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Liu D, Cui J, Liu Y, Niu M, Wang F, Zhao Q, Cai B, Zhang H, Wei J. Ultraconserved elements from transcriptome and genome data provide insight into the phylogenomics of Sternorrhyncha (Insecta: Hemiptera). Cladistics 2024. [PMID: 38808591 DOI: 10.1111/cla.12585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 04/30/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024] Open
Abstract
Sternorrhyncha, one of the four major suborders of Hemiptera, is a phytophagous taxon inclusive of nearly 18 000 described species. The phylogenetic relationships within the taxon and the earliest-branching lineage of its infraorders remain incompletely understood. This study attempted to illuminate the phylogenetic relationships within Sternorrhyncha through the use of maximum likelihood, Bayesian inference and maximum parsimony analyses, employing ultraconserved element (UCE) data from 39 genomic and 62 transcriptomic datasets and thereby representing most families within the taxon. The probe set Hemiptera 2.7Kv1 was used to recover a total of 2731 UCE loci: from 547 to 1699 (with an average of 1084) across all genomic datasets and from 108 to 849 (with an average of 329) across all transcriptomic datasets. All three types of phylogenetic analyses employed in this study produced robust statistical support for Sternorrhyncha being a monophyletic group. The different methods of phylogenetic analysis produced inconsistent descriptions of topological structure at the infraorder level: while maximum likelihood and Bayesian inference analyses produced strong statistical evidence (100%) indicating the clade Psylloidea + Aleyrodoidea to be a sister of the clade Aphidoidea (Aphidomorpha) + Coccoidea (Coccomorpha), the maximum parsimony analysis failed to recover a similar result. Our results also provide detail on the phylogenetic relationships within each infraorder. This study presents the first use of UCE data to investigate the phylogeny of Sternorrhyncha. It also shows the viability of amalgamating genomic and transcriptomic data in studies of phylogenetic relationships, potentially highlighting a resource-efficient approach for future inquiries into diverse taxa through the integration of varied data sources.
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Affiliation(s)
- Dajun Liu
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, 030801, China
- Department of Biology, Xinzhou Normal University, Xinzhou, Shanxi, 034000, China
| | - Jinyu Cui
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, 030801, China
| | - Yubo Liu
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, 030801, China
| | - Minmin Niu
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, 030801, China
| | - Fang Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, China
| | - Qing Zhao
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, 030801, China
| | - Bo Cai
- Post-Entry Quarantine Station for Tropical Plant, Haikou Customs District, No. 9 West Haixiu Road, Haikou, 570311, China
| | - Hufang Zhang
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, 030801, China
- Department of Biology, Xinzhou Normal University, Xinzhou, Shanxi, 034000, China
| | - Jiufeng Wei
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, 030801, China
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Leiva AM, Chittarath K, Lopez-Alvarez D, Vongphachanh P, Gomez MI, Sengsay S, Wang XW, Rodriguez R, Newby J, Cuellar WJ. Mitochondrial Genetic Diversity of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) Associated with Cassava in Lao PDR. INSECTS 2022; 13:861. [PMID: 36292809 PMCID: PMC9604212 DOI: 10.3390/insects13100861] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Cassava Mosaic Disease (CMD) caused by Sri Lankan cassava mosaic virus (SLCMV), has rapidly spread in Southeast Asia (SEA) since 2016. Recently it has been documented in Lao PDR. Previous reports have identified whitefly species of B. tabaci as potential vectors of CMD in SEA, but their occurrence and distribution in cassava fields is not well known. We conducted a countrywide survey in Lao PDR for adult whiteflies in cassava fields, and determined the abundance and genetic diversity of the B. tabaci species complex using mitochondrial cytochrome oxidase I (mtCOI) sequencing. In order to expedite the process, PCR amplifications were performed directly on whitefly adults without DNA extraction, and mtCOI sequences obtained using nanopore portable-sequencing technology. Low whitefly abundances and two cryptic species of the B. tabaci complex, Asia II 1 and Asia II 6, were identified. This is the first work on abundance and genetic identification of whiteflies associated with cassava in Lao PDR. This study indicates currently only a secondary role for Asia II in spreading CMD or as a pest. Routine monitoring and transmission studies on Asia II 6 should be carried out to establish its potential role as a vector of SLCMV in this region.
