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Boucheffa S, Kheyar-Kraouche N, Djermouni M, Bettihi S, Sellal A, Cheraft N, Berboucha M, Rovellini P, Kelebek H, Tamendjari A. Extra Virgin Olive Oil's Main Components' Antioxidant Activity and in Silico Effect on AKT1. Chem Biodivers 2024:e202302074. [PMID: 38923341 DOI: 10.1002/cbdv.202302074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 06/08/2024] [Accepted: 06/21/2024] [Indexed: 06/28/2024]
Abstract
The study compared the chemical composition of various olive oils from the northern Algerian province of Bejaia. The research focused on the antioxidant activities of the oil's main constituents and their ability to inhibit the AKT1 protein, which is implicated in the development of colorectal cancer. The findings revealed that all of the examined oils fell within the extra virgin olive oil (EVOO) category and exhibited a high oleic acid content, particularly for samples from wild olives. These oils include high amount of ligstroside and oleocanthal, two important phenolic compounds. Wild olive oils stand out from cultivated ones due to their higher bitterness index. In addition, these oils have the highest concentrations of α-tocopherols and the best oxidative stability. Olive oil extracts demonstrated their antioxidant properties by neutralizing DPPH and ABTS radicals and converting ferric ions (Fe3+) to ferrous ions (Fe2+) for FRAP assay. Molecular docking was applied to assess the interaction between the main compounds identified in the analyzed olive oils and the human AKT1 protein, which is involved in the genesis of colorectal cancer. The findings revealed that lutein, oleuropein aglycone, and ligstroside aglycone had the highest binding affinity for the AKT1 protein. The present study could provide the theoretical foundation for further research on the interaction between AKT1 protein and EVOO compounds.
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Affiliation(s)
- Saliha Boucheffa
- Laboratory of Applied Biochemistry, Faculty of Natural and Life Sciences, University Ferhat Abbas Sétif, 19000, Sétif, Algeria
| | - Naouel Kheyar-Kraouche
- Laboratory of Plant Biotechnology and Ethnobotany, Faculty of Nature and Life Sciences, University A/Mira University, Bejaia, 06000, Algeria
| | - Meriem Djermouni
- Laboratory of Applied Biochemistry, Faculty of Natural and Life Sciences, University Ferhat Abbas Sétif, 19000, Sétif, Algeria
| | - Sarra Bettihi
- Département de biochimie, Faculté des Sciences de la Nature et de la Vie, Université de Ferhat Abbas, 19000, Sétif, Algérie
| | - Abdelhakim Sellal
- Naturel and Life Sciences Faculty, University of Sétif 1, Sétif, Algeria
- Laboratory of Health and Environment, El Bachir El Ibrahimi University of Bordj, Bou Arreridj, Algeria
| | - Nassima Cheraft
- Laboratoire de Biochimie Appliquée, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, 06000, Algérie
| | - Meriem Berboucha
- Laboratoire de Biochimie Appliquée, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, 06000, Algérie
| | - Pierangela Rovellini
- INNOVHUB - SSIAzienda Speciale dellaCamera di Commercio di MilanoDivisione SSOG - Milano
| | - Hasim Kelebek
- Department of Food Engineering, Faculty of Engineering and Natural Sciences, Adana Alparslan Turkes Science and Technology University, 01110, Adana, Turkey
| | - Abderezak Tamendjari
- Laboratoire de Biochimie Appliquée, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, 06000, Algérie
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Yao Y, Shi Y, Feng K, Du J, Chang Y, Xue Y, Li W. The mitochondrial genome of Homoneura picta (Diptera: Lauxaniidae) and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:828-831. [PMID: 38919812 PMCID: PMC11198121 DOI: 10.1080/23802359.2024.2333560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 03/15/2024] [Indexed: 06/27/2024] Open
Abstract
Homoneura picta belongs to the Homoneurinae subfamily of Lauxaniidae, and it is widely distributed and common in China. This study reports the newly sequenced mitochondrial genome of H. picta. The sequence is 15,469 bp long and contains 37 genes (13 protein-coding, 22 tRNA, and 2 rRNA genes) and a control region. The overall base composition is 38.4% for A, 37.7% for T, 14.1% for C, and 9.8% for G, with a bias toward A + T (76.1%). Phylogenetic analysis show that Homoneura is a sister genus of Cestrotus. We have successfully sequenced the mitochondrial genome of H. picta, which can be useful in investigating the phylogenetic status of Homoneurinae. Our results provide data for further studies of phylogeny in Diptera.
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Affiliation(s)
- Yao Yao
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Yedi Shi
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Keli Feng
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Jiaoyi Du
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Yiming Chang
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Yaoyao Xue
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Wenliang Li
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
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Nardi F, Boschi S, Funari R, Cucini C, Cardaioli E, Potter D, Asano SI, Toubarro D, Meier M, Paoli F, Carapelli A, Frati F. The direction, timing and demography of Popillia japonica (Coleoptera) invasion reconstructed using complete mitochondrial genomes. Sci Rep 2024; 14:7120. [PMID: 38531924 DOI: 10.1038/s41598-024-57667-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 03/20/2024] [Indexed: 03/28/2024] Open
Abstract
The Japanese beetle Popillia japonica is a pest insect that feeds on hundreds of species of wild and cultivated plants including important fruit, vegetable, and field crops. Native to Japan, the pest has invaded large areas of the USA, Canada, the Azores (Portugal), Italy, and Ticino (Switzerland), and it is considered a priority for control in the European Union. We determined the complete mitochondrial genome sequence in 86 individuals covering the entire distribution of the species. Phylogenetic analysis supports a major division between South Japan and Central/North Japan, with invasive samples coming from the latter. The origin of invasive USA samples is incompatible, in terms of the timing of the event, with a single introduction, with multiple Japanese lineages having been introduced and one accounting for most of the population expansion locally. The origin of the two invasive European populations is compatible with two different invasions followed by minimal differentiation locally. Population analyses provide the possibility to estimate the rate of sequence change from the data and to date major invasion events. Demographic analysis identifies a population expansion followed by a period of contraction prior to the invasion. The present study adds a time and demographic dimension to available reconstructions.
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Affiliation(s)
- Francesco Nardi
- Department of Life Sciences, University of Siena, via Aldo Moro 2, 53100, Siena, Italy.
- NBFC, National Biodiversity Future Center, Palermo, Italy.
- BAT-Center, Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, Portici, Italy.
| | - Sara Boschi
- Department of Life Sciences, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Rebecca Funari
- Department of Life Sciences, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Claudio Cucini
- Department of Life Sciences, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Elena Cardaioli
- Department of Life Sciences, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Daniel Potter
- Department of Entomology, University of Kentucky, Lexington, USA
| | - Shin-Ichiro Asano
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Duarte Toubarro
- Biotechnology Centre of Azores, University of the Azores, Ponta Delgada, Portugal
| | - Michela Meier
- Servizio fitosanitario cantonale, Dipartimento delle finanze e dell'economia, Bellinzona, Switzerland
| | - Francesco Paoli
- Council for Agricultural Research and Agricultural Economy Analysis (CREA), Florence, Italy
| | - Antonio Carapelli
- Department of Life Sciences, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- BAT-Center, Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, Portici, Italy
| | - Francesco Frati
- Department of Life Sciences, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- BAT-Center, Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, Portici, Italy
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Vizzarri V, Lombardo L, Novellis C, Rizzo P, Pellegrino M, Cruceli G, Godino G, Zaffina F, Ienco A. Testing the Single and Combined Effect of Kaolin and Spinosad against Bactrocera oleae and Its Natural Antagonist Insects in an Organic Olive Grove. Life (Basel) 2023; 13:life13030607. [PMID: 36983763 PMCID: PMC10056781 DOI: 10.3390/life13030607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/10/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
The presence and infestation level of Bactrocera oleae was monitored in an organic olive orchard divided into differently treated parcels with kaolin (K), spinosad (S) and with kaolin and spinosad (K + S) in alternate rows. The treatments did not seem to affect olive fruit fly population dynamics, while statistically significant protective effects were recorded against total and harmful infestation, but not against the active one. Eventually, neither kaolin nor spinosad were shown to have a particular detrimental effect against naturally occurring B. oleae parasitoids.
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Vast Gene Flow among the Spanish Populations of the Pest Bactrocera oleae (Diptera, Tephritidae), Phylogeography of a Metapopulation to Be Controlled and Its Mediterranean Genetic Context. INSECTS 2022; 13:insects13070642. [PMID: 35886818 PMCID: PMC9322173 DOI: 10.3390/insects13070642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/10/2022] [Accepted: 07/15/2022] [Indexed: 02/04/2023]
Abstract
Simple Summary The output of olive industry at the Mediterranean Basin, headed by Spain, is huge worldwide. The olive fruit fly Bactrocera oleae is the major pest of olive orchards. The damages it causes become in considerable economic losses as well as a decrease in oil quantity and quality. A key question for the success of pest control strategies is the further knowledge about the species, and genetic data becomes essential for this purpose. The present work analyses more than 250 fruit flies from six different Mediterranean countries, showing relevant data about the genetic structure and gene flow of this damaging pest. These findings are helpful to improve the integrated pest management strategies according to the current European Guidelines. Abstract Spain is the leading producer of olives and olive oil. Ninety-five percent of world production originate from Spain and other regions of the Mediterranean Basin. However, these olive-growing countries face a major problem, the harmful fly Bactrocera oleae, the main pest of olive crops. To improve its control, one of the challenges is the further knowledge of the species and populations dynamics in this area. A phylogeographic work is necessary to further characterise the levels and distribution patterns of genetic diversity of the Spanish populations and their genetic relationships with other Mediterranean populations. A 1151 bp fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene has been analysed in over 250 specimens of the six main Mediterranean countries via sequencing. Genetic diversity parameters were high; 51 new haplotypes have been identified showing a geographical pattern across the Mediterranean area. The data revealed that olive fruit fly populations have been long time established in the Mediterranean Basin with two genetic groups. Gene flow seems to be the main process in shaping this genetic structure as well as fly’s colonisation routes that have paralleled those of the olive tree.
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Xu Y, Dong Y, Cheng W, Wu K, Gao H, Liu L, Xu L, Gong B. Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Diospyros oleifera, the first representative from the family Ebenaceae. Heliyon 2022; 8:e09870. [PMID: 35847622 PMCID: PMC9283892 DOI: 10.1016/j.heliyon.2022.e09870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/18/2022] [Accepted: 06/30/2022] [Indexed: 01/30/2023] Open
Abstract
Plant mitochondrial genomes are a valuable source of genetic information for a better understanding of phylogenetic relationships. However, no mitochondrial genome of any species in Ebenaceae has been reported. In this study, we reported the first mitochondrial genome of an Ebenaceae model plant Diospyros oleifera. The mitogenome was 493,958 bp in length, contained 39 protein-coding genes, 27 transfer RNA genes, and 3 ribosomal RNA genes. The rps2 and rps11 genes were missing in the D. oleifera mt genome, while the rps10 gene was identified. The length of the repetitive sequence in the D. oleifera mt genome was 31 kb, accounting for 6.33%. A clear bias in RNA-editing sites were found in the D. oleifera mt genome. We also detected 28 chloroplast-derived fragments significantly associated with D. oleifera mt genes, indicating intracellular tRNA genes transferred frequently from chloroplasts to mitochondria in D. oleifera. Phylogenetic analysis based on the mt genomes of D. oleifera and 27 other taxa reflected the exact evolutionary and taxonomic status of D. oleifera. Ka/Ks analysis revealed that 95.16% of the protein-coding genes in the D. oleifera mt genome had undergone negative selections. But, the rearrangement of mitochondrial genes has been widely occur among D. oleifera and these observed species. These results will lay the foundation for identifying further evolutionary relationships within Ebenaceae.
