1
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Alotaibi NJ, Alsufyani T, M’sakni NH, Almalki MA, Alghamdi EM, Spiteller D. Rapid Identification of Aphid Species by Headspace GC-MS and Discriminant Analysis. INSECTS 2023; 14:589. [PMID: 37504595 PMCID: PMC10380428 DOI: 10.3390/insects14070589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023]
Abstract
Aphids are a ubiquitous group of pests in agriculture that cause serious losses. For sustainable aphid identification, it is necessary to develop a precise and fast aphid identification tool. A new simple chemotaxonomy approach to rapidly identify aphids was implemented. The method was calibrated in comparison to the established phylogenetic analysis. For chemotaxonomic analysis, aphids were crushed, their headspace compounds were collected through closed-loop stripping (CLS) and analysed using gas chromatography-mass spectrometry (GC-MS). GC-MS data were then subjected to a discriminant analysis using CAP12.exe software, which identified key biomarkers that distinguish aphid species. A dichotomous key taking into account the presence and absence of a set of species-specific biomarkers was derived from the discriminant analysis which enabled rapid and reliable identification of aphid species. As the method overcomes the limits of morphological identification, it works with aphids at all life stages and in both genders. Thus, our method enables entomologists to assign aphids to growth stages and identify the life history of the investigated aphids, i.e., the food plant(s) they fed on. Our experiments clearly showed that the method could be used as a software to automatically identify aphids.
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Affiliation(s)
- Noura J. Alotaibi
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Taghreed Alsufyani
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (N.H.M.); (M.A.A.)
| | - Nour Houda M’sakni
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (N.H.M.); (M.A.A.)
| | - Mona A. Almalki
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (N.H.M.); (M.A.A.)
| | - Eman M. Alghamdi
- Chemistry Department, Faculty of Science, King AbdulAziz University, P.O. Box 80200, Jeddah 21589, Saudi Arabia;
| | - Dieter Spiteller
- Chemical Ecology/Biological Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany;
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2
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Kapantaidaki DE, Krokida A, Evangelou V, Milonas P, Papachristos DP. A Molecular Diagnostic Assay for the Discrimination of Aphid Species (Hemiptera: Aphididae) Infesting Citrus. JOURNAL OF ECONOMIC ENTOMOLOGY 2022; 115:2075-2082. [PMID: 36269118 DOI: 10.1093/jee/toac158] [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: 03/09/2022] [Indexed: 06/16/2023]
Abstract
Aphid species (Hemiptera: Aphididae) are among the most serious pests for citrus cultivation throughout the world causing substantial crop damages. Accurate identification of aphids to the species level can be difficult, though being crucial for their effective management. In this study, a molecular diagnostic assay for distinguishing eleven aphid species was developed. A fragment of the mitochondrial Cytochrome Oxidase I (mtCOI) gene was used and a Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-FLP) analysis with five restriction enzymes, based on DNA sequence polymorphisms, was applied to differentiate the eleven aphid species. This molecular technique allows aphid species at any life stage to be discriminated accurately and simply and can be a useful tool for monitoring the populations of economically important aphid species.
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Affiliation(s)
- Despoina Ev Kapantaidaki
- Benaki Phytopathological Institute, Scientific Directorate of Entomology and Agricultural Zoology, 8 Stefanou Delta Street, Kifissia, Attica, Greece
| | - Afroditi Krokida
- Benaki Phytopathological Institute, Scientific Directorate of Entomology and Agricultural Zoology, 8 Stefanou Delta Street, Kifissia, Attica, Greece
| | - Vasiliki Evangelou
- Benaki Phytopathological Institute, Scientific Directorate of Entomology and Agricultural Zoology, 8 Stefanou Delta Street, Kifissia, Attica, Greece
| | - Panagiotis Milonas
- Benaki Phytopathological Institute, Scientific Directorate of Entomology and Agricultural Zoology, 8 Stefanou Delta Street, Kifissia, Attica, Greece
| | - Dimitrios P Papachristos
- Benaki Phytopathological Institute, Scientific Directorate of Entomology and Agricultural Zoology, 8 Stefanou Delta Street, Kifissia, Attica, Greece
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3
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Massimino Cocuzza GE, Magoga G, Montagna M, Nieto Nafría JM, Barbagallo S. European and Mediterranean Myzocallidini Aphid Species: DNA Barcoding and Remarks on Ecology with Taxonomic Modifications in An Integrated Framework. INSECTS 2022; 13:1006. [PMID: 36354832 PMCID: PMC9693350 DOI: 10.3390/insects13111006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
The genus Myzocallis Passerini (Hemiptera, Aphididae, Calaphidinae, Myzocallidini) is a rather primitive group of aphids currently comprising 45 species and 3 subspecies, subdivided into ten subgenera, three of them having a West Palaearctic distribution. The majority of the species inhabit Fagales plants and some of them are considered pests. Despite their ecological interest and the presence of some taxonomic controversies, there are only a few molecular studies on the group. Here, the main aims were to develop a DNA barcodes library for the molecular identification of West Palaearctic Myzocallis species, to evaluate the congruence among their morphological, ecological and DNA-based delimitation, and verify the congruence of the subgeneric subdivision presently adopted by comparing the results with those obtained for other Panaphidini species. These study findings indicate that Myzocallis (Agrioaphis) leclanti, originally described as a subspecies of M. (A.) castanicola and M. (M.) schreiberi, considered as a subspecies of M. (M.) boerneri, should be regarded at a rank of full species, and the subgenera Agrioaphis, Lineomyzocallis, Neomyzocallis, Pasekia were elevated to the rank of genus, while Myzocallis remain as such.