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Affiliation(s)
- Ana M. Leiva
- Cassava Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), The Americas Hub, Km 17 Recta Cali-Palmira, Cali 763537, Colombia
| | - Khonesavanh Chittarath
- Plant Protection Center (PPC), Department of Agriculture, Ministry of Agriculture and Forestry, Vientiane P.O. Box 811, Laos
| | - Diana Lopez-Alvarez
- Department of Biological Sciences, Universidad Nacional de Colombia UNAL-Palmira, Palmira 763533, Colombia
| | - Pinkham Vongphachanh
- Plant Protection Center (PPC), Department of Agriculture, Ministry of Agriculture and Forestry, Vientiane P.O. Box 811, Laos
| | - Maria Isabel Gomez
- Cassava Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), The Americas Hub, Km 17 Recta Cali-Palmira, Cali 763537, Colombia
| | - Somkhit Sengsay
- Plant Protection Center (PPC), Department of Agriculture, Ministry of Agriculture and Forestry, Vientiane P.O. Box 811, Laos
| | - Xiao-Wei Wang
- Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Rafael Rodriguez
- Cassava Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), The Americas Hub, Km 17 Recta Cali-Palmira, Cali 763537, Colombia
| | - Jonathan Newby
- Cassava Program Asia Office, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Laos Country Office, Vientiane P.O. Box 783, Laos
| | - Wilmer J. Cuellar
- Cassava Program, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), The Americas Hub, Km 17 Recta Cali-Palmira, Cali 763537, Colombia
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Assessment of genetic diversity, detection of strain-specific single nucleotide polymorphisms and identification of the Bangladesh and Vietnam strain of Channa striata by PCR-RFLP analysis of the mitochondrial COI gene fragment. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2020.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Distribution and Molecular Diversity of Whitefly Species Colonizing Cassava in Kenya. INSECTS 2021; 12:insects12100875. [PMID: 34680644 PMCID: PMC8541676 DOI: 10.3390/insects12100875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/02/2021] [Accepted: 09/04/2021] [Indexed: 11/25/2022]
Abstract
Simple Summary The whitefly, Bemisia tabaci (Gennadium, Hemiptera) is a crop pest and plant-virus vector known to transmit more than 300 plant viruses. Among other plant viruses, the vector transmits viruses that cause the two major devastating viral diseases of cassava in sub-Saharan Africa namely cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). In order to achieve effective implementation of whitefly management programs including prevention of spread of the species, accurate species identification is vital. Morphological identification approaches toward whitefly species limits the capacity to accurately identify new species, especially the presence of cryptic species such as the numerous B. tabaci genetic groups. Using the mitochondrial DNA cytochrome oxidase 1 (mtCO1) sequences, four distinct whitefly species namely Bemisia tabaci, Bemisia afer, Aleurodicus dispersus and Paraleyrodes bondari were identified in samples collected from major cassava growing regions in Kenya. The study presents the first report of P. bondari (Bondar’s nesting whitefly) on cassava in Kenya. We found three B. tabaci genetic groups of SSA1, SSA2 and Indian Ocean (IO) putative species colonizing cassava in Kenya. The information is useful to inform better management strategies of the whitefly vectors to reduce the impact of cassava viral diseases, which continue to be a threat to food security in major cassava growing regions. Abstract The whitefly, Bemisia tabaci (Gennadium, Hemiptera) has been reported to transmit viruses that cause cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) in many parts of sub-Saharan Africa (SSA). Currently, there is limited information on the distribution, species and haplotype composition of the whitefly populations colonizing cassava in Kenya. A study was conducted in the major cassava growing regions of Kenya to address this gap. Analyses of mitochondrial DNA cytochrome oxidase 1 (mtCO1) sequences revealed the presence of four distinct whitefly species: Bemisia tabaci, Bemisia afer, Aleurodicus dispersus and Paraleyrodes bondari in Kenya. The B. tabaci haplotypes were further resolved into SSA1, SSA2 and Indian Ocean (IO) putative species. The SSA1 population had three haplogroups of SSA1-SG1, SSA-SG2 and SSA1-SG3. Application of KASP genotyping grouped the Bemisia tabaci into two haplogroups namely sub-Saharan Africa East and Southern Africa (SSA-ESA) and sub-Saharan Africa East and Central Africa (SSA-ECA). The study presents the first report of P. bondari (Bondar’s nesting whitefly) on cassava in Kenya. Bemisia tabaci was widely distributed in all the major cassava growing regions in Kenya. The increased detection of different whitefly species on cassava and genetically diverse B. tabaci mitotypes indicates a significant influence on the dynamics of cassava virus epidemics in the field. The study highlights the need for continuous monitoring of invasive whitefly species population on cassava for timely application of management practices to reduce the impact of cassava viral diseases and prevent potential yield losses.