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Affiliation(s)
- Yang Xu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
| | - Yi Dong
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
| | - Wenqiang Cheng
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
| | - Kaiyun Wu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
| | - Haidong Gao
- Genepioneer Biotechnologies Co. Ltd, Nanjing, 210023, China
| | - Lei Liu
- Genepioneer Biotechnologies Co. Ltd, Nanjing, 210023, China
| | - Lei Xu
- Genepioneer Biotechnologies Co. Ltd, Nanjing, 210023, China
| | - Bangchu Gong
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
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7
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The Impact of Fast Radiation on the Phylogeny of Bactrocera Fruit Flies as Revealed by Multiple Evolutionary Models and Mutation Rate-Calibrated Clock. INSECTS 2022; 13:insects13070603. [PMID: 35886779 PMCID: PMC9319077 DOI: 10.3390/insects13070603] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/22/2022] [Accepted: 06/28/2022] [Indexed: 11/16/2022]
Abstract
Several true fruit flies (Tephritidae) cause major damage to agriculture worldwide. Among them, species of the genus Bactrocera are extensively studied to understand the traits associated with their invasiveness and ecology. Comparative approaches based on a reliable phylogenetic framework are particularly effective, but several nodes of the Bactrocera phylogeny are still controversial, especially concerning the reciprocal affinities of the two major pests B. dorsalis and B. tryoni. Here, we analyzed a newly assembled genomic-scaled dataset using different models of evolution to infer a phylogenomic backbone of ten representative Bactrocera species and two outgroups. We further provide the first genome-scaled inference of their divergence by calibrating the clock using fossil records and the spontaneous mutation rate. The results reveal a closer relationship of B. dorsalis with B. latifrons than to B. tryoni, contrary to what was previously supported by mitochondrial-based phylogenies. By employing coalescent-aware and heterogeneous evolutionary models, we show that this incongruence likely derives from a hitherto undetected systematic error, exacerbated by incomplete lineage sorting and possibly hybridization. This agrees with our clock analysis, which supports a rapid and recent radiation of the clade to which B. dorsalis, B. latifrons and B. tryoni belong. These results provide a new picture of Bactrocera phylogeny that can serve as the basis for future comparative analyses.
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Kawai K, Fujita H, Umino T. The complete mitochondrial genome of Acanthopagrus pacificus (Perciformes, Sparidae) from Iriomotejima Island, Okinawa, Japan. Mitochondrial DNA B Resour 2022; 7:1027-1029. [PMID: 35756456 PMCID: PMC9225699 DOI: 10.1080/23802359.2022.2080606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Kentaro Kawai
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Hiroki Fujita
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Tetsuya Umino
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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Nobre T. Olive fruit fly and its obligate symbiont Candidatus Erwinia dacicola: Two new symbiont haplotypes in the Mediterranean basin. PLoS One 2021; 16:e0256284. [PMID: 34495983 PMCID: PMC8425570 DOI: 10.1371/journal.pone.0256284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/03/2021] [Indexed: 11/19/2022] Open
Abstract
The olive fruit fly, specialized to become monophagous during several life stages, remains the most important olive tree pest with high direct production losses, but also affecting the quality, composition, and inherent properties of the olives. Thought to have originated in Africa is nowadays present wherever olive groves are grown. The olive fruit fly evolved to harbor a vertically transmitted and obligate bacterial symbiont -Candidatus Erwinia dacicola- leading thus to a tight evolutionary history between olive tree, fruit fly and obligate, vertical transmitted symbiotic bacterium. Considering this linkage, the genetic diversity (at a 16S fragment) of this obligate symbiont was added in the understanding of the distribution pattern of the holobiont at nine locations throughout four countries in the Mediterranean Basin. This was complemented with mitochondrial (four mtDNA fragments) and nuclear (ten microsatellites) data of the host. We focused on the previously established Iberian cluster for the B. oleae structure and hypothesised that the Tunisian samples would fall into a differentiated cluster. From the host point of view, we were unable to confirm this hypothesis. Looking at the symbiont, however, two new 16S haplotypes were found exclusively in the populations from Tunisia. This finding is discussed in the frame of host-symbiont specificity and transmission mode. To understand olive fruit fly population diversity and dispersion, the dynamics of the symbiont also needs to be taken into consideration, as it enables the fly to, so efficiently and uniquely, exploit the olive fruit resource.
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Affiliation(s)
- Tânia Nobre
- MED - Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada, Universidade de Évora, Pólo da Mitra, Évora, Portugal
- * E-mail:
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10
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Cucini C, Leo C, Iannotti N, Boschi S, Brunetti C, Pons J, Fanciulli PP, Frati F, Carapelli A, Nardi F. EZmito: a simple and fast tool for multiple mitogenome analyses. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1101-1109. [PMID: 33796755 PMCID: PMC7995877 DOI: 10.1080/23802359.2021.1899865] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Complete mitochondrial genome data are frequently applied to address phylogenetic/phylogeographic issues at different taxonomic levels in ecology and evolution. While sample preparation/sequencing is becoming more and more straightforward thanks to dropping costs for next-generation sequencing (NGS), data preparation and visualization remains a manually intensive step that may lead to errors if improperly conducted. We have elaborated, and here introduce, EZmito, a simple and intuitive, freely accessible Web Server aimed at automating some of these tasks. EZmito is divided into three main tools: EZpipe that assembles DNA matrices for phylo-mitogenomic analyses; EZskew that calculates genome, strand, and codon nucleotide compositional skews and EZcodon which computes Relative Synonymous Codon Usage statistics as well as amino acid usage frequency over multiple mitogenomes. Output is produced in tabular format as well as publication-quality graphics.
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Affiliation(s)
- Claudio Cucini
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Chiara Leo
- Department of Life Sciences, Imperial College London, London, UK
| | - Nicola Iannotti
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Sara Boschi
- Department of Life Sciences, University of Siena, Siena, Italy
| | | | - Joan Pons
- Department de Biodiversitat Animal i Microbiana, Institut Mediterrani d'Estudis Avancats, Esporles, Spain
| | | | - Francesco Frati
- Department of Life Sciences, University of Siena, Siena, Italy
| | | | - Francesco Nardi
- Department of Life Sciences, University of Siena, Siena, Italy
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Wang X, Walton VM, Hoelmer KA, Pickett CH, Blanchet A, Straser RK, Kirk AA, Daane KM. Exploration for olive fruit fly parasitoids across Africa reveals regional distributions and dominance of closely associated parasitoids. Sci Rep 2021; 11:6182. [PMID: 33731743 PMCID: PMC7971055 DOI: 10.1038/s41598-021-85253-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/24/2021] [Indexed: 11/09/2022] Open
Abstract
The olive fruit fly, Bactrocera oleae, has been a key pest of olives in Europe and North America. We conducted the largest exploration for parasitoids associated with the fly across Sub-Saharan Africa (Kenya, Namibia, and South Africa) including some of the fly’s adjoining regions (Canary Islands, Morocco, Réunion Island and Tunisia). From Sub-Saharan regions, four braconids were collected: Bracon celer, Psytallia humilis, P. lounsburyi, and Utetes africanus. Results showed that their regional dominance was related to climate niches, with P. humilis dominant in hot semi-arid areas of Namibia, P. lounsburyi dominant in more tropical areas of Kenya, and U. africanus prevalent in Mediterranean climates of South Africa. Psytallia concolor was found in the Canary Islands, Morocco and Tunisian, and the Afrotropical braconid Diachasmimorpha sp. near fullawayi on Réunion Island. Furthermore, we monitored the seasonal dynamics of the fly and parasitoids in Cape Province of South Africa. Results showed that fruit maturity, seasonal variations in climates and interspecific interactions shape the local parasitoid diversity that contribute to the low fly populations. The results are discussed with regard to ecological adaptations of closely associated parasitoids, and how their adaptations impact biocontrol.
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Affiliation(s)
- Xingeng Wang
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720, USA. .,USDA-ARS Beneficial Insects Introduction Research Unit, Newark, DE, 19713, USA.
| | - Vaughn M Walton
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720, USA.,Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
| | - Kim A Hoelmer
- USDA-ARS, European Biological Control Laboratory, Montferrier, France.,USDA-ARS Beneficial Insects Introduction Research Unit, Newark, DE, 19713, USA
| | - Charles H Pickett
- California Department of Food and Agriculture, Sacramento, CA, 95832, USA
| | - Arnaud Blanchet
- USDA-ARS, European Biological Control Laboratory, Montferrier, France
| | - Robert K Straser
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720, USA.,Department of Entomology, University of California, Riverside, Riverside, CA, 92521, USA
| | - Alan A Kirk
- USDA-ARS, European Biological Control Laboratory, Montferrier, France
| | - Kent M Daane
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720, USA.
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Powell C, Caleca V, Rhode C, Teixeira da Costa L, van Asch B. New Mitochondrial Gene Rearrangement in Psyttalia concolor, P. humilis and P. lounsburyi (Hymenoptera: Braconidae), Three Parasitoid Species of Economic Interest. INSECTS 2020; 11:E854. [PMID: 33276418 PMCID: PMC7761351 DOI: 10.3390/insects11120854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/02/2022]
Abstract
The family Braconidae consists mostly of specialized parasitoids, some of which hold potential in biocontrol of agricultural pests. Psyttalia concolor, Psyttalia humilis and Psyttalia lounsburyi are parasitoids associated with Bactrocera oleae, a major pest of cultivated olives. The native range of Psyttalia concolor is the Mediterranean, and P. humilis and P. lounsburyi are native to sub-Saharan Africa. This study reports the mitochondrial genomes of the three species, thus laying the foundation for mitogenomic analyses in the genus Psyttalia. Comparative mitogenomics within Braconidae showed a novel gene arrangement in Psyttalia in involving translocation and inversion of transfer RNA genes. The placement of Psyttalia in the subfamily Opiinae was well-supported, and the divergence between Psyttalia and its closest relative (Diachasmimorpha longicaudata) was at ~55 MYA [95% highest posterior density (HPD): 34-83 MYA]. Psyttalia lounsburyi occupied the most basal position among the three Psyttalia, having diverged from the other two species ~11 MYA (95% HPD: 6-17 MYA). Psyttalia concolor and P. humilis were recovered as sister species diverged at ~2 MYA (95% HPD: 1.1-3.6 MYA). This phylogeny combining new sequences and a set of 31 other cyclostomes and non-cyclostomes highlights the importance of a comprehensive taxonomic coverage of Braconidae mitogenomes to overcome the lack of robustness in the placement of several subfamilies.
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Affiliation(s)
- Chanté Powell
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; (C.P.); (C.R.)
| | - Virgilio Caleca
- Department of Agricultural, Food and Forest Sciences, Università degli Studi di Palermo, Viale delle Scienze, Edificio 5, 90128 Palermo, Italy;
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; (C.P.); (C.R.)
| | - Luis Teixeira da Costa
- Unit for Cardiac and Cardiovascular Genetics, Department of Medical Genetics, Oslo University Hospital, Postboks 4956 Nydalen, 0424 Oslo, Norway
- Norsk Entomologisk Forening, Naturhistorisk Museum, Universitetet i Oslo, Postboks 1172 Blindern, 0318 Oslo, Norway
| | - Barbara van Asch
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; (C.P.); (C.R.)