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Affiliation(s)
| | - Giulia Magoga
- Dipartimento di Scienze Agrarie ed Ambientali (DISAA), Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
| | - Matteo Montagna
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Via Università 100, 80055 Portici, Italy
- BAT Center–Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Napoli Federico II, Via Università 100, 80055 Portici, Italy
| | | | - Sebastiano Barbagallo
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy
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4
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Liu T, Chen J, Jiang L, Qiao G. Phylogeny and species reassessment of
Hyalopterus
(Aphididae, Aphidinae). ZOOL SCR 2020. [DOI: 10.1111/zsc.12444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Tongyi Liu
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Sciences University of Chinese Academy of Sciences Beijing China
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Liyun Jiang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Sciences University of Chinese Academy of Sciences Beijing China
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5
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Voronova NV, Levykina S, Warner D, Shulinski R, Bandarenka Y, Zhorov D. Characteristic and variability of five complete aphid mitochondrial genomes: Aphis fabae mordvilkoi, Aphis craccivora, Myzus persicae, Therioaphis tenera and Appendiseta robiniae (Hemiptera; Sternorrhyncha; Aphididae). Int J Biol Macromol 2020; 149:187-206. [PMID: 31917211 DOI: 10.1016/j.ijbiomac.2019.12.276] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/31/2019] [Accepted: 12/31/2019] [Indexed: 02/06/2023]
Abstract
The complete mitochondrial genomes of aphids Aphis fabae mordvilkoi, A. craccivora, Myzus persicae from Aphidinae as well as Therioaphis tenera and Appendiseta robiniae from Calaphidinae were sequenced and compared with the genomes of other aphid species. A. fabae mordvilkoi, Th. tenera and A. robiniae mitogenomes were sequenced and analyzed for the first time. The annotation of A. craccivora and M. persicae were corrected compared to what was previously published. According to our data there is no translocation of tRNA-Tyr gene in A. craccivora mitogenome and this aphid species has an ancestral type of mitochondrial gene order. A + T content in all 5 mitogenomes was higher than 80%. A + T content in the Th. tenera CR was 59.5% which is untypically low. CRs of all 5 studied mitogenomes had 2 conserved motifs at their ends and extended G + C rich region. A. craccivora, M. persicae and Th. tenera had large tandem repeats inside the CRs. Detailed molecular analysis of all 5 aphid mitochondrial genomes showed the importance of a deep understanding of the molecular organization of all the functional regions of the mitochondrial DNA, which helps to avoid mistakes during genome annotation.
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Affiliation(s)
- Nina V Voronova
- Zoology Department, Belarusian State University, Minsk, Belarus.