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Marín DV, Castillo DK, López-Lavalle LAB, Chalarca JR, Pérez CR. An optimized high-quality DNA isolation protocol for spodoptera frugiperda J. E. smith (Lepidoptera: Noctuidae). MethodsX 2021; 8:101255. [PMID: 34434778 PMCID: PMC8374285 DOI: 10.1016/j.mex.2021.101255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 01/28/2021] [Indexed: 11/27/2022] Open
Abstract
An optimized high-quality DNA isolation protocol was developed using body segment tissue from the Fall Armyworm (Spodoptera frugiperda), that will allow documenting genetic variability based on biotypes, facilitating studies on the appearance, distribution and population dynamics of the fall armyworm at the molecular level. The resulting protocol is an easy-to-use, timesaving method that can rapidly achieve high quality, high-yielding total genomic DNA, using chemicals and everyday consumables available in a molecular laboratory. This new method of DNA extraction avoids the contamination of polysaccharides, salts, phenols, proteins and other cellular by-products that can interfere with subsequent reactions. DNA purity estimates reveal A260: A280 ratios greater than 1.9, which were evidenced by quality test on agarose gel, observing complete integrity and high purity of the resulting samples, and yielded 30–99 µg/g of total DNA. Therefore, the quality of the DNA produced from this extraction is suitable for subsequent molecular applications: (i) next generation whole genome sequencing, (ii) conventional polymerase chain reaction for genotyping, (iii) barcodes and (iv) gene cloning. In addition, to become an anticipating diagnostic tool for invasive lepidopteran larval stages:The resulting protocol is an easy-to-use time-saving method. This new extraction method prevents contamination from polysaccharides, salts, phenols, proteins, and other cellular sub-products. DNA purity estimations reveal A260:A280 ratios above 1.9.
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Affiliation(s)
- Diana Victoria Marín
- Universidad Nacional de Colombia, Sede Palmira, Palmira, Valle del Cauca, Colombia.,The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Recta Cali-Palmira km 17, Valle del Cauca, Colombia
| | - Diana Katherine Castillo
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Recta Cali-Palmira km 17, Valle del Cauca, Colombia
| | - Luis Augusto Becerra López-Lavalle
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Recta Cali-Palmira km 17, Valle del Cauca, Colombia
| | - Jairo Rodríguez Chalarca
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Recta Cali-Palmira km 17, Valle del Cauca, Colombia
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Khamis FM, Ombura FLO, Ajene IJ, Akutse KS, Subramanian S, Mohamed SA, Dubois T, Tanga CM, Ekesi S. Mitogenomic analysis of diversity of key whitefly pests in Kenya and its implication to their sustainable management. Sci Rep 2021; 11:6348. [PMID: 33737698 PMCID: PMC7973771 DOI: 10.1038/s41598-021-85902-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/08/2021] [Indexed: 01/31/2023] Open
Abstract
Whiteflies (Hemiptera: Aleyrodidae) are devastating agricultural pests of economic importance vectoring pathogenic plant viruses. Knowledge on their diversity and distribution in Kenya is scanty, limiting development of effective sustainable management strategies. The present study is aimed at identifying whitefly pest species present in Kenya across different agroecological zones and establish predictive models for the most abundant species in Africa. Whiteflies were sampled in Kenya from key crops known to be severely infested and identified using 16S rRNA markers and complete mitochondrial genomes. Four whitefly species were identified: Aleyrodes proletella, Aleurodicus dispersus, Bemisia afer and Trialeurodes vaporariorum, the latter being the most dominant species across all the agroecology. The assembly of complete mitogenomes and comparative analysis of all 13 protein coding genes confirmed the identities of the four species. Furthermore, prediction spatial models indicated high climatic suitability of T. vaporariorum in Africa, Europe, Central America, parts of Southern America, parts of Australia, New Zealand and Asia. Consequently, our findings provide information to guide biosecurity agencies on protocols to be adopted for precise identification of pest whitefly species in Kenya to serve as an early warning tool against T. vaporariorum invasion into unaffected areas and guide appropriate decision-making on their management.