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Blacket MJ, Agarwal A, Zheng L, Cunningham JP, Britton D, Schneider I, Rodoni BC. A LAMP assay for the detection of Bactrocera tryoni Queensland fruit fly (Diptera: Tephritidae). Sci Rep 2020; 10:9554. [PMID: 32533005 PMCID: PMC7293347 DOI: 10.1038/s41598-020-65715-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/29/2020] [Indexed: 11/30/2022] Open
Abstract
LAMP assays are targeted molecular tests for the rapid detection of species in the laboratory and field. We developed a LAMP assay for an economically important fruit fly species, Queensland fruit fly, Bactrocera tryoni. This assay was assessed against a broad panel of target and non-target species and found to be specific, only amplifying the target species and closest relatives, in a portable real-time fluorometer (Genie III) in under 15 minutes with an anneal derivative temperature of 82.5 oC. The assay is sensitive to low levels of target DNA (>0.016 ng/µl), performing equally to the existing qPCR test. To enable retention of a physical voucher specimen, for potential morphological confirmation of LAMP results, a novel whole-specimen non-destructive DNA extraction method was developed, suitable for LAMP in the field. The stability of DNA extraction and LAMP reagents was tested under simulated and actual field conditions and shown to be robust. Our new assay now provides a portable molecular tool for the detection of this significant tephritid fruit fly pest species of biosecurity/quarantine concern. This has already proven invaluable for in-field diagnostics, providing real-time support influencing immediate actions, with negative results allowing the release of fruit produce, and positive results initiating fruit fly control measures.
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Affiliation(s)
- Mark J Blacket
- Agriculture Victoria Research, AgriBio, 5 Ring Road, Bundoora, Victoria, 3083, Australia.
| | - Arati Agarwal
- Agriculture Victoria Research, AgriBio, 5 Ring Road, Bundoora, Victoria, 3083, Australia
| | - Linda Zheng
- Agriculture Victoria Research, AgriBio, 5 Ring Road, Bundoora, Victoria, 3083, Australia
| | - J Paul Cunningham
- Agriculture Victoria Research, AgriBio, 5 Ring Road, Bundoora, Victoria, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3083, Australia
| | - David Britton
- Department of Agriculture, Water and the Environment, Northern Australian Quarantine Strategy (NAQS), Cairns, Queensland, 4870, Australia
| | - Isarena Schneider
- Department of Agriculture, Water and the Environment, Northern Australian Quarantine Strategy (NAQS), Cairns, Queensland, 4870, Australia
| | - Brendan C Rodoni
- Agriculture Victoria Research, AgriBio, 5 Ring Road, Bundoora, Victoria, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3083, Australia
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14
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Hidden Genetic Variability, Can the Olive Moth Prays oleae (Lepidoptera: Yponomeutidae or Praydidae?) be a Species' Complex? INSECTS 2020; 11:insects11040204. [PMID: 32225064 PMCID: PMC7240722 DOI: 10.3390/insects11040204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/14/2020] [Accepted: 03/16/2020] [Indexed: 11/17/2022]
Abstract
Prays oleae is the second most important pest in Mediterranean olive groves, causing substantial damage on olive production. We used mitochondrial [cytochrome c oxidase subunit I (COI), and NADH dehydrogenase subunit 5 (nad5)] and nuclear [ribosomal protein S5 (RpS5)] amplicons to assess the population variability in five main olive producing regions from Tunisia, to support or dismiss the existence of two non-monophyletic groups within the species, as found within Portugal. Our phylogenetic analysis with cytochrome c oxidase subunit I (COI) indeed displayed two distinct and well-supported clades of P. oleae, which were corroborated by the haplotype network reconstructed with both mitochondrial and nuclear amplicons. We were also able to dismiss the hypothesis that one of the clades would not develop on olive fruits. No correlation was observed between clades differentiation and geographic distribution. The existence of cryptic species can impact on the management of agroecosystems and on the perception of how these moths responds to environmental changes.
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15
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Krosch MN, Strutt F, Blacket MJ, Batovska J, Starkie M, Clarke AR, Cameron SL, Schutze MK. Development of internal COI primers to improve and extend barcoding of fruit flies (Diptera: Tephritidae: Dacini). INSECT SCIENCE 2020; 27:143-158. [PMID: 29873880 DOI: 10.1111/1744-7917.12612] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 04/30/2018] [Accepted: 05/17/2018] [Indexed: 06/08/2023]
Abstract
Accurate species-level identifications underpin many aspects of basic and applied biology; however, identifications can be hampered by a lack of discriminating morphological characters, taxonomic expertise or time. Molecular approaches, such as DNA "barcoding" of the cytochrome c oxidase (COI) gene, are argued to overcome these issues. However, nuclear encoding of mitochondrial genes (numts) and poor amplification success of suboptimally preserved specimens can lead to erroneous identifications. One insect group for which these molecular and morphological problems are significant are the dacine fruit flies (Diptera: Tephritidae: Dacini). We addressed these issues associated with COI barcoding in the dacines by first assessing several "universal" COI primers against public mitochondrial genome and numt sequences for dacine taxa. We then modified a set of four primers that more closely matched true dacine COI sequence and amplified two overlapping portions of the COI barcode region. Our new primers were tested alongside universal primers on a selection of dacine species, including both fresh preserved and decades-old dry specimens. Additionally, Bactrocera tryoni mitochondrial and nuclear genomes were compared to identify putative numts. Four numt clades were identified, three of which were amplified using existing universal primers. In contrast, our new primers preferentially amplified the "true" mitochondrial COI barcode in all dacine species tested. The new primers also successfully amplified partial barcodes from dry specimens for which full length barcodes were unobtainable. Thus we recommend these new primers be incorporated into the suites of primers used by diagnosticians and quarantine labs for the accurate identification of dacine species.
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Affiliation(s)
- Matt N Krosch
- School of Earth, Environmental & Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Plant Biosecurity Co-operative Research Centre, Bruce, Australian Capital Territory, Australia
| | - Francesca Strutt
- School of Earth, Environmental & Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Plant Biosecurity Co-operative Research Centre, Bruce, Australian Capital Territory, Australia
| | - Mark J Blacket
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Jana Batovska
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Melissa Starkie
- School of Earth, Environmental & Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Anthony R Clarke
- School of Earth, Environmental & Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Stephen L Cameron
- School of Earth, Environmental & Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Plant Biosecurity Co-operative Research Centre, Bruce, Australian Capital Territory, Australia
- Department of Entomology, Purdue University, West Lafayette, Indiana, USA
| | - Mark K Schutze
- School of Earth, Environmental & Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Plant Biosecurity Co-operative Research Centre, Bruce, Australian Capital Territory, Australia
- Department of Agriculture & Fisheries, Queensland Primary Industries Insect Collection (QDPC), Dutton Park, Queensland, Australia
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16
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Solecki AM, Skevington JH, Buddle CM, Wheeler TA. Phylogeography of higher Diptera in glacial and postglacial grasslands in western North America. BMC Ecol 2019; 19:53. [PMID: 31861996 PMCID: PMC6923875 DOI: 10.1186/s12898-019-0266-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 11/22/2019] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Pleistocene glaciations have had an important impact on the species distribution and community composition of the North American biota. Species survived these glacial cycles south of the ice sheets and/or in other refugia, such as Beringia. In this study, we assessed, using mitochondrial DNA from three Diptera species, whether flies currently found in Beringian grasslands (1) survived glaciation as disjunct populations in Beringia and in the southern refugium; (2) dispersed northward postglacially from the southern refugium; or (3) arose by a combination of the two. Samples were collected in grasslands in western Canada: Prairies in Alberta and Manitoba; the Peace River region (Alberta); and the southern Yukon Territory. We sequenced two gene regions (658 bp of cytochrome c oxidase subunit I, 510 bp of cytochrome b) from three species of higher Diptera: one with a continuous distribution across grassland regions, and two with disjunct populations between the regions. We used a Bayesian approach to determine population groupings without a priori assumptions and performed analysis of molecular variance (AMOVA) and exact tests of population differentiation (ETPD) to examine their validity. Molecular dating was used to establish divergence times. RESULTS Two geographically structured populations were found for all species: a southern Prairie and Peace River population, and a Yukon population. Although AMOVA did not show significant differentiation between populations, ETPD did. Divergence time between Yukon and southern populations predated the Holocene for two species; the species with an ambiguous divergence time had high haplotype diversity, which could suggest survival in a Beringian refugium. CONCLUSIONS Populations of Diptera in Yukon grasslands could have persisted in steppe habitats in Beringia through Pleistocene glaciations. Current populations in the region appear to be a mix of Beringian relict populations and, to a lesser extent, postglacial dispersal northward from southern prairie grasslands.
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Affiliation(s)
- Anna M. Solecki
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1 Canada
- Natural Resource Sciences, McGill University, Macdonald Campus, Ste-Anne-De-Bellevue, QC H9X 3V9 Canada
| | - Jeffrey H. Skevington
- Agriculture and Agri-Food Canada, Canadian National Collection of Insects, Arachnids, and Nematodes, 960 Carling Ave, Ottawa, ON K1A 0C6 Canada
| | - Christopher M. Buddle
- Natural Resource Sciences, McGill University, Macdonald Campus, Ste-Anne-De-Bellevue, QC H9X 3V9 Canada
| | - Terry A. Wheeler
- Natural Resource Sciences, McGill University, Macdonald Campus, Ste-Anne-De-Bellevue, QC H9X 3V9 Canada
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17
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Choo A, Nguyen TNM, Ward CM, Chen IY, Sved J, Shearman D, Gilchrist AS, Crisp P, Baxter SW. Identification of Y-chromosome scaffolds of the Queensland fruit fly reveals a duplicated gyf gene paralogue common to many Bactrocera pest species. INSECT MOLECULAR BIOLOGY 2019; 28:873-886. [PMID: 31150140 DOI: 10.1111/imb.12602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/22/2019] [Accepted: 05/28/2019] [Indexed: 06/09/2023]
Abstract
Bactrocera tryoni (Queensland fruit fly) are polyphagous horticultural pests of eastern Australia. Heterogametic males contain a sex-determining Y-chromosome thought to be gene poor and repetitive. Here, we report 39 Y-chromosome scaffolds (~700 kb) from B. tryoni identified using genotype-by-sequencing data and whole-genome resequencing. Male diagnostic PCR assays validated eight Y-scaffolds, and one (Btry4096) contained a novel gene with five exons that encode a predicted 575 amino acid protein. The Y-gene, referred to as typo-gyf, is a truncated Y-chromosome paralogue of X-chromosome gene gyf (1773 aa). The Y-chromosome contained ~41 copies of typo-gyf, and expression occurred in male flies and embryos. Analysis of 13 tephritid transcriptomes confirmed typo-gyf expression in six additional Bactrocera species, including Bactrocera latifrons, Bactrocera dorsalis and Bactrocera zonata. Molecular dating estimated typo-gyf evolved within the past 8.02 million years (95% highest posterior density 10.56-5.52 million years), after the split with Bactrocera oleae. Phylogenetic analysis also highlighted complex evolutionary histories among several Bactrocera species, as discordant nuclear (116 genes) and mitochondrial (13 genes) topologies were observed. B. tryoni Y-sequences may provide useful sites for future transgene insertions, and typo-gyf could act as a Y-chromosome diagnostic marker for many Bactrocera species, although its function is unknown.
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Affiliation(s)
- Amanda Choo
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Thu N M Nguyen
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Christopher M Ward
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Isabel Y Chen
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- South Australian Research and Development Institute, Adelaide, South Australia, Australia
| | - John Sved
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Deborah Shearman
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Anthony S Gilchrist
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Peter Crisp
- South Australian Research and Development Institute, Adelaide, South Australia, Australia
| | - Simon W Baxter
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
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18
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Drosopoulou E, Syllas A, Goutakoli P, Zisiadis GA, Konstantinou T, Pangea D, Sentis G, van Sauers-Muller A, Wee SL, Augustinos AA, Zacharopoulou A, Bourtzis K. Τhe Complete Mitochondrial Genome of Bactrocera carambolae (Diptera: Tephritidae): Genome Description and Phylogenetic Implications. INSECTS 2019; 10:E429. [PMID: 31795125 PMCID: PMC6955806 DOI: 10.3390/insects10120429] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 11/15/2019] [Accepted: 11/21/2019] [Indexed: 01/09/2023]
Abstract
Bactrocera carambolae is one of the approximately 100 sibling species of the Bactrocera dorsalis complex and considered to be very closely related to B. dorsalis. Due to their high morphological similarity and overlapping distribution, as well as to their economic impact and quarantine status, the development of reliable markers for species delimitation between the two taxa is of great importance. Here we present the complete mitochondrial genome of B. carambolae sourced from its native range in Malaysia and its invaded territory in Suriname. The mitogenome of B. carambolae presents the typical organization of an insect mitochondrion. Comparisons of the analyzed B. carambolae sequences to all available complete mitochondrial sequences of B. dorsalis revealed several species-specific polymorphic sites. Phylogenetic analysis based on Bactrocera mitogenomes supports that B. carambolae is a differentiated taxon though closely related to B. dorsalis. The present complete mitochondrial sequences of B. carambolae could be used, in the frame of Integrative Taxonomy, for species discrimination and resolution of the phylogenetic relationships within this taxonomically challenging complex, which would facilitate the application of species-specific population suppression strategies, such as the sterile insect technique.
