and non-admixed Asian FAW individuals, all of which suggested multiple introductions underpinning the pest’s global spread. Directional gene flow from the East into eastern Africa was also detected, in contrast to the west-to-east spread hypothesis. Our study demonstrated the potential of population genomic approaches via international partnership to address global emerging pest threats and biosecurity challenges. This population genomics study identifies the complex multiple introduction history of Spodoptera frugiperda (fall armyworm) from the Americas, into Africa and Asia. This provides new insight into the ‘east-to-west’ directionality of gene flow, and suggests ample genomic exchange at the nuclear level.
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Petrone JR, Muñoz-Beristain A, Glusberger PR, Russell JT, Triplett EW. Unamplified, Long-Read Metagenomic Sequencing Approach to Close Endosymbiont Genomes of Low-Biomass Insect Populations. Microorganisms 2022; 10:microorganisms10030513. [PMID: 35336091 PMCID: PMC8948638 DOI: 10.3390/microorganisms10030513] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/23/2022] [Accepted: 02/23/2022] [Indexed: 02/04/2023] Open
Abstract
With the current advancements in DNA sequencing technology, the limiting factor in long-read metagenomic assemblies is now the quantity and quality of input DNA. Although these requirements can be met through the use of axenic bacterial cultures or large amounts of biological material, insect systems that contain unculturable bacteria or that contain a low amount of available DNA cannot fully utilize the benefits of third-generation sequencing. The citrus greening disease insect vector Diaphorina citri is an example that exhibits both of these limitations. Although endosymbiont genomes have mostly been closed after the short-read sequencing of amplified template DNA, creating de novo long-read genomes from the unamplified DNA of an insect population may benefit communities using bioinformatics to study insect pathosystems. Here all four genomes of the infected D. citri microbiome were sequenced to closure using unamplified template DNA and two long-read sequencing technologies. Avoiding amplification bias and using long reads to assemble the bacterial genomes allowed for the circularization of the Wolbachia endosymbiont of Diaphorina citri for the first time and paralleled the annotation context of all four reference genomes without utilizing a traditional hybrid assembly. The strategies detailed here are suitable for the sequencing of other insect systems for which the input DNA, time, and cost are an issue.
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Elfekih S, Tay WT, Polaszek A, Gordon KHJ, Kunz D, Macfadyen S, Walsh TK, Vyskočilová S, Colvin J, De Barro PJ. On species delimitation, hybridization and population structure of cassava whitefly in Africa. Sci Rep 2021; 11:7923. [PMID: 33846476 PMCID: PMC8041820 DOI: 10.1038/s41598-021-87107-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 03/17/2021] [Indexed: 01/03/2023] Open
Abstract
The Bemisia cassava whitefly complex includes species that cause severe crop damage through vectoring cassava viruses in eastern Africa. Currently, this whitefly complex is divided into species and subgroups (SG) based on very limited molecular markers that do not allow clear definition of species and population structure. Based on 14,358 genome-wide SNPs from 62 Bemisia cassava whitefly individuals belonging to sub-Saharan African species (SSA1, SSA2 and SSA4), and using a well-curated mtCOI gene database, we show clear incongruities in previous taxonomic approaches underpinned by effects from pseudogenes. We show that the SSA4 species is nested within SSA2, and that populations of the SSA1 species comprise well-defined south-eastern (Madagascar, Tanzania) and north-western (Nigeria, Democratic Republic of Congo, Burundi) putative sub-species. Signatures of allopatric incipient speciation, and the presence of a 'hybrid zone' separating the two putative sub-species were also detected. These findings provide insights into the evolution and molecular ecology of a highly cryptic hemipteran insect complex in African, and allow the systematic use of genomic data to be incorporated in the development of management strategies for this cassava pest.