| | - Sofiya Levykina
- Zoology Department, Belarusian State University, Minsk, Belarus
| | - Derek Warner
- DNA Sequencing Core Facility, University of Utah, Salt Lake City, UT, United States of America
| | - Raman Shulinski
- Zoology Department, Belarusian State University, Minsk, Belarus
| | - Yury Bandarenka
- Zoology Department, Belarusian State University, Minsk, Belarus
| | - Dmitrii Zhorov
- Zoology Department, Belarusian State University, Minsk, Belarus
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6
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Naseem MT, Ashfaq M, Khan AM, Rasool A, Asif M, Hebert PDN. BIN overlap confirms transcontinental distribution of pest aphids (Hemiptera: Aphididae). PLoS One 2019; 14:e0220426. [PMID: 31821347 PMCID: PMC6903727 DOI: 10.1371/journal.pone.0220426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/24/2019] [Indexed: 11/25/2022] Open
Abstract
DNA barcoding is highly effective for identifying specimens once a reference sequence library is available for the species assemblage targeted for analysis. Despite the great need for an improved capacity to identify the insect pests of crops, the use of DNA barcoding is constrained by the lack of a well-parameterized reference library. The current study begins to address this limitation by developing a DNA barcode reference library for the pest aphids of Pakistan. It also examines the affinities of these species with conspecific populations from other geographic regions based on both conventional taxonomy and Barcode Index Numbers (BINs). A total of 809 aphids were collected from a range of plant species at sites across Pakistan. Morphological study and DNA barcoding allowed 774 specimens to be identified to one of 42 species while the others were placed to a genus or subfamily. Sequences obtained from these specimens were assigned to 52 BINs whose monophyly were supported by neighbor-joining (NJ) clustering and Bayesian inference. The 42 species were assigned to 41 BINs with 38 showing BIN concordance. These species were represented on BOLD by 7,870 records from 69 countries. Combining these records with those from Pakistan produced 60 BINs with 12 species showing a BIN split and three a BIN merger. Geo-distance correlations showed that intraspecific divergence values for 49% of the species were not affected by the distance between populations. Forty four of the 52 BINs from Pakistan had counterparts in 73 countries across six continents, documenting the broad distributions of pest aphids.
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Affiliation(s)
- Muhammad Tayyib Naseem
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Muhammad Ashfaq
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
- * E-mail:
| | - Arif Muhammad Khan
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Akhtar Rasool
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Zoology, University of Swat, Swat, Pakistan
| | - Muhammad Asif
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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7
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Kinyanjui G, Khamis FM, Ombura FLO, Kenya EU, Ekesi S, Mohamed SA. Infestation Levels and Molecular Identification Based on Mitochondrial COI Barcode Region of Five Invasive Gelechiidae Pest Species in Kenya. JOURNAL OF ECONOMIC ENTOMOLOGY 2019; 112:872-882. [PMID: 30476129 DOI: 10.1093/jee/toy357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Indexed: 06/09/2023]
Abstract
Invasive Gelechiidae pest species, namely Tuta absoluta, Phthorimaea operculella, Aproaerema simplixella, Sitotroga cerealella, and Pectinophora gossypiella are among the major constraints hampering agricultural economy in Kenya. Infestation levels were determined on respective host crops sampled from different localities and P. operculella recorded the highest infestation of 68.00 ± 4.92% on stored potato. Aproaerema simplixella and T. absoluta accounted for 61.33 ± 5.35% and 51.56 ± 5.22% maximal infestation on groundnuts and tomato leaves, respectively. Stored maize was significantly infested by S. cerealella (54.33 ± 5.31%) while no infestation was observed on the freshly harvested grains. Infestation on open bolls by P. gossypiella was relatively low (6.11 ± 3.46%) compared to Anatrachyntis simplex (45.67 ± 7.84%) that emerged as the key pest of cotton. The species were discriminated based on sequence similarities, evolutionary divergences, and phylogenetic analyses. A 658-bp fragment of mitochondrial cytochrome c oxidase subunit I (COI) gene was obtained from 302 specimens. Generally, genetic variations were low within and between Gelechiid populations, with an average of 0.02% and all intraspecific divergences were less than 2% except for S. cerealella. The Gelechiids data set generated eight Barcode Index Numbers (BINs), five of which were concordant and three belonging to S. cerealella were singleton. All species were separated into distinct clusters on a maximum likelihood tree. Data on infestation levels will be useful in defining the pest status of these Gelechiids in Kenya. DNA barcoding is also presented as a valuable tool to complement traditional taxonomy for rapid and accurate identification of these species of agronomic interest.