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Affiliation(s)
- Elena Drosopoulou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.S.); (P.G.); (G.-A.Z.); (T.K.); (D.P.); (G.S.)
| | - Alexandros Syllas
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.S.); (P.G.); (G.-A.Z.); (T.K.); (D.P.); (G.S.)
| | - Panagiota Goutakoli
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.S.); (P.G.); (G.-A.Z.); (T.K.); (D.P.); (G.S.)
| | - Georgios-Alkis Zisiadis
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.S.); (P.G.); (G.-A.Z.); (T.K.); (D.P.); (G.S.)
| | - Theodora Konstantinou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.S.); (P.G.); (G.-A.Z.); (T.K.); (D.P.); (G.S.)
| | - Dimitra Pangea
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.S.); (P.G.); (G.-A.Z.); (T.K.); (D.P.); (G.S.)
| | - George Sentis
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.S.); (P.G.); (G.-A.Z.); (T.K.); (D.P.); (G.S.)
| | - Alies van Sauers-Muller
- Consultant, retired from Ministry of Agriculture, Animal Husbandry and Fisheries, Carambola Fruit Fly Project, Damboentong 282, Tijgerkreek, Saramacca, Suriname;
| | - Suk-Ling Wee
- Center for Insect Systematics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia;
| | - Antonios A. Augustinos
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, A-1400 Vienna, Austria; (A.A.A.); (K.B.)
| | | | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, A-1400 Vienna, Austria; (A.A.A.); (K.B.)
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19
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The first two complete mitochondrial genome of Dacus bivittatus and Dacus ciliatus (Diptera: Tephritidae) by next-generation sequencing and implications for the higher phylogeny of Tephritidae. Int J Biol Macromol 2019; 140:469-476. [DOI: 10.1016/j.ijbiomac.2019.08.076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 07/22/2019] [Accepted: 08/07/2019] [Indexed: 11/18/2022]
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20
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Mitochondrial Genome Diversity in Collembola: Phylogeny, Dating and Gene Order. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11090169] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Collembola (springtails) are an early diverging class of apterygotes, and mark the first substantial radiation of hexapods on land. Despite extensive work, the relationships between major collembolan lineages are still debated and, apart from the Early Devonian fossil Rhyniella praecursor, which demonstrates their antiquity, the time frame of springtail evolution is unknown. In this study, we sequence two new mitochondrial genomes and reanalyze all known Collembola mt-genomes, including selected metagenomic data, to produce an improved phylogenetic hypothesis for the group, develop a tentative time frame for their differentiation, and provide a comprehensive overview of gene order diversity. Our analyses support most taxonomically recognized entities. We find support for an Entomobryomorpha + Symphypleona clade, while the position of Neelipleona could not be assessed with confidence. A Silurian time frame for their basal diversification is recovered, with an indication that divergence times may be fairly old overall. The distribution of mitochondrial gene order indicates the pancrustacean arrangement as plesiomorphic and dominant in the group, with the exception of the family Onychiuridae. We distinguished multiple instances of different arrangements in individual genomes or small clusters. We further discuss the opportunities and drawbacks associated with the inclusion of metagenomic data in a classic study on mitochondrial genome diversity.
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21
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Güler A, Karakoç E, Gökdere G, Doğaç E, Taşkin V. Genetic structure of Mediterranean fruit fly (Diptera: Tephritidae) populations from Turkey revealed by mitochondrial DNA markers. J Genet 2019. [DOI: 10.1007/s12041-019-1106-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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The complete mitochondrial genome of Bactrocera biguttula (Bezzi) (Diptera: Tephritidae) and phylogenetic relationships with other Dacini. Int J Biol Macromol 2019; 126:130-140. [DOI: 10.1016/j.ijbiomac.2018.12.186] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 11/19/2022]
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23
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Powell C, Caleca V, Sinno M, van Staden M, van Noort S, Rhode C, Allsopp E, van Asch B. Barcoding of parasitoid wasps (Braconidae and Chalcidoidea) associated with wild and cultivated olives in the Western Cape of South Africa. Genome 2019; 62:183-199. [DOI: 10.1139/gen-2018-0068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Wild and cultivated olives harbor and share a diversity of insects, some of which are considered agricultural pests, such as the olive fruit fly. The assemblage of olive-associated parasitoids and seed wasps is rich and specialized in sub-Saharan Africa, with native species possibly coevolving with their hosts. Although historical entomological surveys reported on the diversity of olive wasp species in the Western Cape Province of South Africa, no comprehensive study has been performed in the region in the molecular era. In this study, a dual approach combining morphological and DNA-based methods was used for the identification of adult specimens reared from olive fruits. Four species of Braconidae and six species of Chalcidoidea were identified, and DNA barcoding methodologies were used to investigate conspecificity among individuals, based on randomly selected representative specimens. Morphological identifications were congruent with DNA data, as NJ and ML trees correctly placed the sequences for each species either at the genus or species level, depending on the available taxa coverage, and genetic distances strongly supported conspecificity. No clear evidence of cryptic diversity was found. Overall seed infestation and parasitism rates were higher in wild olives compared to cultivated olives, and highest for Eupelmus spermophilus and Utetes africanus. These results can be used for early DNA-based detection of wasp larvae in olives and to further investigate the biology and ecology of these species.
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Affiliation(s)
- Chante Powell
- Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa
| | - Virgilio Caleca
- Department of Agricultural and Forestry Sciences, University of Palermo, Italy
| | - Martina Sinno
- Department of Agricultural Sciences, University of Naples “Federico II”, Naples, Italy
| | - Michaela van Staden
- Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa
| | - Simon van Noort
- Division of Entomology, Department of Natural History, Iziko South African Museum, Cape Town, South Africa
| | - Clint Rhode
- Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa
| | - Elleunorah Allsopp
- Agricultural Research Council, Infruitec-Nietvoorbij, Stellenbosch, South Africa
| | - Barbara van Asch
- Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa
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Estes AM, Hearn DJ, Agrawal S, Pierson EA, Dunning Hotopp JC. Comparative genomics of the Erwinia and Enterobacter olive fly endosymbionts. Sci Rep 2018; 8:15936. [PMID: 30374192 PMCID: PMC6205999 DOI: 10.1038/s41598-018-33809-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 10/04/2018] [Indexed: 11/09/2022] Open
Abstract
The pestivorous tephritid olive fly has long been known as a frequent host of the obligately host-associated bacterial endosymbiont, Erwinia dacicola, as well as other facultative endosymbionts. The genomes of Erwinia dacicola and Enterobacter sp. OLF, isolated from a California olive fly, encode the ability to supplement amino acids and vitamins missing from the olive fruit on which the larvae feed. The Enterobacter sp. OLF genome encodes both uricase and ureases, and the Er. dacicola genome encodes an allantoate transport pathway, suggesting that bird feces or recycling the fly's waste products may be important sources of nitrogen. No homologs to known nitrogenases were identified in either bacterial genome, despite suggestions of their presence from experiments with antibiotic-treated flies. Comparisons between the olive fly endosymbionts and their free-living relatives revealed similar GC composition and genome size. The Er. dacicola genome has fewer genes for amino acid metabolism, cell motility, and carbohydrate transport and metabolism than free-living Erwinia spp. while having more genes for cell division, nucleotide metabolism and replication as well as mobile elements. A 6,696 bp potential lateral gene transfer composed primarily of amino acid synthesis and transport genes was identified that is also observed in Pseudomonas savastanoii pv savastanoii, the causative agent of olive knot disease.
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Affiliation(s)
- Anne M Estes
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. .,Department of Biological Sciences, Towson University, Baltimore, MD, 21252, USA.
| | - David J Hearn
- Department of Biological Sciences, Towson University, Baltimore, MD, 21252, USA
| | - Sonia Agrawal
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Elizabeth A Pierson
- Department of Horticultural Sciences, Texas A & M University, College Station, TX, 77843, USA
| | - Julie C Dunning Hotopp
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. .,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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25
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The first complete mitochondrial genome of Bactrocera tsuneonis (Miyake) (Diptera: Tephritidae) by next-generation sequencing and its phylogenetic implications. Int J Biol Macromol 2018; 118:1229-1237. [PMID: 29944944 DOI: 10.1016/j.ijbiomac.2018.06.099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/20/2018] [Accepted: 06/21/2018] [Indexed: 11/20/2022]
Abstract
Bactrocera tsuneonis (Miyake), generally known as the Japanese orange fly, is considered to be a major pest of commercial citrus crops. It has a limited distribution in China, Japan and Vietnam, but it has the potential to invade areas outside of Asia. More genetic information of B. tsuneonis should be obtained in order to develop effective methodologies for rapid and accurate molecular identification due to the difficulty of distinguishing it from Bactrocera minax based on morphological features. We report here the whole mitochondrial genome of B. tsuneonis sequenced by next-generation sequencing. This mitogenome sequence had a total length of 15,865 bp, a typical circular molecule comprising 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a non-coding region (A + T-rich control region). The structure and organization of the molecule were typical and similar compared with the published homologous sequences of other fruit flies in Tephritidae. The phylogenetic analyses based on the mitochondrial genome data presented a close genetic relationship between B. tsuneonis and B. minax. This is the first report of the complete mitochondrial genome of B. tsuneonis, and it can be used in further studies of species diagnosis, evolutionary biology, prevention and control.
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26
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Chen YH, Schoville SD. Editorial overview: Ecology: Ecological adaptation in agroecosystems: novel opportunities to integrate evolutionary biology and agricultural entomology. CURRENT OPINION IN INSECT SCIENCE 2018; 26:iv-viii. [PMID: 29764669 DOI: 10.1016/j.cois.2018.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Yolanda H Chen
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin, Madison, WI, USA
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Besnard G, Terral JF, Cornille A. On the origins and domestication of the olive: a review and perspectives. ANNALS OF BOTANY 2018; 121:385-403. [PMID: 29293871 PMCID: PMC5838823 DOI: 10.1093/aob/mcx145] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/12/2017] [Indexed: 05/18/2023]
Abstract
Background Unravelling domestication processes is crucial for understanding how species respond to anthropogenic pressures, forecasting crop responses to future global changes and improving breeding programmes. Domestication processes for clonally propagated perennials differ markedly from those for seed-propagated annual crops, mostly due to long generation times, clonal propagation and recurrent admixture with local forms, leading to a limited number of generations of selection from wild ancestors. However, additional case studies are required to document this process more fully. Scope The olive is an iconic species in Mediterranean cultural history. Its multiple uses and omnipresence in traditional agrosystems have made this species an economic pillar and cornerstone of Mediterranean agriculture. However, major questions about the domestication history of the olive remain unanswered. New paleobotanical, archeological, historical and molecular data have recently accumulated for olive, making it timely to carry out a critical re-evaluation of the biogeography of wild olives and the history of their cultivation. We review here the chronological history of wild olives and discuss the questions that remain unanswered, or even unasked, about their domestication history in the Mediterranean Basin. We argue that more detailed ecological genomics studies of wild and cultivated olives are crucial to improve our understanding of olive domestication. Multidisciplinary research integrating genomics, metagenomics and community ecology will make it possible to decipher the evolutionary ecology of one of the most iconic domesticated fruit trees worldwide. Conclusion The olive is a relevant model for improving our knowledge of domestication processes in clonally propagated perennial crops, particularly those of the Mediterranean Basin. Future studies on the ecological and genomic shifts linked to domestication in olive and its associated community will provide insight into the phenotypic and molecular bases of crop adaptation to human uses.