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Affiliation(s)
- S Elfekih
- Australian Centre for Disease Preparedness, CSIRO, Geelong, VIC, Australia
| | - W T Tay
- Black Mountain Laboratories, CSIRO, Canberra, ACT, Australia.
| | - A Polaszek
- Department of Life Sciences, Natural History Museum, London, UK
| | - K H J Gordon
- Black Mountain Laboratories, CSIRO, Canberra, ACT, Australia
| | - D Kunz
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - S Macfadyen
- Black Mountain Laboratories, CSIRO, Canberra, ACT, Australia
| | - T K Walsh
- Black Mountain Laboratories, CSIRO, Canberra, ACT, Australia
| | - S Vyskočilová
- Natural Resources Institute, University of Greenwich, Kent, UK
| | - J Colvin
- Natural Resources Institute, University of Greenwich, Kent, UK
| | - P J De Barro
- CSIRO, Ecosciences Precinct, Brisbane, Australia
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Popa-Báez ÁD, Lee SF, Yeap HL, Westmore G, Crisp P, Li D, Catullo R, Cameron EC, Edwards OR, Taylor PW, Oakeshott JG. Tracing the origins of recent Queensland fruit fly incursions into South Australia, Tasmania and New Zealand. Biol Invasions 2021. [DOI: 10.1007/s10530-020-02422-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Krause-Sakate R, Watanabe LFM, Gorayeb ES, da Silva FB, Alvarez DDL, Bello VH, Nogueira AM, de Marchi BR, Vicentin E, Ribeiro-Junior MR, Marubayashi JM, Rojas-Bertini CA, Muller C, Bueno RCODF, Rosales M, Ghanim M, Pavan MA. Population Dynamics of Whiteflies and Associated Viruses in South America: Research Progress and Perspectives. INSECTS 2020; 11:insects11120847. [PMID: 33260578 PMCID: PMC7760982 DOI: 10.3390/insects11120847] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/30/2020] [Accepted: 11/26/2020] [Indexed: 11/16/2022]
Abstract
Simple Summary Whiteflies are one of the most important and widespread pests in the world. In South America, the currently most important species occurring are Bemisia afer,Trialeurodes vaporariorum, and the cryptic species Middle East-Asia Minor 1, Mediterranean, and New World, from Bemisia tabaci complex. The present review compiles information from several studies conducted in South America regarding these insects, providing data related to the dynamics and distribution of whiteflies, the associated viruses, and the management strategies to keep whiteflies under the economic damage threshold. Abstract By having an extensive territory and suitable climate conditions, South America is one of the most important agricultural regions in the world, providing different kinds of vegetable products to different regions of the world. However, such favorable conditions for plant production also allow the development of several pests, increasing production costs. Among them, whiteflies (Hemiptera: Aleyrodidae) stand out for their potential for infesting several crops and for being resistant to insecticides, having high rates of reproduction and dispersal, besides their efficient activity as virus vectors. Currently, the most important species occurring in South America are Bemisia afer, Trialeurodes vaporariorum, and the cryptic species Middle East-Asia Minor 1, Mediterranean, and New World, from Bemisia tabaci complex. In this review, a series of studies performed in South America were compiled in an attempt to unify the advances that have been developed in whitefly management in this continent. At first, a background of the current whitefly distribution in South American countries as well as factors affecting them are shown, followed by a background of the whitefly transmitted viruses in South America, addressing their location and association with whiteflies in each country. Afterwards, a series of management strategies are proposed to be implemented in South American fields, including cultural practices and biological and chemical control, finalizing with a section containing future perspectives and directions for further research.
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Affiliation(s)
- Renate Krause-Sakate
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
- Correspondence: ; Tel.: +55-14-3880-7487
| | - Luís Fernando Maranho Watanabe
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Eduardo Silva Gorayeb
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
- Facultad de Agronomía e Ingeniería, Pontificia Universidad Católica de Chile, Forestal, Vicuña Mackena, 4860, Macul, Santiago 7820436, Chile; (C.A.R.-B.); (M.R.)
| | - Felipe Barreto da Silva
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Daniel de Lima Alvarez
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Vinicius Henrique Bello
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Angélica Maria Nogueira
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | | | - Eduardo Vicentin
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Marcos Roberto Ribeiro-Junior
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Julio Massaharu Marubayashi
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Claudia Andrea Rojas-Bertini
- Facultad de Agronomía e Ingeniería, Pontificia Universidad Católica de Chile, Forestal, Vicuña Mackena, 4860, Macul, Santiago 7820436, Chile; (C.A.R.-B.); (M.R.)