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Affiliation(s)
- Fathiya M. Khamis
- grid.419326.b0000 0004 1794 5158Plant Health Theme, International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya
| | - Fidelis L. O. Ombura
- grid.419326.b0000 0004 1794 5158Plant Health Theme, International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya
| | - Inusa J. Ajene
- grid.419326.b0000 0004 1794 5158Plant Health Theme, International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya
| | - Komivi S. Akutse
- grid.419326.b0000 0004 1794 5158Plant Health Theme, International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya
| | - Sevgan Subramanian
- grid.419326.b0000 0004 1794 5158Plant Health Theme, International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya
| | - Samira A. Mohamed
- grid.419326.b0000 0004 1794 5158Plant Health Theme, International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya
| | - Thomas Dubois
- grid.419326.b0000 0004 1794 5158Plant Health Theme, International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya
| | - Chrysantus M. Tanga
- grid.419326.b0000 0004 1794 5158Plant Health Theme, International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya
| | - Sunday Ekesi
- grid.419326.b0000 0004 1794 5158Plant Health Theme, International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya
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7
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Low Genetic Variability in Bemisia tabaci MEAM1 Populations within Farmscapes of Georgia, USA. INSECTS 2020; 11:insects11120834. [PMID: 33255960 PMCID: PMC7760769 DOI: 10.3390/insects11120834] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 11/25/2022]
Abstract
Simple Summary Sweetpotato whitefly, Bemisia tabaci Gennadius, is a serious pest of many agricultural crops worldwide. Numerous studies have examined the genetic structure of whitefly populations separated by geographical barriers; however, very few have assessed the population structure of B. tabaci at a farmscape level. A farmscape in this study is defined as heterogenous habitat with crop and non-crop areas spanning approximately 8 square kilometers. To assess the roles of farmscapes as drivers of B. tabaci genetic variation, thirty-five populations of the sweetpotato whitefly were collected from crop and non-crop plant species from fifteen farmscapes. Using mitochondrial COI gene sequences (mtCOI) and six nuclear microsatellite markers, the genetic diversity and genetic differentiation among collected B. tabaci MEAM1 populations were examined. Haplotype analysis using mtCOI sequences revealed the presence of a single B. tabaci MEAM1 haplotype across farmscapes of Georgia. Results from microsatellite markers further showed no significant genetic structuring among populations that corresponded to plant species or farmscapes from which they were collected. Annual whitefly population explosions and subsequent dispersal might have facilitated the persistence of a single panmictic B. tabaci population over all sampled farmscapes in this region. Abstract Bemisia tabaci is a whitefly species complex comprising important phloem feeding insect pests and plant virus vectors of many agricultural crops. Middle East–Asia Minor 1 (MEAM1) and Mediterranean (MED) are the two most invasive members of the B. tabaci species complex worldwide. The diversity of agroecosystems invaded by B. tabaci could potentially influence their population structure, but this has not been assessed at a farmscape level. A farmscape in this study is defined as heterogenous habitat with crop and non-crop areas spanning ~8 square kilometers. In this study, mitochondrial COI gene (mtCOI) sequences and six microsatellite markers were used to examine the population structure of B. tabaci MEAM1 colonizing different plant species at a farmscape level in Georgia, United States. Thirty-five populations of adult whiteflies on row and vegetable crops and weeds across major agricultural regions of Georgia were collected from fifteen farmscapes. Based on morphological features and mtCOI sequences, five species/cryptic species of whiteflies (B. tabaci MEAM1, B. tabaci MED, Dialeurodes citri, Trialeurodes abutiloneus, T. vaporariorum) were found. Analysis of 102 mtCOI sequences revealed the presence of a single B. tabaci MEAM1 haplotype across farmscapes in Georgia. Population genetics analyses (AMOVA, PCA and STRUCTURE) of B. tabaci MEAM1 (microsatellite data) revealed only minimal genetic differences among collected populations within and among farmscapes. Overall, our results suggest that there is a high level of gene flow among B. tabaci MEAM1 populations among farmscapes in Georgia. Frequent whitefly population explosions driven by a single or a few major whitefly-suitable hosts planted on a wide spatial scale may be the key factor behind the persistence of a single panmictic population over Georgia’s farmscapes. These population structuring effects are useful for delineating the spatial scale at which whiteflies must be managed and predicting the speed at which alleles associated with insecticide resistance might spread.