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Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENSFEA-IRD, EDB, UMR 5174, Université Paul Sabatier, Toulouse Cedex , France
| | - Jean-Frédéric Terral
- ISEM, UMR 5554, CNRS-Université de Montpellier-IRD-EPHE, Equipe Dynamique de la Biodiversité, Anthropo-écologie, Montpellier Cedex, France
- International Associated Laboratory (LIA, CNRS) EVOLea, Zürich, Switzerland
| | - Amandine Cornille
- Center for Adaptation to a Changing Environment, ETH Zürich, Zürich, Switzerland
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
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28
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Jiang F, Liang L, Li Z, Yu Y, Wang J, Wu Y, Zhu S. A conserved motif within cox 2 allows broad detection of economically important fruit flies (Diptera: Tephritidae). Sci Rep 2018; 8:2077. [PMID: 29391551 PMCID: PMC5794786 DOI: 10.1038/s41598-018-20555-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 01/19/2018] [Indexed: 11/09/2022] Open
Abstract
The genera Anastrepha, Bactrocera, Ceratitis, Dacus and Rhagoletis in the family Tephritidae order Diptera are economically important, worldwide distributed and cause damage to a large number of commercially produced fruits and vegetables. China had regulated these five genera as quarantine pests, including the species Carpomya vesuviana. An accurate molecular method not depending on morphology able to detect all the quarantine fruit flies simultaneously is required for quarantine monitoring. This study contributes a comparative analysis of 146 mitochondrial genomes of Diptera species and found variable sites at the mt DNA cox2 gene only conserved in economically important fruit flies species. Degenerate primers (TephFdeg/TephR) were designed specific for the economically important fruit flies. A 603 bp fragment was amplified after testing each of the 40 selected representative species belonging to each economically important Tephritid genera, no diagnostic fragments were detected/amplified in any of the other Tephritidae and Diptera species examined. PCR sensitivity assays demonstrated the limit of detection of targeted DNA was 0.1 ng/μl. This work contributes an innovative approach for detecting all reported economically important fruit flies in a single-step PCR specific for reported fruit fly species of quarantine concern in China.
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Affiliation(s)
- Fan Jiang
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Liang Liang
- Key Laboratory of Agro-Products Postharvest Handling, Ministry of Agriculture, Chinese Academy of Agricultural Engineering, Beijing, 100121, China
| | - Zhihong Li
- College of Plant Protection, China Agricultural University, Beijing, 100193, China.
| | - Yanxue Yu
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Jun Wang
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Yuping Wu
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China.
| | - Shuifang Zhu
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China.
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29
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Yong HS, Song SL, Lim PE, Eamsobhana P. Complete mitochondrial genome of Zeugodacus tau (Insecta: Tephritidae) and differentiation of Z. tau species complex by mitochondrial cytochrome c oxidase subunit I gene. PLoS One 2017; 12:e0189325. [PMID: 29216281 PMCID: PMC5720772 DOI: 10.1371/journal.pone.0189325] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 11/23/2017] [Indexed: 01/19/2023] Open
Abstract
The tephritid fruit fly Zeugodacus tau (Walker) is a polyphagous fruit pest of economic importance in Asia. Studies based on genetic markers indicate that it forms a species complex. We report here (1) the complete mitogenome of Z. tau from Malaysia and comparison with that of China as well as the mitogenome of other congeners, and (2) the relationship of Z. tau taxa from different geographical regions based on sequences of cytochrome c oxidase subunit I gene. The complete mitogenome of Z. tau had a total length of 15631 bp for the Malaysian specimen (ZT3) and 15835 bp for the China specimen (ZT1), with similar gene order comprising 37 genes (13 protein-coding genes-PCGs, 2 rRNA genes, and 22 tRNA genes) and a non-coding A + T-rich control region (D-loop). Based on 13 PCGs and 15 mt-genes, Z. tau NC_027290 (China) and Z. tau ZT1 (China) formed a sister group in the lineage containing also Z. tau ZT3 (Malaysia). Phylogenetic analysis based on partial sequences of cox1 gene indicates that the taxa from China, Japan, Laos, Malaysia, Bangladesh, India, Sri Lanka, and Z. tau sp. A from Thailand belong to Z. tau sensu stricto. A complete cox1 gene (or 13 PCGs or 15 mt-genes) instead of partial sequence is more appropriate for determining phylogenetic relationship.
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Affiliation(s)
- Hoi-Sen Yong
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Sze-Looi Song
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Phaik-Eem Lim
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Praphathip Eamsobhana
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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30
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Eti CN, Dogac E, Gocmen Taskin B, Gokdere G, Taskin V. Population structure and patterns of geographic differentiation of Bactrocera oleae (Diptera: Tephritidae) in Eastern Mediterranean Basin. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:1051-1062. [PMID: 29157052 DOI: 10.1080/24701394.2017.1404045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The olive fly (Bactrocera oleae) is the most destructive pest of olives in most commercial olive-growing regions worldwide. Significant economic damage to olive production is caused by the larvae of this fly, which feed on the pulp of Olea fruits. Studying the genetic structure of insect pest populations is essential for the success of pest management strategies. Our primary goal in the present study was to examine the population structures of olive flies collected over a wide geographic area from Turkey, a representative of eastern Mediterranean region, using two mitochondrial DNA sequences as genetic markers. The data revealed a high level of genetic variability in olive fly populations and a moderate level of genetic differentiation between Mediterranean and Aegean populations in Turkey. We also merged the sequences obtained in the present study with previously published sequences from across the world into the data matrix. Strong population substructure and a significant correlation between genetic and geographic distances were detected in northern Mediterranean basin populations of B. oleae, indicating the possibility of a westward expansion of the species in the continent. In addition, our results revealed a very close genetic relationship between the Aegean and Iranian populations, which suggests that B. oleae was introduced to Iran from western parts of Turkey. However, additional markers and analytical approaches are required to determine the exact colonization route of olive fly.
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Affiliation(s)
- Ceren Naz Eti
- a Department of Biology, Faculty of Science , Muğla Sıtkı Kocman University , Kotekli , Turkey
| | - Ersin Dogac
- b Department of Medicinal and Aromatic Plants , Koycegiz Vocational School, Mugla Sitki Kocman University , Mugla , Turkey
| | - Belgin Gocmen Taskin
- a Department of Biology, Faculty of Science , Muğla Sıtkı Kocman University , Kotekli , Turkey
| | - Güven Gokdere
- a Department of Biology, Faculty of Science , Muğla Sıtkı Kocman University , Kotekli , Turkey
| | - Vatan Taskin
- a Department of Biology, Faculty of Science , Muğla Sıtkı Kocman University , Kotekli , Turkey
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31
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Grasso F, Coppola M, Carbone F, Baldoni L, Alagna F, Perrotta G, Pérez-Pulido AJ, Garonna A, Facella P, Daddiego L, Lopez L, Vitiello A, Rao R, Corrado G. The transcriptional response to the olive fruit fly (Bactrocera oleae) reveals extended differences between tolerant and susceptible olive (Olea europaea L.) varieties. PLoS One 2017; 12:e0183050. [PMID: 28797083 PMCID: PMC5552259 DOI: 10.1371/journal.pone.0183050] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/30/2017] [Indexed: 11/23/2022] Open
Abstract
The olive fruit fly Bactrocera oleae (Diptera: Tephritidae) is the most devastating pest of cultivated olive (Olea europaea L.). Intraspecific variation in plant resistance to B. oleae has been described only at phenotypic level. In this work, we used a transcriptomic approach to study the molecular response to the olive fruit fly in two olive cultivars with contrasting level of susceptibility. Using next-generation pyrosequencing, we first generated a catalogue of more than 80,000 sequences expressed in drupes from approximately 700k reads. The assembled sequences were used to develop a microarray layout with over 60,000 olive-specific probes. The differential gene expression analysis between infested (i.e. with II or III instar larvae) and control drupes indicated a significant intraspecific variation between the more tolerant and susceptible cultivar. Around 2500 genes were differentially regulated in infested drupes of the tolerant variety. The GO annotation of the differentially expressed genes implies that the inducible resistance to the olive fruit fly involves a number of biological functions, cellular processes and metabolic pathways, including those with a known role in defence, oxidative stress responses, cellular structure, hormone signalling, and primary and secondary metabolism. The difference in the induced transcriptional changes between the cultivars suggests a strong genetic role in the olive inducible defence, which can ultimately lead to the discovery of factors associated with a higher level of tolerance to B. oleae.
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Affiliation(s)
- Filomena Grasso
- Dipartimento di Agraria, Università degli Studi di Napoli “Federico II”, Portici (NA), Italy
| | - Mariangela Coppola
- Dipartimento di Agraria, Università degli Studi di Napoli “Federico II”, Portici (NA), Italy
| | - Fabrizio Carbone
- Centro di Ricerca per l’Olivicoltura e l’Industria Olearia, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria (CREA), Rende (CS), Italy
| | - Luciana Baldoni
- Institute of Biosciences and Bioresources (IBBR), CNR, Perugia, Italy
| | - Fiammetta Alagna
- Institute of Biosciences and Bioresources (IBBR), CNR, Perugia, Italy
| | - Gaetano Perrotta
- Trisaia Research Center, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Rotondella (MT), Italy
| | - Antonio J. Pérez-Pulido
- Departamento Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
| | - Antonio Garonna
- Dipartimento di Agraria, Università degli Studi di Napoli “Federico II”, Portici (NA), Italy
| | - Paolo Facella
- Trisaia Research Center, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Rotondella (MT), Italy
| | - Loretta Daddiego
- Trisaia Research Center, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Rotondella (MT), Italy
| | - Loredana Lopez
- Trisaia Research Center, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Rotondella (MT), Italy
| | - Alessia Vitiello
- Dipartimento di Agraria, Università degli Studi di Napoli “Federico II”, Portici (NA), Italy
| | - Rosa Rao
- Dipartimento di Agraria, Università degli Studi di Napoli “Federico II”, Portici (NA), Italy
- * E-mail: (RR); (CG)
| | - Giandomenico Corrado
- Dipartimento di Agraria, Università degli Studi di Napoli “Federico II”, Portici (NA), Italy
- * E-mail: (RR); (CG)
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32
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Drosopoulou E, Pantelidou C, Gariou-Papalexiou A, Augustinos AA, Chartomatsidou T, Kyritsis GA, Bourtzis K, Mavragani-Tsipidou P, Zacharopoulou A. The chromosomes and the mitogenome of Ceratitis fasciventris (Diptera: Tephritidae): two genetic approaches towards the Ceratitis FAR species complex resolution. Sci Rep 2017; 7:4877. [PMID: 28687799 PMCID: PMC5501848 DOI: 10.1038/s41598-017-05132-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/25/2017] [Indexed: 11/29/2022] Open
Abstract
Ceratitis fasciventris is a serious agricultural pest of the Tephritidae family that belongs to the African Ceratitis FAR species complex. Species limits within the FAR complex are obscure and multidisciplinary approaches have attempted to resolve phylogenetic relationships among its members. These studies support the existence of at least three additional species in the complex, C. anonnae, C. rosa and C. quilicii, while they indicate the presence of two structured populations (F1 and F2) within the C. fasciventris species. In the present study we present the mitotic karyotype, polytene chromosome maps, in situ hybridization data and the complete mitochondrial genome sequence of an F2 population of C. fasciventris. This is the first polytene chromosome map and complete mitogenome of a member of the FAR complex and only the second reported for the Ceratitis genus. Both polytene chromosomes and mitochondrial sequence could provide valuable information and be used as reference for comparative analysis among the members of the complex towards the clarification of their phylogenetic relationships.