| | | | - Regiane Cristina Oliveira de Freitas Bueno
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Marlene Rosales
- Facultad de Agronomía e Ingeniería, Pontificia Universidad Católica de Chile, Forestal, Vicuña Mackena, 4860, Macul, Santiago 7820436, Chile; (C.A.R.-B.); (M.R.)
| | - Murad Ghanim
- Department of Entomology, Institute of Plant Protection, The Volcani Center, Rishon LeZion 7505101, Israel;
| | - Marcelo Agenor Pavan
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
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Walsh TK, Perera O, Anderson C, Gordon K, Czepak C, McGaughran A, Zwick A, Hackett D, Tay WT. Mitochondrial DNA genomes of five major Helicoverpa pest species from the Old and New Worlds (Lepidoptera: Noctuidae). Ecol Evol 2019; 9:2933-2944. [PMID: 30891227 PMCID: PMC6405535 DOI: 10.1002/ece3.4971] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/18/2018] [Accepted: 10/29/2018] [Indexed: 12/16/2022] Open
Abstract
Five species of noctuid moths, Helicoverpa armigera, H. punctigera, H. assulta, H. zea, and H. gelotopoeon, are major agricultural pests inhabiting various and often overlapping global distributions. Visual identification of these species requires a great deal of expertise and misidentification can have repercussions for pest management and agricultural biosecurity. Here, we report on the complete mitochondrial genomes of H. assulta assulta and H. assulta afra, H. gelotopoeon, H. punctigera, H. zea, and H. armigera armigera and H. armigera conferta' assembled from high-throughput sequencing data. This study significantly increases the mitogenome resources for these five agricultural pests with sequences assembled from across different continents, including an H. armigera individual collected from an invasive population in Brazil. We infer the phylogenetic relationships of these five Helicoverpa species based on the 13 mitochondrial DNA protein-coding genes (PCG's) and show that two publicly available mitogenomes of H. assulta (KP015198 and KR149448) have been misidentified or incorrectly assembled. We further consolidate existing PCR-RFLP methods to cover all five Helicoverpa pest species, providing an updated method that will contribute to species differentiation and to future monitoring efforts of Helicoverpa pest species across different continents. We discuss the value of Helicoverpa mitogenomes to assist with species identification in view of the context of the rapid spread of H. armigera in the New World. With this work, we provide the molecular resources necessary for future studies of the evolutionary history and ecology of these species.
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Affiliation(s)
- Tom K. Walsh
- CSIROBlack Mountain LaboratoriesCanberraACTAustralia
| | - Omaththage Perera
- USDA‐ARS Southern Insect Management Research UnitStonevilleMississippi
| | - Craig Anderson
- CSIROBlack Mountain LaboratoriesCanberraACTAustralia
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, Western General HospitalUniversity of EdinburghEdinburghUK
| | - Karl Gordon
- CSIROBlack Mountain LaboratoriesCanberraACTAustralia
| | - Cecilia Czepak
- Escola de AgronomiaUniversidade Federal de GoiásGoiâniaBrazil
| | - Angela McGaughran
- CSIROBlack Mountain LaboratoriesCanberraACTAustralia
- Division of Ecology and Evolution, Research School of BiologyAustralian National UniversityCanberraACTAustralia
| | - Andreas Zwick
- CSIROBlack Mountain LaboratoriesCanberraACTAustralia
| | | | - Wee Tek Tay
- CSIROBlack Mountain LaboratoriesCanberraACTAustralia
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12
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Tay WT, Gordon KHJ. Going global - genomic insights into insect invasions. CURRENT OPINION IN INSECT SCIENCE 2019; 31:123-130. [PMID: 31109665 DOI: 10.1016/j.cois.2018.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/03/2018] [Accepted: 12/05/2018] [Indexed: 06/09/2023]
Abstract
The spread of invasive insect pests is becoming an increasing problem for agriculture globally. We discuss a number of invasive insects, already of major economic significance that have recently expanded their range to become truly global threats. These include the noctuid moths Helicoverpa and Spodoptera, whose caterpillars have long been among the worst pests in their native Old and New World habitats, respectively, and the whitefly Bemisia, a major vector of plant virus diseases. Importantly, genomic resources for these species have recently become available, allowing research to move beyond the restrictions imposed by earlier approaches limited to a single or few mitochondrial and nuclear markers, to employ genome-wide genotyping and resequencing protocols. These studies have shown hybridisation within the various species complexes, identified regions under selection in agricultural environments, and enable monitoring of genes important as biosecurity risks through introgression into established populations free of the genes. In all cases studied, global trade has emerged as the probable cause of insect spread, making it ever more important that biosecurity protocols and agencies work with researchers to make the most effective use of emerging genomic resources and tools.