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Affiliation(s)
- G Kinyanjui
- Plant Health Theme, International Centre of Insect Physiology and Ecology (icipe), GPO, Nairobi, Kenya
- Department of Biological Sciences, University of Embu, Embu, Kenya
| | - F M Khamis
- Plant Health Theme, International Centre of Insect Physiology and Ecology (icipe), GPO, Nairobi, Kenya
| | - F L O Ombura
- Plant Health Theme, International Centre of Insect Physiology and Ecology (icipe), GPO, Nairobi, Kenya
| | - E U Kenya
- Department of Biological Sciences, University of Embu, Embu, Kenya
| | - S Ekesi
- Plant Health Theme, International Centre of Insect Physiology and Ecology (icipe), GPO, Nairobi, Kenya
| | - S A Mohamed
- Plant Health Theme, International Centre of Insect Physiology and Ecology (icipe), GPO, Nairobi, Kenya
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8
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Li ZQ, Cai XM, Luo ZX, Bian L, Xin ZJ, Liu Y, Chu B, Chen ZM. Geographical Distribution of Ectropis grisescens (Lepidoptera: Geometridae) and Ectropis obliqua in China and Description of an Efficient Identification Method. JOURNAL OF ECONOMIC ENTOMOLOGY 2019; 112:277-283. [PMID: 30508146 DOI: 10.1093/jee/toy358] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Indexed: 06/09/2023]
Abstract
Ectropis grisescens Warren 1894 (Lepidopotera: Geometridae) and Ectropis obliqua Prout 1915 (Lepidopotera: Geometridae) are the most destructive chewing pests in China's tea plantations. Ectropis grisescens sex pheromone lures and E. obliqua nucleopolyhedrosis virus (EoNPV) are two species-specific and effective bio-control technologies to control these pests. Because these two species are morphologically similar, tea growers are unable to discriminate them by visual inspection. Hence, determining whether to use E. grisescens sex pheromone lures or EoNPV is difficult without knowledge on the geographical distribution of these two Ectropis species in China. In this study, we developed an efficient identification method, which is considerably cheaper and faster than sequencing the cytochrome c oxidase I gene. Overall, 2,588 E. grisescens and E. obliqua samples, collected from 13 provinces and municipalities in China covering the major regions where these pests have been reported, were identified. All insect samples from southern Jiangsu Province were identified as E. obliqua. Both Ectropis species were mix-distributed at the Anhui-Zhejiang Province border areas, whereas E. grisescens was mostly collected from the other sampling sites. Thus, E. obliqua might be mainly distributed at the junction of Jiangsu, Anhui, and Zhejiang Provinces. In contrast, E. grisescens has a considerably wide distribution area and is the main lepidopteran pest in the tea plantations of China. Our results contribute to improve the management of E. grisescens and E. obliqua populations and provide new insights for further studies on these two species.
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Affiliation(s)
- Zhao-Qun Li
- Key Laboratory of Tea Biology and Resource Utilization, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Science, Hangzhou, People's Republic of China
| | - Xiao-Ming Cai
- Key Laboratory of Tea Biology and Resource Utilization, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Science, Hangzhou, People's Republic of China
| | - Zong-Xiu Luo
- Key Laboratory of Tea Biology and Resource Utilization, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Science, Hangzhou, People's Republic of China
| | - Lei Bian
- Key Laboratory of Tea Biology and Resource Utilization, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Science, Hangzhou, People's Republic of China
| | - Zhao-Jun Xin
- Key Laboratory of Tea Biology and Resource Utilization, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Science, Hangzhou, People's Republic of China
| | - Yan Liu
- Key Laboratory of Tea Biology and Resource Utilization, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Science, Hangzhou, People's Republic of China
| | - Bo Chu
- Key Laboratory of Tea Biology and Resource Utilization, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Science, Hangzhou, People's Republic of China
| | - Zong-Mao Chen
- Key Laboratory of Tea Biology and Resource Utilization, Ministry of Agriculture, Tea Research Institute, Chinese Academy of Agricultural Science, Hangzhou, People's Republic of China
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9
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Hua HQ, Zhao ZY, Zhang Y, Hu J, Zhang F, Li YX. Inter- and Intra-Specific Differentiation of Trichogramma (Hymenoptera: Trichogrammatidae) Species Using PCR-RFLP Targeting COI. JOURNAL OF ECONOMIC ENTOMOLOGY 2018; 111:1860-1867. [PMID: 29718401 DOI: 10.1093/jee/toy119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Indexed: 06/08/2023]
Abstract
The identification of Trichogramma (Hymenoptera: Trichogrammatidae) species is problematic due to their small size and lack of distinct morphological characters. In this study, we combined morphological characters of the male genitalia and molecular methods using the mitochondrial cytochrome oxidase I (COI) gene as a molecular marker to identify eight species from 16 geographic populations: T. evanescens Westwood, T. cacoeciae Marchal, T. ostriniae Pang et Chen, T. chilonis Ishii, T. japonicum Ashmead, T. brassicae Bezdenko, T. bilingensis He et Pang, and T. dendrolimi Matsumura. We developed a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method targeting the mitochondrial COI to distinguish the eight Trichogramma species using three restriction enzymes. We further analyzed 109 COI fragments from 18 Trichogramma species and found that the PCR-RFLP method could distinguish both intra- and inter-specific genetic variation among most of the species using four additional restriction enzymes.