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Affiliation(s)
- Elena Drosopoulou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | - Christina Pantelidou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Antonios A Augustinos
- Department of Biology, University of Patras, Patras, Greece.,Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, Vienna, Austria
| | - Tatiana Chartomatsidou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgios A Kyritsis
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, Vienna, Austria
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, Vienna, Austria
| | - Penelope Mavragani-Tsipidou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
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33
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Li X, Li W, Ding S, Cameron SL, Mao M, Shi L, Yang D. Mitochondrial Genomes Provide Insights into the Phylogeny of Lauxanioidea (Diptera: Cyclorrhapha). Int J Mol Sci 2017; 18:E773. [PMID: 28420076 PMCID: PMC5412357 DOI: 10.3390/ijms18040773] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/23/2017] [Accepted: 04/01/2017] [Indexed: 11/17/2022] Open
Abstract
The superfamily Lauxanioidea is a significant dipteran clade including over 2500 known species in three families: Lauxaniidae, Celyphidae and Chamaemyiidae. We sequenced the first five (three complete and two partial) lauxanioid mitochondrial (mt) genomes, and used them to reconstruct the phylogeny of this group. The lauxanioid mt genomes are typical of the Diptera, containing all 37 genes usually present in bilaterian animals. A total of three conserved intergenic sequences have been reported across the Cyclorrhapha. The inferred secondary structure of 22 tRNAs suggested five substitution patterns among the Cyclorrhapha. The control region in the Lauxanioidea has apparently evolved very fast, but four conserved structural elements were detected in all three complete mt genome sequences. Phylogenetic relationships based on the mt genome data were inferred by Maximum Likelihood and Bayesian methods. The traditional relationships between families within the Lauxanioidea, (Chamaemyiidae + (Lauxaniidae + Celyphidae)), were corroborated; however, the higher-level relationships between cyclorrhaphan superfamilies are mostly poorly supported.
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Affiliation(s)
- Xuankun Li
- Department of Entomology, China Agricultural University, Beijing 100193, China.
| | - Wenliang Li
- College of Forestry, Henan University of Science and Technology, Luoyang 471023, China.
| | - Shuangmei Ding
- Department of Entomology, China Agricultural University, Beijing 100193, China.
| | - Stephen L Cameron
- Department of Entomology, Purdue University, West Lafayette, IN 47907, USA.
| | - Meng Mao
- Department of Plant and Environmental Protection Science, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
| | - Li Shi
- College of Agronomy, Inner Mongolia Agricultural University, Hohhot 010018, China.
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing 100193, China.
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Jeong SY, Kim MJ, Kim JS, Kim I. Complete mitochondrial genome of the pumpkin fruit fly, Bactrocera depressa (Diptera: Tephritidae). Mitochondrial DNA B Resour 2017; 2:85-87. [PMID: 33473724 PMCID: PMC7800232 DOI: 10.1080/23802359.2017.1285212] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this study, we sequenced the complete mitochondrial genome (mitogenome) of the pumpkin fruit fly, Bactrocera depressa (Diptera: Tephritidae), which is an economically damaging pest of pumpkin and turban squash. The 15,832-bp-long complete mitogenome of the species consists of a typical set of genes, with an arrangement typical of insects. Of the 13 protein-coding genes (PCGs), 12 have a typical ATN start codon, whereas the COI gene begins with TCG, which has been identified as the start codon for all Bactrocera COI genes. The 1004-bp A + T-rich region of B. depressa is the third longest, after B. minax and B. scutellata, of the Bactrocera species for which the whole mitogenome has been sequenced. Phylogenetic analysis using the 13 PCGs of Bactrocera species indicated that B. depressa is a sister to the sister group containing B. tau and B. cucurbitae with the highest nodal support (Bayesian posterior probability =1.0).
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Affiliation(s)
- Su Yeon Jeong
- College of Agriculture & Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Min Jee Kim
- College of Agriculture & Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Jong Seok Kim
- College of Agriculture & Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Iksoo Kim
- College of Agriculture & Life Sciences, Chonnam National University, Gwangju, Republic of Korea
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35
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Jiang F, Pan X, Li X, Yu Y, Zhang J, Jiang H, Dou L, Zhu S. The first complete mitochondrial genome of Dacus longicornis (Diptera: Tephritidae) using next-generation sequencing and mitochondrial genome phylogeny of Dacini tribe. Sci Rep 2016; 6:36426. [PMID: 27812024 PMCID: PMC5095552 DOI: 10.1038/srep36426] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/14/2016] [Indexed: 11/09/2022] Open
Abstract
The genus Dacus is one of the most economically important tephritid fruit flies. The first complete mitochondrial genome (mitogenome) of Dacus species - D. longicornis was sequenced by next-generation sequencing in order to develop the mitogenome data for this genus. The circular 16,253 bp mitogenome is the typical set and arrangement of 37 genes present in the ancestral insect. The mitogenome data of D. longicornis was compared to all the published homologous sequences of other tephritid species. We discovered the subgenera Bactrocera, Daculus and Tetradacus differed from the subgenus Zeugodacus, the genera Dacus, Ceratitis and Procecidochares in the possession of TA instead of TAA stop codon for COI gene. There is a possibility that the TA stop codon in COI is the synapomorphy in Bactrocera group in the genus Bactrocera comparing with other Tephritidae species. Phylogenetic analyses based on the mitogenome data from Tephritidae were inferred by Bayesian and Maximum-likelihood methods, strongly supported the sister relationship between Zeugodacus and Dacus.
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MESH Headings
- Animals
- Base Sequence
- Bayes Theorem
- Codon, Terminator
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/isolation & purification
- DNA, Mitochondrial/metabolism
- Electron Transport Complex IV/chemistry
- Electron Transport Complex IV/genetics
- Genome, Mitochondrial
- High-Throughput Nucleotide Sequencing
- Mitochondria/genetics
- Phylogeny
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- Sequence Analysis, DNA
- Tephritidae/classification
- Tephritidae/genetics
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Affiliation(s)
- Fan Jiang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Xubin Pan
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Xuankun Li
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Yanxue Yu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Junhua Zhang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Hongshan Jiang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Liduo Dou
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Shuifang Zhu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
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36
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Wang K, Li X, Ding S, Wang N, Mao M, Wang M, Yang D. The complete mitochondrial genome of the Atylotus miser (Diptera: Tabanomorpha: Tabanidae), with mitochondrial genome phylogeny of lower Brachycera (Orthorrhapha). Gene 2016; 586:184-96. [PMID: 27063560 DOI: 10.1016/j.gene.2016.04.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/22/2016] [Accepted: 04/05/2016] [Indexed: 11/25/2022]
Abstract
Brachycera is a clade with over 80,000 described species and originated from the Mesozoic, and its larvae employ comprehensive feeding strategies. The phylogeny of the lower Brachycera has been studied intensively over the past decades. In order to supplement the lack of genetic data in this important group, we sequenced the complete mitochondrial (mt) genome of Atylotus miser as well as the nearly complete mt genomes of another 11 orthorrhaphous flies. The mt genome of A. miser is 15,858bp, which is typical of Diptera, with 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a 993bp control region. The rest of the orthorrhaphous mt genomes in our study have the similar structure with A. miser. Additionally, we conducted a phylogenetic analysis of 20 mt genomes using Maximum-likelihood and Bayesian methods in order to reconstruct the evolutionary relationship of Orthorrhapha. The results show that all infraorders of Brachycera are monophyletic, and a relationship of Tabanomorpha+((Xylophagomorpha+Stratiomyomorpha)+Muscomorpha) has been proposed. Within Xylophagomorpha, Nemestrinoidae forms the sister group of Xylophagidae.
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Affiliation(s)
- Kai Wang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Xuankun Li
- Department of Entomology, China Agricultural University, Beijing, China
| | - Shuangmei Ding
- Department of Entomology, China Agricultural University, Beijing, China
| | - Ning Wang
- Department of Entomology, China Agricultural University, Beijing, China; Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Meng Mao
- School of Biological Sciences, University of Wollongong, Wollongong, Australia
| | - Mengqing Wang
- Department of Entomology, China Agricultural University, Beijing, China; Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing, China.
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Medjkouh L, Tamendjari A, Keciri S, Santos J, Nunes MA, Oliveira MBPP. The effect of the olive fruit fly (Bactrocera oleae) on quality parameters, and antioxidant and antibacterial activities of olive oil. Food Funct 2016; 7:2780-8. [DOI: 10.1039/c6fo00295a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
This study shows the importance of controlling the fly attack because it causes a decrease in the beneficial health effects of olive oils.
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Affiliation(s)
- Lynda Medjkouh
- Laboratoire de Biochimie Appliquée
- Faculté des Sciences de la Nature et de la Vie
- Université de Bejaia
- Algérie
| | - Abderezak Tamendjari
- Laboratoire de Biochimie Appliquée
- Faculté des Sciences de la Nature et de la Vie
- Université de Bejaia
- Algérie
| | - Sonia Keciri
- Technical Institute of Arboriculture of Fruits and Vine (TIAFV)
- Bejaia
- Algeria
| | - Joana Santos
- REQUIMTE/LAQV
- Department of Chemical Sciences
- Faculty of Pharmacy
- University of Porto
- Portugal
| | - M. Antónia Nunes
- REQUIMTE/LAQV
- Department of Chemical Sciences
- Faculty of Pharmacy
- University of Porto
- Portugal
| | - M. B. P. P. Oliveira
- REQUIMTE/LAQV
- Department of Chemical Sciences
- Faculty of Pharmacy
- University of Porto
- Portugal
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Doğaç E, Kandemir İ, Taşkın V. Geographical distribution and frequencies of organophosphate-resistant Ace alleles and morphometric variations in olive fruit fly populations. PEST MANAGEMENT SCIENCE 2015; 71:1529-1539. [PMID: 25491602 DOI: 10.1002/ps.3958] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 10/25/2014] [Accepted: 12/03/2014] [Indexed: 06/04/2023]
Abstract
BACKGROUND In the Mediterranean basin, organophosphate (OP) insecticides have been used intensively to control olive fly populations. Acetylcholinesterase (Ace) is the molecular target of OP insecticides, and three resistance-associated mutations that confer different levels of OP insensitivity have been identified. In this study, genotypes of olive fly Ace were determined in field-collected populations from broad geographical areas in Turkey. In addition, the levels of asymmetry of wing and leg characters were compared in these populations. RESULTS Our study revealed the existence of a genetically smooth stratification pattern in OP resistance allele distribution in the olive fly populations of Turkey. In contrast to earlier findings, the frequency of Δ3Q was found to be lower in the Aegean region, where the populations have been subjected to high selection pressure. Results based on the morphological differences among the samples revealed a similar pattern for both sides and did not demonstrate a clear separation. CONCLUSION The frequencies and geographic range of resistance alleles indicate that they were selected in the Aegean coast of Turkey and then spread westward towards Europe. One possible explanation for the absence of morphological asymmetry in olive fly samples might be the presence of modifier allele(s) that compensate for the increase in asymmetry.