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Affiliation(s)
- Wee Tek Tay
- CSIRO Black Mountain Laboratories, Clunies Ross Street, ACT 2601, Australia
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13
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Kunz D, Tay WT, Court LN, Elfekih S, Gordon KHJ, Evans GA, De Barro PJ. Draft mitochondrial DNA genome of a 1920 Barbados cryptic Bemisia tabaci ‘New World’ species (Hemiptera: Aleyrodidae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1591197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- D. Kunz
- CSIRO Black Mountain Laboratories, ACT, Australia
| | - W. T. Tay
- CSIRO Black Mountain Laboratories, ACT, Australia
| | - L. N. Court
- CSIRO Black Mountain Laboratories, ACT, Australia
| | - S. Elfekih
- CSIRO Black Mountain Laboratories, ACT, Australia
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14
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Rossitto De Marchi B, Kinene T, Mbora Wainaina J, Krause-Sakate R, Boykin L. Comparative transcriptome analysis reveals genetic diversity in the endosymbiont Hamiltonella between native and exotic populations of Bemisia tabaci from Brazil. PLoS One 2018; 13:e0201411. [PMID: 30052670 PMCID: PMC6063447 DOI: 10.1371/journal.pone.0201411] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/14/2018] [Indexed: 12/22/2022] Open
Abstract
The whitefly, Bemisia tabaci, is a species complex of more than 40 cryptic species and a major agricultural pest. It causes extensive damage to plants mainly by transmitting plant viruses. There is still a lack of genomic data available for the different whitefly species found in Brazil and their bacterial endosymbionts. Understanding the genetic and transcriptomic composition of these insect pests, the viruses they transmit and the microbiota is crucial to sustainable solutions for farmers to control whiteflies. Illumina RNA-Seq was used to obtain the transcriptome of individual whiteflies from 10 different populations from Brazil including Middle East-Asia Minor 1 (MEAM1), Mediterranean (MED) and New World 2 (NW2). Raw reads were assembled using CLC Genomics Workbench and subsequently mapped to reference genomes. We obtained whitefly complete mitochondrial genomes and draft genomes from the facultative bacterial endosymbiont Hamiltonella for further phylogenetic analyses. In addition, nucleotide sequences of the GroEL chaperonin gene from Hamiltonella from different populations were obtained and analysed. There was concordance in the species clustering using the whitefly complete mitogenome and the mtCOI gene tree. On the other hand, the phylogenetic analysis using the 12 ORF's of Hamiltonella clustered the native species NW2 apart from the exotics MEAM1 and MED. In addition, the amino acid analysis of GroEL chaperonin revealed a deletion only in Hamiltonella infecting NW2 among whiteflies populations analysed which was further confirmed by PCR and Sanger sequencing. The genomic data obtained in this study will aid understanding the functions that Hamiltonella may have in whitefly biology and serve as a reference for further studies regarding whiteflies in Brazil.