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Ovalle TM, Vásquez-Ordóñez AA, Jimenez J, Parsa S, Cuellar WJ, Becerra Lopez-Lavalle LA. A simple PCR-based method for the rapid and accurate identification of spider mites (Tetranychidae) on cassava. Sci Rep 2020; 10:19496. [PMID: 33177527 PMCID: PMC7658231 DOI: 10.1038/s41598-020-75743-w] [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] [Received: 05/04/2020] [Accepted: 10/14/2020] [Indexed: 11/10/2022] Open
Abstract
The morphological identification of mites entails great challenges. Characteristics such as dorsal setae and aedeagus are widely used, but they show variations between populations, and the technique is time consuming and demands specialized taxonomic expertise that is difficult to access. A successful alternative has been to exploit a region of the mitochondrial cytochrome oxidase I (COI) gene to classify specimens to the species level. We analyzed the COI sequences of four mite species associated with cassava and classified them definitively by detailed morphological examinations. We then developed an identification kit based on the restriction fragment length polymorphism-polymerase chain reaction of subunit I of the COI gene focused on the three restriction enzymes AseI, MboII, and ApoI. This set of enzymes permitted the simple, accurate identification of Mononychellus caribbeanae, M. tanajoa, M. mcgregori, and Tetranychus urticae, rapidly and with few resources. This kit could be a vital tool for the surveillance and monitoring of mite pests in cassava crop protection programs in Africa, Asia, and Latin America.
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Affiliation(s)
- Tatiana M Ovalle
- Centro Internacional de Agricultura Tropical (CIAT), Km 17, Recta Cali-Palmira, 763537, Cali, Valle del Cauca, Colombia.,CGIAR Research Program for Root Tubers and Bananas, Lima, Peru
| | - Aymer Andrés Vásquez-Ordóñez
- Centro Internacional de Agricultura Tropical (CIAT), Km 17, Recta Cali-Palmira, 763537, Cali, Valle del Cauca, Colombia.,Entomology Section, Universidad del Valle, Ciudad Universitaria Melendez, Cali, Valle del Cauca, Colombia
| | - Jenyfer Jimenez
- Centro Internacional de Agricultura Tropical (CIAT), Km 17, Recta Cali-Palmira, 763537, Cali, Valle del Cauca, Colombia.,CGIAR Research Program for Root Tubers and Bananas, Lima, Peru
| | - Soroush Parsa
- Centro Internacional de Agricultura Tropical (CIAT), Km 17, Recta Cali-Palmira, 763537, Cali, Valle del Cauca, Colombia.,International Potato Center (CIP), Av. La Molina 1895, La Molina, Lima, Lima12, Perú
| | - Wilmer J Cuellar
- Centro Internacional de Agricultura Tropical (CIAT), Km 17, Recta Cali-Palmira, 763537, Cali, Valle del Cauca, Colombia.,CGIAR Research Program for Root Tubers and Bananas, Lima, Peru
| | - Luis A Becerra Lopez-Lavalle
- Centro Internacional de Agricultura Tropical (CIAT), Km 17, Recta Cali-Palmira, 763537, Cali, Valle del Cauca, Colombia. .,CGIAR Research Program for Root Tubers and Bananas, Lima, Peru.