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Affiliation(s)
- Ersin Doğaç
- Department of Biology, Faculty of Science, Muğla Sıtkı Kocman University, Kotekli, Muğla, Turkey
| | - İrfan Kandemir
- Department of Biology, Faculty of Science, Ankara University, Beşevler, Ankara, Turkey
| | - Vatan Taşkın
- Department of Biology, Faculty of Science, Muğla Sıtkı Kocman University, Kotekli, Muğla, Turkey
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Liu JH, Xu J, Li YH, Dan W, Pan Y. Complete mitochondrial genome of the guava fruit fly, Bactrocera correcta (Diptera: Tephritidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4553-4554. [PMID: 26513144 DOI: 10.3109/19401736.2015.1101559] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Bactrocera correcta (Diptera: Tephritidae) is one of the most serious pest insects in south China and surrounding Southeast Asian countries. The family Tephritidae includes over 4257 species distributed worldwide, so the complete mitochondrial genome would be helpful for bio-identification, biogeography and phylogeny. The B. correcta genome consists of 15 936 bp. Annotation indicated that the structure and orientation of 13 protein-coding genes (PCGs), 22 tRNA and 2 rRNA sequences were typical of, and similar to, the ten closely related tephritid species. The nucleotide composition shows heavily biased toward As and Ts accounting 73.2% and exhibits a slightly positive AT skew, which is similar to other known tephritid species and other insects. The phylogenetic tree indicated the presence of three distinct families (Tephritidae, Muscidae, Drosophilidae) in Order Diptera.
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Affiliation(s)
- Jian-Hong Liu
- a College of Forestry, Southwest Forestry University , Kunming , China.,b Yunnan Provincial Key Laboratory of Forest Disaster Warning and Control , Kunming , China , and
| | - Jin Xu
- c Agriculture School, Yunnan University , Kunming , China
| | - Yong-He Li
- a College of Forestry, Southwest Forestry University , Kunming , China.,b Yunnan Provincial Key Laboratory of Forest Disaster Warning and Control , Kunming , China , and
| | - Wenli Dan
- a College of Forestry, Southwest Forestry University , Kunming , China
| | - Yongzhi Pan
- a College of Forestry, Southwest Forestry University , Kunming , China.,b Yunnan Provincial Key Laboratory of Forest Disaster Warning and Control , Kunming , China , and
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Yong HS, Song SL, Lim PE, Chan KG, Chow WL, Eamsobhana P. Complete mitochondrial genome of Bactrocera arecae (Insecta: Tephritidae) by next-generation sequencing and molecular phylogeny of Dacini tribe. Sci Rep 2015; 5:15155. [PMID: 26472633 PMCID: PMC4607999 DOI: 10.1038/srep15155] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/15/2015] [Indexed: 11/09/2022] Open
Abstract
The whole mitochondrial genome of the pest fruit fly Bactrocera arecae was obtained from next-generation sequencing of genomic DNA. It had a total length of 15,900 bp, consisting of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a non-coding region (A + T-rich control region). The control region (952 bp) was flanked by rrnS and trnI genes. The start codons included 6 ATG, 3 ATT and 1 each of ATA, ATC, GTG and TCG. Eight TAA, two TAG, one incomplete TA and two incomplete T stop codons were represented in the protein-coding genes. The cloverleaf structure for trnS1 lacked the D-loop, and that of trnN and trnF lacked the TΨC-loop. Molecular phylogeny based on 13 protein-coding genes was concordant with 37 mitochondrial genes, with B. arecae having closest genetic affinity to B. tryoni. The subgenus Bactrocera of Dacini tribe and the Dacinae subfamily (Dacini and Ceratitidini tribes) were monophyletic. The whole mitogenome of B. arecae will serve as a useful dataset for studying the genetics, systematics and phylogenetic relationships of the many species of Bactrocera genus in particular, and tephritid fruit flies in general.
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Affiliation(s)
- Hoi-Sen Yong
- Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia.,Chancellery High Impact Research, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Sze-Looi Song
- Chancellery High Impact Research, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Phaik-Eem Lim
- Institute of Ocean and Earth Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia.,Chancellery High Impact Research, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Wan-Loo Chow
- Science Vision Sdn Bhd, Setia Avenue, 33A-4 Jalan Setia Prima S, U13/S, Setia Alam, Seksyen U13, 40170 Shah Alam, Selangor Darul Ehsan, Malaysia
| | - Praphathip Eamsobhana
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
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41
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Ye F, Liu T, King SD, You P. Mitochondrial genomes of two phlebotomine sand flies, Phlebotomus chinensis and Phlebotomus papatasi (Diptera: Nematocera), the first representatives from the family Psychodidae. Parasit Vectors 2015; 8:472. [PMID: 26381614 PMCID: PMC4573934 DOI: 10.1186/s13071-015-1081-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 09/10/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Leishmaniasis is a worldwide but neglected disease of humans and animal transmitted by sand flies, vectors that also transmit other important diseases. Mitochondrial genomes contain abundant information for population genetic and phylogenetic studies, important in disease management. However, the available mitochondrial sequences of these crucial vectors are limited, emphasizing the need for developing more mitochondrial genetic markers. METHODS The complete mitochondrial genome of Phlebotomus chinensis was amplified in eight fragments and sequenced using primer walking. The mitochondrial genome of Phlebotomus papatasi was reconstructed from whole-genome sequencing data available on Genbank. The phylogenetic relationship of 24 selected representatives of Diptera was deduced from codon positions 1 and 2 for 13 protein coding genes, using Bayesian inference (BI) and maximum likelihood (ML) methods. RESULTS We provide the first Phlebotomus (P. chinensis and P. papatasi) mitochondrial genomes. Both genomes contain 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and an A + T-rich region. The gene order of Phlebotomus mitochondrial genomes is identical with the ancestral gene order of insect. Phylogenetic analyses demonstrated that Psychodidae and Tanyderidae are sister taxa. Potential markers for population genetic study of Phlebotomus species were also revealed. CONCLUSION The generated mitochondrial genomes of P. chinensis and P. papatasi represent a useful resource for comparative genomic studies and provide valuable future markers for the population genetic study of these important Leishmania vectors. Our results also preliminary demonstrate the phylogenetic placement of Psychodidae based on their mitochondrial genomes.
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Affiliation(s)
- Fei Ye
- Co-Innovation Center for Qinba regions' sustainable development, College of Life Science, Shaanxi Normal University, Xi'an, 710062, China.
| | - Ting Liu
- Co-Innovation Center for Qinba regions' sustainable development, College of Life Science, Shaanxi Normal University, Xi'an, 710062, China.
| | - Stanley D King
- Department of Biology, Dalhousie University, Halifax, NS, Canada, B3H 4J1.
| | - Ping You
- Co-Innovation Center for Qinba regions' sustainable development, College of Life Science, Shaanxi Normal University, Xi'an, 710062, China.
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Godefroid M, Cruaud A, Rossi JP, Rasplus JY. Assessing the Risk of Invasion by Tephritid Fruit Flies: Intraspecific Divergence Matters. PLoS One 2015; 10:e0135209. [PMID: 26274582 PMCID: PMC4537207 DOI: 10.1371/journal.pone.0135209] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/19/2015] [Indexed: 11/28/2022] Open
Abstract
Widely distributed species often show strong phylogeographic structure, with lineages potentially adapted to different biotic and abiotic conditions. The success of an invasion process may thus depend on the intraspecific identity of the introduced propagules. However, pest risk analyses are usually performed without accounting for intraspecific diversity. In this study, we developed bioclimatic models using MaxEnt and boosted regression trees approaches, to predict the potential distribution in Europe of six economically important Tephritid pests (Ceratitis fasciventris (Bezzi), Bactrocera oleae (Rossi), Anastrepha obliqua (Macquart), Anastrepha fraterculus (Wiedemann), Rhagoletis pomonella (Walsh) and Bactrocera cucurbitae (Coquillet)). We considered intraspecific diversity in our risk analyses by independently modeling the distributions of conspecific lineages. The six species displayed different potential distributions in Europe. A strong signal of intraspecific climate envelope divergence was observed in most species. In some cases, conspecific lineages differed strongly in potential distributions suggesting that taxonomic resolution should be accounted for in pest risk analyses. No models (lineage- and species-based approaches) predicted high climatic suitability in the entire invaded range of B. oleae—the only species whose intraspecific identity of invading populations has been elucidated—in California. Host availability appears to play the most important role in shaping the geographic range of this specialist pest. However, climatic suitability values predicted by species-based models are correlated with population densities of B. oleae globally reported in California. Our study highlights how classical taxonomic boundaries may lead to under- or overestimation of the potential pest distributions and encourages accounting for intraspecific diversity when assessing the risk of biological invasion.
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Affiliation(s)
- Martin Godefroid
- Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, Montferriez-sur-Lez, France
| | - Astrid Cruaud
- Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, Montferriez-sur-Lez, France
| | - Jean-Pierre Rossi
- Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, Montferriez-sur-Lez, France
| | - Jean-Yves Rasplus
- Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, Montferriez-sur-Lez, France
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Malheiro R, Casal S, Baptista P, Pereira JA. A review of Bactrocera oleae (Rossi) impact in olive products: From the tree to the table. Trends Food Sci Technol 2015. [DOI: 10.1016/j.tifs.2015.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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44
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Ding S, Li X, Wang N, Cameron SL, Mao M, Wang Y, Xi Y, Yang D. The Phylogeny and Evolutionary Timescale of Muscoidea (Diptera: Brachycera: Calyptratae) Inferred from Mitochondrial Genomes. PLoS One 2015; 10:e0134170. [PMID: 26225760 PMCID: PMC4520480 DOI: 10.1371/journal.pone.0134170] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/06/2015] [Indexed: 11/19/2022] Open
Abstract
Muscoidea is a significant dipteran clade that includes house flies (Family Muscidae), latrine flies (F. Fannidae), dung flies (F. Scathophagidae) and root maggot flies (F. Anthomyiidae). It is comprised of approximately 7000 described species. The monophyly of the Muscoidea and the precise relationships of muscoids to the closest superfamily the Oestroidea (blow flies, flesh flies etc) are both unresolved. Until now mitochondrial (mt) genomes were available for only two of the four muscoid families precluding a thorough test of phylogenetic relationships using this data source. Here we present the first two mt genomes for the families Fanniidae (Euryomma sp.) (family Fanniidae) and Anthomyiidae (Delia platura (Meigen, 1826)). We also conducted phylogenetic analyses containing of these newly sequenced mt genomes plus 15 other species representative of dipteran diversity to address the internal relationship of Muscoidea and its systematic position. Both maximum-likelihood and Bayesian analyses suggested that Muscoidea was not a monophyletic group with the relationship: (Fanniidae + Muscidae) + ((Anthomyiidae + Scathophagidae) + (Calliphoridae + Sarcophagidae)), supported by the majority of analysed datasets. This also infers that Oestroidea was paraphyletic in the majority of analyses. Divergence time estimation suggested that the earliest split within the Calyptratae, separating (Tachinidae + Oestridae) from the remaining families, occurred in the Early Eocene. The main divergence within the paraphyletic muscoidea grade was between Fanniidae + Muscidae and the lineage ((Anthomyiidae + Scathophagidae) + (Calliphoridae + Sarcophagidae)) which occurred in the Late Eocene.