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Affiliation(s)
| | - Tonny Kinene
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA, Australia
| | - James Mbora Wainaina
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA, Australia
| | - Renate Krause-Sakate
- UNESP–Universidade Estadual Paulista, Faculdade de Ciências Agronomicas, Botucatu-SP, Brazil
| | - Laura Boykin
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA, Australia
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15
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Vyskočilová S, Tay WT, van Brunschot S, Seal S, Colvin J. An integrative approach to discovering cryptic species within the Bemisia tabaci whitefly species complex. Sci Rep 2018; 8:10886. [PMID: 30022040 PMCID: PMC6052153 DOI: 10.1038/s41598-018-29305-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/05/2018] [Indexed: 11/26/2022] Open
Abstract
Bemisia tabaci is a cryptic whitefly-species complex that includes some of the most damaging pests and plant-virus vectors of a diverse range of food and fibre crops worldwide. We combine experimental evidence of: (i) differences in reproductive compatibility, (ii) hybrid verification using a specific nuclear DNA marker and hybrid fertility confirmation and (iii) high-throughput sequencing-derived mitogenomes, to show that the "Mediterranean" (MED) B. tabaci comprises at least two distinct biological species; the globally invasive MED from the Mediterranean Basin and the "African silver-leafing" (ASL) from sub-Saharan Africa, which has no associated invasion records. We demonstrate that, contrary to its common name, the "ASL" does not induce squash silver-leafing symptoms and show that species delimitation based on the widely applied 3.5% partial mtCOI gene sequence divergence threshold produces discordant results, depending on the mtCOI region selected. Of the 292 published mtCOI sequences from MED/ASL groups, 158 (54%) are low quality and/or potential pseudogenes. We demonstrate fundamental deficiencies in delimiting cryptic B. tabaci species, based solely on partial sequences of a mitochondrial barcoding gene. We advocate an integrative approach to reveal the true species richness within cryptic species complexes, which is integral to the deployment of effective pest and disease management strategies.
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Affiliation(s)
- Soňa Vyskočilová
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, ME4 4TB, United Kingdom.
| | - Wee Tek Tay
- CSIRO Black Mountain Laboratories, Clunies Ross Street, ACT 2601, Canberra, Australia
| | - Sharon van Brunschot
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, ME4 4TB, United Kingdom
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Susan Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, ME4 4TB, United Kingdom
| | - John Colvin
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, ME4 4TB, United Kingdom
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Tay WT, Elfekih S, Court LN, Gordon KHJ, Delatte H, De Barro PJ. The Trouble with MEAM2: Implications of Pseudogenes on Species Delimitation in the Globally Invasive Bemisia tabaci (Hemiptera: Aleyrodidae) Cryptic Species Complex. Genome Biol Evol 2018; 9:2732-2738. [PMID: 28985301 PMCID: PMC5647793 DOI: 10.1093/gbe/evx173] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2017] [Indexed: 11/23/2022] Open
Abstract
Molecular species identification using suboptimal PCR primers can over-estimate species diversity due to coamplification of nuclear mitochondrial (NUMT) DNA/pseudogenes. For the agriculturally important whitefly Bemisia tabaci cryptic pest species complex, species identification depends primarily on characterization of the mitochondrial DNA cytochrome oxidase I (mtDNA COI) gene. The lack of robust PCR primers for the mtDNA COI gene can undermine correct species identification which in turn compromises management strategies. This problem is identified in the B. tabaci Africa/Middle East/Asia Minor clade which comprises the globally invasive Mediterranean (MED) and Middle East Asia Minor I (MEAM1) species, Middle East Asia Minor 2 (MEAM2), and the Indian Ocean (IO) species. Initially identified from the Indian Ocean island of Réunion, MEAM2 has since been reported from Japan, Peru, Turkey and Iraq. We identified MEAM2 individuals from a Peruvian population via Sanger sequencing of the mtDNA COI gene. In attempting to characterize the MEAM2 mitogenome, we instead characterized mitogenomes of MEAM1. We also report on the mitogenomes of MED, AUS, and IO thereby increasing genomic resources for members of this complex. Gene synteny (i.e., same gene composition and orientation) was observed with published B. tabaci cryptic species mitogenomes. Pseudogene fragments matching MEAM2 partial mtDNA COI gene exhibited low frequency single nucleotide polymorphisms that matched low copy number DNA fragments (<3%) of MEAM1 genomes, whereas presence of internal stop codons, loss of expected stop codons and poor primer annealing sites, all suggested MEAM2 as a pseudogene artifact and so not a real species.