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9
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Santos-Garcia D, Mestre-Rincon N, Ouvrard D, Zchori-Fein E, Morin S. Portiera Gets Wild: Genome Instability Provides Insights into the Evolution of Both Whiteflies and Their Endosymbionts. Genome Biol Evol 2020; 12:2107-2124. [PMID: 33049039 PMCID: PMC7821994 DOI: 10.1093/gbe/evaa216] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2020] [Indexed: 12/12/2022] Open
Abstract
Whiteflies (Hemiptera: Sternorrhyncha: Aleyrodidae) are a superfamily of small phloem-feeding insects. They rely on their primary endosymbionts "Candidatus Portiera aleyrodidarum" to produce essential amino acids not present in their diet. Portiera has been codiverging with whiteflies since their origin and therefore reflects its host's evolutionary history. Like in most primary endosymbionts, the genome of Portiera stays stable across the Aleyrodidae superfamily after millions of years of codivergence. However, Portiera of the whitefly Bemisia tabaci has lost the ancestral genome order, reflecting a rare event in the endosymbiont evolution: the appearance of genome instability. To gain a better understanding of Portiera genome evolution, identify the time point in which genome instability appeared and contribute to the reconstruction of whitefly phylogeny, we developed a new phylogenetic framework. It targeted five Portiera genes and determined the presence of the DNA polymerase proofreading subunit (dnaQ) gene, previously associated with genome instability, and two alternative gene rearrangements. Our results indicated that Portiera gene sequences provide a robust tool for studying intergenera phylogenetic relationships in whiteflies. Using these new framework, we found that whitefly species from the Singhiella, Aleurolobus, and Bemisia genera form a monophyletic tribe, the Aleurolobini, and that their Portiera exhibit genome instability. This instability likely arose once in the common ancestor of the Aleurolobini tribe (at least 70 Ma), drawing a link between the appearance of genome instability in Portiera and the switch from multibacteriocyte to a single-bacteriocyte mode of inheritance in this tribe.
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Affiliation(s)
- Diego Santos-Garcia
- Department of Entomology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Natividad Mestre-Rincon
- Department of Entomology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - David Ouvrard
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Entomology and Invasive Plants Unit, Plant Health Laboratory, ANSES, Montferrier-sur-Lez, France
| | - Einat Zchori-Fein
- Department of Entomology, Newe-Ya'ar Research Center, ARO, Ramat-Yishai, Israel
| | - Shai Morin
- Department of Entomology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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Gómez-Díaz JS, Montoya-Lerma J, Muñoz-Valencia V. Prevalence and Diversity of Endosymbionts in Cassava Whiteflies (Hemiptera: Aleyrodidae) From Colombia. JOURNAL OF INSECT SCIENCE (ONLINE) 2019; 19:5494810. [PMID: 31115477 PMCID: PMC6529905 DOI: 10.1093/jisesa/iez047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Indexed: 05/30/2023]
Abstract
Whiteflies cause huge economic losses for cassava (Manihot esculenta Crantz) cultivation. Damage can be caused directly when the insects feed on the phloem and/or indirectly by the transmission of viruses. It has been found that whiteflies maintain a close relationship with some endosymbiotic bacteria and that this interaction produces different effects on host biology and can also facilitate viral transmission. This study aimed to characterize the diversity of secondary endosymbionts (SE) present in whiteflies associated with cassava. Whitefly adults and nymphs were collected from cassava crops at nine locations in Southwestern Colombia. Molecular identification of insects and endosymbionts was carried out using specific mtCOI, wsp, 23s rRNA, and 16s rRNA primers. Phylogenetic trees were constructed from these sequences, both for whitefly species and the endosymbionts found. In addition, morphological identification of whitefly species was made using last instar nymphs. Molecular and morphological evaluation revealed that the most abundant whitefly species was Trialeurodes variabilis (Quaintance) followed by Aleurotrachelus socialis Bondar and Bemisia tuberculata Bondar. One hundred percent of the individuals contained the primary endosymbiont Portiera. The SE Rickettsia, Hamiltonella, Wolbachia, and Fritschea were not detected in the samples tested. Prevalence of Cardinium and Arsenophonus were variable at each locality, Cardinium being most prevalent in A. socialis adults. This study is the first report on the presence of Cardinium and Arsenophonus in A. socialis and T. variabilis. It is also the first report of endosymbiotic diversity in whiteflies associated with cassava in Colombia.