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Affiliation(s)
- Hai-Qing Hua
- Department of Entomology, Nanjing Agricultural University, Xuanwu District, Nanjing, China
| | - Zi-Yi Zhao
- Department of Entomology, Nanjing Agricultural University, Xuanwu District, Nanjing, China
| | - Yang Zhang
- Department of Entomology, Nanjing Agricultural University, Xuanwu District, Nanjing, China
| | - Jin Hu
- Department of Entomology, Nanjing Agricultural University, Xuanwu District, Nanjing, China
| | - Fan Zhang
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yuan-Xi Li
- Department of Entomology, Nanjing Agricultural University, Xuanwu District, Nanjing, China
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10
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Khamis FM, Rwomushana I, Ombura LO, Cook G, Mohamed SA, Tanga CM, Nderitu PW, Borgemeister C, Sétamou M, Grout TG, Ekesi S. DNA Barcode Reference Library for the African Citrus Triozid, Trioza erytreae (Hemiptera: Triozidae): Vector of African Citrus Greening. JOURNAL OF ECONOMIC ENTOMOLOGY 2017; 110:2637-2646. [PMID: 29045665 DOI: 10.1093/jee/tox283] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Indexed: 06/07/2023]
Abstract
Citrus (Citrus spp.) production continues to decline in East Africa, particularly in Kenya and Tanzania, the two major producers in the region. This decline is attributed to pests and diseases including infestation by the African citrus triozid, Trioza erytreae (Del Guercio) (Hemiptera: Triozidae). Besides direct feeding damage by adults and immature stages, T. erytreae is the main vector of 'Candidatus Liberibacter africanus', the causative agent of Greening disease in Africa, closely related to Huanglongbing. This study aimed to generate a novel barcode reference library for T. erytreae in order to use DNA barcoding as a rapid tool for accurate identification of the pest to aid phytosanitary measures. Triozid samples were collected from citrus orchards in Kenya, Tanzania, and South Africa and from alternative host plants. Sequences generated from populations in the study showed very low variability within acceptable ranges of species. All samples analyzed were linked to T. erytreae of GenBank accession number KU517195. Phylogeny of samples in this study and other Trioza reference species was inferred using the Maximum Likelihood method. The phylogenetic tree was paraphyletic with two distinct branches. The first branch had two clusters: 1) cluster of all populations analyzed with GenBank accession of T. erytreae and 2) cluster of all the other GenBank accession of Trioza species analyzed except T. incrustata Percy, 2016 (KT588307.1), T. eugeniae Froggatt (KY294637.1), and T. grallata Percy, 2016 (KT588308.1) that occupied the second branch as outgroups forming sister clade relationships. These results were further substantiated with genetic distance values and principal component analyses.