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Affiliation(s)
- Wee Tek Tay
- CSIRO, Black Mountain Science and Innovation Park, Acton, Australia
| | - Samia Elfekih
- CSIRO, Black Mountain Science and Innovation Park, Acton, Australia
| | - Leon N Court
- CSIRO, Black Mountain Science and Innovation Park, Acton, Australia
| | - Karl H J Gordon
- CSIRO, Black Mountain Science and Innovation Park, Acton, Australia
| | | | - Paul J De Barro
- CSIRO, Ecosciences Precinct, Brisbane, Queensland, Australia
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17
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Elfekih S, Etter P, Tay WT, Fumagalli M, Gordon K, Johnson E, De Barro P. Genome-wide analyses of the Bemisia tabaci species complex reveal contrasting patterns of admixture and complex demographic histories. PLoS One 2018; 13:e0190555. [PMID: 29364919 PMCID: PMC5783331 DOI: 10.1371/journal.pone.0190555] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 12/16/2017] [Indexed: 12/21/2022] Open
Abstract
Once considered a single species, the whitefly, Bemisia tabaci, is a complex of numerous morphologically indistinguishable species. Within the last three decades, two of its members (MED and MEAM1) have become some of the world's most damaging agricultural pests invading countries across Europe, Africa, Asia and the Americas and affecting a vast range of agriculturally important food and fiber crops through both feeding-related damage and the transmission of numerous plant viruses. For some time now, researchers have relied on a single mitochondrial gene and/or a handful of nuclear markers to study this species complex. Here, we move beyond this by using 38,041 genome-wide Single Nucleotide Polymorphisms, and show that the two invasive members of the complex are closely related species with signatures of introgression with a third species (IO). Gene flow patterns were traced between contemporary invasive populations within MED and MEAM1 species and these were best explained by recent international trade. These findings have profound implications for delineating the B. tabaci species status and will impact quarantine measures and future management strategies of this global pest.
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Affiliation(s)
- S. Elfekih
- CSIRO, Black Mountain Laboratories, ACT, Australia
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - P. Etter
- Institute of Molecular Biology, University of Oregon, Eugene, OR, United States of America
| | - W. T. Tay
- CSIRO, Black Mountain Laboratories, ACT, Australia
| | - M. Fumagalli
- Department of Life Sciences, Silwood Park campus, Imperial College London, Ascot, United Kingdom
| | - K. Gordon
- CSIRO, Black Mountain Laboratories, ACT, Australia
| | - E. Johnson
- Institute of Molecular Biology, University of Oregon, Eugene, OR, United States of America
| | - P. De Barro
- CSIRO Ecosciences Precinct, Brisbane, QLD, Australia
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18
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Elfekih S, Tay WT, Gordon K, Court LN, De Barro PJ. Standardized molecular diagnostic tool for the identification of cryptic species within the Bemisia tabaci complex. PEST MANAGEMENT SCIENCE 2018; 74:170-173. [PMID: 28736873 DOI: 10.1002/ps.4676] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 07/18/2017] [Accepted: 07/18/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The whitefly Bemisia tabaci complex harbours over 40 cryptic species that have been placed in 11 phylogenetically distinct clades based on the molecular characterization of partial mitochondrial DNA COI (mtCOI) gene region. Four cryptic species are currently within the invasive clade, i.e. MED, MEAM1, MEAM2 and IO. Correct identification of these species is a critical step towards implementing reliable measures for plant biosecurity and border protection; however, no standardized B. tabaci-specific primers are currently available which has caused inconsistencies in the species identification processes. RESULTS We report three sets of polymerase chain reaction (PCR) primers developed to amplify the mtCOI region which can be used for genotyping MED, MEAM1 and IO species, and tested these primers on 91 MED, 35 MEAM1 and five IO individuals. PCR and sequencing of amplicons identified a total of 21, six and one haplotypes in MED, MEAM1 and IO respectively, of which six haplotypes were new to the B. tabaci database. CONCLUSION These primer pairs enabled standardization and robust molecular species identification via mtCOI screening of the targeted invasive cryptic species and will improve quarantine decisions. Use of this diagnostic tool could be extended to other species within the complex. © 2017 Society of Chemical Industry.
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Affiliation(s)
| | - Wee Tek Tay
- CSIRO, Black Mountain Laboratories, ACT, Australia
| | - Karl Gordon
- CSIRO, Black Mountain Laboratories, ACT, Australia
| | - Leon N Court
- CSIRO, Black Mountain Laboratories, ACT, Australia
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