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11
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Ashfaq M, Hebert PDN. DNA barcodes for bio-surveillance: regulated and economically important arthropod plant pests. Genome 2016; 59:933-945. [PMID: 27753511 DOI: 10.1139/gen-2016-0024] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Many of the arthropod species that are important pests of agriculture and forestry are impossible to discriminate morphologically throughout all of their life stages. Some cannot be differentiated at any life stage. Over the past decade, DNA barcoding has gained increasing adoption as a tool to both identify known species and to reveal cryptic taxa. Although there has not been a focused effort to develop a barcode library for them, reference sequences are now available for 77% of the 409 species of arthropods documented on major pest databases. Aside from developing the reference library needed to guide specimen identifications, past barcode studies have revealed that a significant fraction of arthropod pests are a complex of allied taxa. Because of their importance as pests and disease vectors impacting global agriculture and forestry, DNA barcode results on these arthropods have significant implications for quarantine detection, regulation, and management. The current review discusses these implications in light of the presence of cryptic species in plant pests exposed by DNA barcoding.
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Affiliation(s)
- Muhammad Ashfaq
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada.,Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada.,Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
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The establishment of species-specific primers for the molecular identification of ten stored-product psocids based on ITS2 rDNA. Sci Rep 2016; 6:21022. [PMID: 26880378 PMCID: PMC4754681 DOI: 10.1038/srep21022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/14/2016] [Indexed: 11/23/2022] Open
Abstract
Psocids are important stored product pests found worldwide that can be spread through grain trade. Most stored-product psocids, including eggs, nymphs, and adults, are very small (~1 mm) and difficult to identify morphologically. Here, we collected 10 economically important stored-product Liposcelis spp. psocids (L. bostrychophila, L. entomophila, L. decolor, L. paeta, L. brunnea, L. corrodens, L. mendax, L. rufa, L. pearmani, and L. tricolor) from 35 geographical locations in 5 countries (China, Czech Republic, Denmark, Germany, and the United States). The ITS2 rDNA gene was extracted and sequenced. The interspecific genetic distance of the stored-product psocids was significantly higher than the intraspecific genetic distance according to the barcoding gap analysis. Ten pairs of species-specific primers based on the ITS2 rDNA were developed for psocid identification. The sensitivity estimation indicated that the species-specific primers could correctly amplify the target ITS2 gene and successfully identify psocids at 1.0 ng/mL. Additionally, these species-specific primers could quantify specificity and identify 10 stored-product psocids; this approach could also be used to accurately identify other stored-product psocids. This work provides a practical approach for the precise examination of 10 stored-product psocid species and also contributes to the development of an identification method using ITS2 rDNA.
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Löhr B, Vásquez-Ordóñez AA, Becerra Lopez-Lavalle LA. Rhynchophorus palmarum in Disguise: Undescribed Polymorphism in the "Black" Palm Weevil. PLoS One 2015; 10:e0143210. [PMID: 26683205 PMCID: PMC4684280 DOI: 10.1371/journal.pone.0143210] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 11/02/2015] [Indexed: 11/18/2022] Open
Abstract
During studies to adapt pheromone trapping of Rhynchophorus palmarum to the special coconut growing conditions at the Colombian Pacific coast, 152 atypically-colored specimens were captured in a total collection of 53,802 of the normally completely black weevil. Five specimens had the typical coloration of Rhynchophorus ferrugineus, an invasive species recently introduced to Aruba and Curação. A regional expansion of this invasion to the South American continent was feared and all atypical specimens were submitted to taxonomic analysis. Both conventional and molecular methods were employed. Conventional taxonomics confirmed the samples as belonging to R. palmarum but registered undescribed and species-atypical morphological variability in the subgular suture (wide vs. narrow), the ratio between intraocular distance and width of antennal scrobes (>0.35 vs. < 0.29) and the indentation of the mandibles (up to three mandibular teeth vs. bilobed). Molecular analysis placed all samples inspected, black and reddish alike, firmly within the R. palmarum group and the hypothesis of having inter-specific hybrids was rejected using co-dominant single sequence repeat markers with allelic specificity for both species.