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Affiliation(s)
- F M Khamis
- International Centre of Insect Physiology and Ecology (icipe) Kenya
| | - I Rwomushana
- International Centre of Insect Physiology and Ecology (icipe) Kenya
| | - L O Ombura
- International Centre of Insect Physiology and Ecology (icipe) Kenya
| | - G Cook
- Citrus Research International (Pty) Limited, South Africa
| | - S A Mohamed
- International Centre of Insect Physiology and Ecology (icipe) Kenya
| | - C M Tanga
- International Centre of Insect Physiology and Ecology (icipe) Kenya
| | - P W Nderitu
- International Centre of Insect Physiology and Ecology (icipe) Kenya
| | - C Borgemeister
- Center for Development Research (ZEF), University of Bonn, Germany
| | - M Sétamou
- Texas A&M University-Kingsville Citrus Centre
| | - T G Grout
- Citrus Research International (Pty) Limited, South Africa
| | - S Ekesi
- International Centre of Insect Physiology and Ecology (icipe) Kenya
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11
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Ateka E, Alicai T, Ndunguru J, Tairo F, Sseruwagi P, Kiarie S, Makori T, Kehoe MA, Boykin LM. Unusual occurrence of a DAG motif in the Ipomovirus Cassava brown streak virus and implications for its vector transmission. PLoS One 2017; 12:e0187883. [PMID: 29155849 PMCID: PMC5695790 DOI: 10.1371/journal.pone.0187883] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/28/2017] [Indexed: 11/19/2022] Open
Abstract
Cassava is the main staple food for over 800 million people globally. Its production in eastern Africa is being constrained by two devastating Ipomoviruses that cause cassava brown streak disease (CBSD); Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), with up to 100% yield loss for smallholder farmers in the region. To date, vector studies have not resulted in reproducible and highly efficient transmission of CBSV and UCBSV. Most virus transmission studies have used Bemisia tabaci (whitefly), but a maximum of 41% U/CBSV transmission efficiency has been documented for this vector. With the advent of next generation sequencing, researchers are generating whole genome sequences for both CBSV and UCBSV from throughout eastern Africa. Our initial goal for this study was to characterize U/CBSV whole genomes from CBSD symptomatic cassava plants sampled in Kenya. We have generated 8 new whole genomes (3 CBSV and 5 UCBSV) from Kenya, and in the process of analyzing these genomes together with 26 previously published sequences, we uncovered the aphid transmission associated DAG motif within coat protein genes of all CBSV whole genomes at amino acid positions 52-54, but not in UCBSV. Upon further investigation, the DAG motif was also found at the same positions in two other Ipomoviruses: Squash vein yellowing virus (SqVYV), Coccinia mottle virus (CocMoV). Until this study, the highly-conserved DAG motif, which is associated with aphid transmission was only noticed once, in SqVYV but discounted as being of minimal importance. This study represents the first comprehensive look at Ipomovirus genomes to determine the extent of DAG motif presence and significance for vector relations. The presence of this motif suggests that aphids could potentially be a vector of CBSV, SqVYV and CocMov. Further transmission and ipomoviral protein evolutionary studies are needed to confirm this hypothesis.
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Affiliation(s)
- Elijah Ateka
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Titus Alicai
- National Crops Resources Research Institute (NaCRRI), Kampala, Uganda
| | - Joseph Ndunguru
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam, Tanzania
| | - Fred Tairo
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam, Tanzania
| | - Peter Sseruwagi
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam, Tanzania
| | - Samuel Kiarie
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Timothy Makori
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Monica A. Kehoe
- Department of Primary Industries and Regional Development, DPIRD Diagnostic Laboratory Services, South Perth, WA, Australia
| | - Laura M. Boykin
- School of Molecular Sciences, University of Western Australia, Crawley, Perth, WA, Australia
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Zhu XC, Chen J, Chen R, Jiang LY, Qiao GX. DNA barcoding and species delimitation of Chaitophorinae (Hemiptera, Aphididae). Zookeys 2017:25-50. [PMID: 28331401 PMCID: PMC5345361 DOI: 10.3897/zookeys.656.11440] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/31/2017] [Indexed: 11/12/2022] Open
Abstract
Chaitophorinae aphids are widespread across Eurasia and North America, and include some important agricultural and horticultural pests. So, accurate rapid species identification is very important. Here, we used three mitochondrial genes and one endosymbiont gene to calculate and analyze the genetic distances within different datasets. For species delimitation, two distance-based methods were employed, threshold with NJ (neighbor-joining) and ABGD (Automatic Barcode Gap Discovery), and two tree-based approaches, GMYC (General Mixed Yule Coalescent) and PTP (Poisson Tree Process). The genetic interspecific divergence was clearly larger than the intraspecific divergence for four molecular markers. COI and COII genes were found to be more suitable for Chaitophorinae DNA barcoding. For species delimitation, at least one distance-based method combined with one tree-based method would be preferable. Based on the data for Chaitophorussaliniger and Laingiapsammae, DNA barcoding may also reveal geographical variation.
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Affiliation(s)
- Xi-Chao Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, No. 1-5 Beichen West Road, Chaoyang District, Beijing 100101, P.R. China; College of Life Science, University of Chinese Academy of Sciences, Shijingshan District, Beijing 100049, P.R. China
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, No. 1-5 Beichen West Road, Chaoyang District, Beijing 100101, P.R. China
| | - Rui Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, No. 1-5 Beichen West Road, Chaoyang District, Beijing 100101, P.R. China
| | - Li-Yun Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, No. 1-5 Beichen West Road, Chaoyang District, Beijing 100101, P.R. China
| | - Ge-Xia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, No. 1-5 Beichen West Road, Chaoyang District, Beijing 100101, P.R. China
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