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Affiliation(s)
- Shuangmei Ding
- Department of Entomology, China Agricultural University, Beijing, China
| | - Xuankun Li
- Department of Entomology, China Agricultural University, Beijing, China
| | - Ning Wang
- Department of Entomology, China Agricultural University, Beijing, China
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Stephen L. Cameron
- Earth, Environmental and Biological Sciences School, Science & Engineering Faculty, Queensland University of Technology, Brisbane, Australia
| | - Meng Mao
- Centre for Medical Bioscience, School of Biological Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Yuyu Wang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Yuqiang Xi
- Department of Entomology, China Agricultural University, Beijing, China
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing, China
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45
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Choudhary JS, Naaz N, Prabhakar CS, Rao MS, Das B. The mitochondrial genome of the peach fruit fly, Bactrocera zonata (Saunders) (Diptera: Tephritidae): Complete DNA sequence, genome organization, and phylogenetic analysis with other tephritids using next generation DNA sequencing. Gene 2015; 569:191-202. [PMID: 26031235 DOI: 10.1016/j.gene.2015.05.066] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/13/2015] [Accepted: 05/27/2015] [Indexed: 02/01/2023]
Abstract
Mitochondrial genome can provide information for genomic structure as well as for phylogenetic analysis and evolutionary biology. The complete 15,935 bp mitochondrial genome of Bactrocera zonata (Diptera: Tephritidae), is assembled from Illumina MiSeq read data. The mitogenome information for B. zonata was compared to the homologous sequences of other tephritids. Annotation indicated that the structure and orientation of 13 protein coding genes (PCGs), 22 tRNA and 2 rRNA sequences were typical of, and similar to, the ten closely related tephritid species. The nucleotide composition shows heavily biased toward As and Ts accounting 73.34% and exhibits a slightly positive AT skew, which is similar to other known tephritid species. All PCGs are initiated by ATN codons, except for cox1 with TCG and atp8 with GTG. Nine PCGs use a common stop codon of TAA or TAG, whereas the remaining four use an incomplete termination codon T or TA likely to be completed by adenylation. All tRNAs have the typical clover-leaf structure, with an exception for trnS((AGN)). Four short intergenic spacers showed high degree of conservation among B. zonata and other ten tephritids. A poly(T) stretch at the 5' end followed by [TA(A)]n-like stretch and a tandem repeats of 39 bp has been observed in CR. The analysis of gene evolutionary rate revealed that the cox1 and atp6 exhibits lowest and highest gene substitution rates, respectively than other genes. The phylogenetic relationships based on Maximum Likelihood method using all protein-coding genes and two ribosomal RNA genes confirmed that B. zonata is closely related to Bactrocera correcta, Bactrocera carambolae, Bactrocera papayae, and Bactrocera philippinensis and Bactrocera dorsalis belonging to B. dorsalis species complex forms a monophyletic clade, which is in accordance with the traditional morphological classification and recent molecular works.
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Affiliation(s)
- Jaipal S Choudhary
- ICAR Research Complex for Eastern Region, Research Centre, Plandu, Ranchi 834 010, Jharkhand, India.
| | - Naiyar Naaz
- ICAR Research Complex for Eastern Region, Research Centre, Plandu, Ranchi 834 010, Jharkhand, India.
| | - Chandra S Prabhakar
- ICAR Research Complex for Eastern Region, Research Centre, Plandu, Ranchi 834 010, Jharkhand, India; Department of Entomology, Bihar Agricultural University, Sabour, Bhagalpur 813 210, Bihar, India.
| | - Mathukumalli Srinivasa Rao
- Central Research Institute for Dryland Agriculture (CRIDA), Santoshnagar, Saidabad PO, Hyderabad 500 059, India.
| | - Bikash Das
- ICAR Research Complex for Eastern Region, Research Centre, Plandu, Ranchi 834 010, Jharkhand, India.
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van Asch B, Pereira-Castro I, Rei FT, da Costa LT. Marked Genetic Differentiation between Western Iberian and Italic Populations of the Olive Fly: Southern France as an Intermediate Area. PLoS One 2015; 10:e0126702. [PMID: 25951107 PMCID: PMC4423870 DOI: 10.1371/journal.pone.0126702] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 04/06/2015] [Indexed: 11/18/2022] Open
Abstract
The olive fly, Bactrocera oleae, is the most important pest affecting the olive industry, to which it is estimated to cause average annual losses in excess of one billion dollars. As with other insects with a wide distribution, it is generally accepted that the understanding of B. oleae population structure and dynamics is fundamental for the design and implementation of effective monitoring and control strategies. However, and despite important advances in the past decade, a clear picture of B. oleae's population structure is still lacking. In the Mediterranean basin, where more than 95% of olive production is concentrated, evidence from several studies suggests the existence of three distinct sub-populations, but the geographical limits of their distributions, and the level of interpenetration and gene flow among them remain ill-characterized. Here we use mitochondrial haplotype analysis to show that one of the Mediterranean mitochondrial lineages displays geographically correlated substructure and demonstrate that Italic populations, though markedly distinct from their Iberian and Levantine counterparts are more diverse than previously described. Finally, we show that this distinction does not result from extant hypothetical geographic limits imposed by the Alps or the Pyrenees nor, more generally, does it result from any sharp boundary, as intermixing is observed in a broad area, albeit at variable levels. Instead, Bayesian phylogeographic analysis suggests the interplay between isolation-mediated differentiation during glacial periods and bi-directional dispersal and population intermixing in the interglacials has played a major role in shaping current olive fly population structure.
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Affiliation(s)
- Barbara van Asch
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Isabel Pereira-Castro
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Fernando Trindade Rei
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | - Luís Teixeira da Costa
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
- * E-mail:
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Li X, Ding S, Cameron SL, Kang Z, Wang Y, Yang D. The first mitochondrial genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997 (Diptera: Sciomyzoidea: Sepsidae), with mitochondrial genome phylogeny of cyclorrhapha. PLoS One 2015; 10:e0123594. [PMID: 25826648 PMCID: PMC4380458 DOI: 10.1371/journal.pone.0123594] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 02/20/2015] [Indexed: 11/18/2022] Open
Abstract
Sepsid flies (Diptera: Sepsidae) are important model insects for sexual selection research. In order to develop mitochondrial (mt) genome data for this significant group, we sequenced the first complete mt genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997. The circular 15,878 bp mt genome is typical of Diptera, containing all 37 genes usually present in bilaterian animals. We discovered inaccurate annotations of fly mt genomes previously deposited on GenBank and thus re-annotated all published mt genomes of Cyclorrhapha. These re-annotations were based on comparative analysis of homologous genes, and provide a statistical analysis of start and stop codon positions. We further detected two 18 bp of conserved intergenic sequences from tRNAGlu-tRNAPhe and ND1-tRNASer(UCN) across Cyclorrhapha, which are the mtTERM binding site motifs. Additionally, we compared automated annotation software MITOS with hand annotation method. Phylogenetic trees based on the mt genome data from Cyclorrhapha were inferred by Maximum-likelihood and Bayesian methods, strongly supported a close relationship between Sepsidae and the Tephritoidea.
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Affiliation(s)
- Xuankun Li
- Department of Entomology, China Agricultural University, Beijing, China
| | - Shuangmei Ding
- Department of Entomology, China Agricultural University, Beijing, China
| | - Stephen L Cameron
- Earth, Environmental & Biological Sciences School, Science & Engineering Faculty, Queensland University of Technology, Brisbane, Australia
| | - Zehui Kang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Yuyu Wang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing, China
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A 454 sequencing approach to dipteran mitochondrial genome research. Genomics 2015; 105:53-60. [DOI: 10.1016/j.ygeno.2014.10.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 10/29/2014] [Accepted: 10/31/2014] [Indexed: 01/14/2023]
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Gilchrist AS, Shearman DCA, Frommer M, Raphael KA, Deshpande NP, Wilkins MR, Sherwin WB, Sved JA. The draft genome of the pest tephritid fruit fly Bactrocera tryoni: resources for the genomic analysis of hybridising species. BMC Genomics 2014; 15:1153. [PMID: 25527032 PMCID: PMC4367827 DOI: 10.1186/1471-2164-15-1153] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 12/12/2014] [Indexed: 01/08/2023] Open
Abstract
Background The tephritid fruit flies include a number of economically important pests of horticulture, with a large accumulated body of research on their biology and control. Amongst the Tephritidae, the genus Bactrocera, containing over 400 species, presents various species groups of potential utility for genetic studies of speciation, behaviour or pest control. In Australia, there exists a triad of closely-related, sympatric Bactrocera species which do not mate in the wild but which, despite distinct morphologies and behaviours, can be force-mated in the laboratory to produce fertile hybrid offspring. To exploit the opportunities offered by genomics, such as the efficient identification of genetic loci central to pest behaviour and to the earliest stages of speciation, investigators require genomic resources for future investigations. Results We produced a draft de novo genome assembly of Australia’s major tephritid pest species, Bactrocera tryoni. The male genome (650 -700 Mbp) includes approximately 150Mb of interspersed repetitive DNA sequences and 60Mb of satellite DNA. Assessment using conserved core eukaryotic sequences indicated 98% completeness. Over 16,000 MAKER-derived gene models showed a large degree of overlap with other Dipteran reference genomes. The sequence of the ribosomal RNA transcribed unit was also determined. Unscaffolded assemblies of B. neohumeralis and B. jarvisi were then produced; comparison with B. tryoni showed that the species are more closely related than any Drosophila species pair. The similarity of the genomes was exploited to identify 4924 potentially diagnostic indels between the species, all of which occur in non-coding regions. Conclusions This first draft B. tryoni genome resembles other dipteran genomes in terms of size and putative coding sequences. For all three species included in this study, we have identified a comprehensive set of non-redundant repetitive sequences, including the ribosomal RNA unit, and have quantified the major satellite DNA families. These genetic resources will facilitate the further investigations of genetic mechanisms responsible for the behavioural and morphological differences between these three species and other tephritids. We have also shown how whole genome sequence data can be used to generate simple diagnostic tests between very closely-related species where only one of the species is scaffolded. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1153) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anthony Stuart Gilchrist
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052 Australia.
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Sagri E, Reczko M, Tsoumani KT, Gregoriou ME, Harokopos V, Mavridou AM, Tastsoglou S, Athanasiadis K, Ragoussis J, Mathiopoulos KD. The molecular biology of the olive fly comes of age. BMC Genet 2014; 15 Suppl 2:S8. [PMID: 25472866 PMCID: PMC4255830 DOI: 10.1186/1471-2156-15-s2-s8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background Olive cultivation blends with the history of the Mediterranean countries since ancient times. Even today, activities around the olive tree constitute major engagements of several people in the countryside of both sides of the Mediterranean basin. The olive fly is, beyond doubt, the most destructive pest of cultivated olives. The female fly leaves its eggs in the olive fruit. Upon emergence, the larvae feed on the olive sap, thus destroying the fruit. If untreated, practically all olives get infected. The use of chemical insecticides constitutes the principal olive fly control approach. The Sterile Insect Technique (SIT), an environmentally friendly alternative control method, had been tried in pilot field applications in the 1970's, albeit with no practical success. This was mainly attributed to the low, non-antagonistic quality of the mixed-sex released insects. Many years of experience from successful SIT applications in related species, primarily the Mediterranean fruit fly, Ceratitis capitata, demonstrated that efficient SIT protocols require the availability of fundamental genetic and molecular information. Results Among the primary systems whose understanding can contribute towards novel SIT approaches (or its recently developed alternative RIDL: Release of Insects carrying a Dominant Lethal) is the reproductive, since the ability to manipulate the reproductive system would directly affect the insect's fertility. In addition, the analysis of early embryonic promoters and apoptotic genes would provide tools that confer dominant early-embryonic lethality during mass-rearing. Here we report the identification of several genes involved in these systems through whole transcriptome analysis of female accessory glands (FAGs) and spermathecae, as well as male testes. Indeed, analysis of differentially expressed genes in these tissues revealed higher metabolic activity in testes than in FAGs/spermathecae. Furthermore, at least five olfactory-related genes were shown to be differentially expressed in the female and male reproductive systems analyzed. Finally, the expression profile of the embryonic serendipity-α locus and the pre-apoptotic head involution defective gene were analyzed during embryonic developmental stages. Conclusions Several years of molecular studies on the olive fly can now be combined with new information from whole transcriptome analyses and lead to a deep understanding of the biology of this notorious insect pest. This is a prerequisite for the development of novel embryonic lethality female sexing strains for successful SIT efforts which, combined with improved mass-reared conditions, give new hope for efficient SIT applications for the olive fly.
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