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Affiliation(s)
- Bernhard Löhr
- Corporación Colombiana de Investigación Agropecuaria, Centro de Investigación Palmira, Palmira, Valle del Cauca, Colombia
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Oettl S, Schlink K. Molecular Identification of Two Vector Species, Cacopsylla melanoneura and Cacopsylla picta (Hemiptera: Psyllidae), of Apple Proliferation Disease and Further Common Psyllids of Northern Italy. JOURNAL OF ECONOMIC ENTOMOLOGY 2015; 108:2174-2183. [PMID: 26453706 DOI: 10.1093/jee/tov204] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 06/23/2015] [Indexed: 06/05/2023]
Abstract
The psyllid species Cacopsylla melanoneura (Förster) and Cacopsylla picta (Förster) are vectors of 'Candidatus Phytoplasma mali', the causal agent of apple proliferation, one of the economically most important apple diseases in Europe. Both vectors are present in apple orchards of South Tyrol and Trentino provinces in Northern Italy. As no direct treatment of the disease is possible, monitoring of the psyllids provides information about the vector presence in the orchards and enables targeted control. Thus, fast and reliable identification of the various psyllids occurring in the apple orchards is required. Morphological differentiation is problematic due to extensive resemblance of some psyllid species especially among females and is error-prone for nymphs. Here we present a rapid and cost-effective polymerase chain reaction-restriction fragment length polymorphism method based on the cytochrome c oxidase subunit I region for the molecular identification of the vector species as well as eight further Cacopsylla species present in the orchards. This method was verified through 98.9% consensus with morphologically identified males, through sequencing and subsequent phylogenetic analysis. In case of doubtful morphological identification of females, the method was able to provide a refined species assignment and could also remarkably facilitate the identification of nymphs.
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Affiliation(s)
- Sabine Oettl
- Functional Genomics Division, Research Centre for Agriculture and Forestry Laimburg, Laimburg 6, 39040 Auer/Ora (BZ), Italy.
| | - Katja Schlink
- Functional Genomics Division, Research Centre for Agriculture and Forestry Laimburg, Laimburg 6, 39040 Auer/Ora (BZ), Italy
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Identification of Eastern United States Reticulitermes Termite Species via PCR-RFLP, Assessed Using Training and Test Data. INSECTS 2015; 6:524-37. [PMID: 26463202 PMCID: PMC4553497 DOI: 10.3390/insects6020524] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 05/30/2015] [Accepted: 06/02/2015] [Indexed: 11/29/2022]
Abstract
Reticulitermes termites play key roles in dead wood decomposition and nutrient cycling in forests. They also damage man-made structures, resulting in considerable economic loss. In the eastern United States, five species (R. flavipes, R. virginicus, R. nelsonae, R. hageni and R. malletei) have overlapping ranges and are difficult to distinguish morphologically. Here we present a molecular tool for species identification. It is based on polymerase chain reaction (PCR) amplification of a section of the mitochondrial cytochrome oxidase subunit II gene, followed by a three-enzyme restriction fragment length polymorphism (RFLP) assay, with banding patterns resolved via agarose gel electrophoresis. The assay was designed using a large set of training data obtained from a public DNA sequence database, then evaluated using an independent test panel of Reticulitermes from the Southern Appalachian Mountains, for which species assignments were determined via phylogenetic comparison to reference sequences. After refining the interpretive framework, the PCR-RFLP assay was shown to provide accurate identification of four co-occurring species (the fifth species, R. hageni, was absent from the test panel, so accuracy cannot yet be extended to training data). The assay is cost- and time-efficient, and will help improve knowledge of Reticulitermes species distributions.
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