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Niu M, Liu Y, Xue L, Cai B, Zhao Q, Wei J. Improving DNA barcoding library of armored scale insects (Hemiptera: Diaspididae) in China. PLoS One 2024; 19:e0301499. [PMID: 38814962 PMCID: PMC11139323 DOI: 10.1371/journal.pone.0301499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/18/2024] [Indexed: 06/01/2024] Open
Abstract
DNA barcoding is used to identify cryptic species, survey environmental samples, and estimate phyletic and genetic diversity. Armored scale insects are phytophagous insects and are the most species-rich taxa in the Coccoidea superfamily. This study developed a DNA barcode library for armored scale insect species collected from southern China during 2021-2022. We sequenced a total of 239 specimens, recognized as 50 morphological species, representing two subfamilies and 21 genera. Sequencing analysis revealed that the average G + C content of the cytochrome oxidase subunit I (COI) gene sequence was very low (~18.06%) and that the average interspecific divergence was 10.07% while intraspecific divergence was 3.20%. The intraspecific divergence value was inflated by the high intraspecific divergence in ten taxa, which may indicate novel species overlooked by current taxonomic treatments. All the Automated Barcode Gap Discovery, Assemble Species by Automatic Partitioning, Taxon DNA analysis and Bayesian Poisson Tree Process methods yielded largely consistent results, indicating a robust and credible species delimitation. Based on these results, an intergeneric distance threshold of ≤ 5% was deemed appropriate for the differentiation of armored scale insect species in China. This study establishes a comprehensive barcode library for the identification of armored scale insects, future research, and application.
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Affiliation(s)
- Minmin Niu
- College of Plant Protection, Shanxi Agricultural University, Taigu, China
| | - Yubo Liu
- College of Plant Protection, Shanxi Agricultural University, Taigu, China
| | - Linjia Xue
- College of Plant Protection, Shanxi Agricultural University, Taigu, China
| | - Bo Cai
- Hainan Province Engineering Research Center for Quarantine, Prevention and Control of Exotic Pests, Haikou, China
| | - Qing Zhao
- College of Plant Protection, Shanxi Agricultural University, Taigu, China
| | - Jiufeng Wei
- College of Plant Protection, Shanxi Agricultural University, Taigu, China
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2
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Kirichenko NI, Ageev AA, Astapenko SA, Golovina AN, Kasparyan DR, Kosheleva OV, Timokhov AV, Tselikh EV, Zakharov EV, Musolin DL, Belokobylskij SA. The Diversity of Parasitoids and Their Role in the Control of the Siberian Moth, Dendrolimus sibiricus (Lepidoptera: Lasiocampidae), a Major Coniferous Pest in Northern Asia. Life (Basel) 2024; 14:268. [PMID: 38398777 PMCID: PMC10890493 DOI: 10.3390/life14020268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
The Siberian moth, Dendrolimus sibiricus Tschetv., 1908 (Lepidoptera: Lasiocampidae) is a conifer pest that causes unprecedented forest mortality in Northern Asia, leading to enormous ecological and economic losses. This is the first study summarizing data on the parasitoid diversity and parasitism of this pest over the last 118 years (1905-2022). Based on 860 specimens of freshly reared and archival parasitoids, 16 species from two orders (Hymenoptera and Diptera) were identified morphologically and/or with the use of DNA barcoding. For all of them, data on distribution and hosts and images of parasitoid adults are provided. Among them, the braconid species, Meteorus versicolor (Wesmael, 1835), was documented as a parasitoid of D. sibiricus for the first time. The eastern Palaearctic form, Aleiodes esenbeckii (Hartig, 1838) dendrolimi (Matsumura, 1926), status nov., was resurrected from synonymy as a valid subspecies, and a key for its differentiation from the western Palaearctic subspecies Aleiodes esenbeckii ssp. esenbecki is provided. DNA barcodes of 11 parasitoid species from Siberia, i.e., nine hymenopterans and two dipterans, represented novel records and can be used for accurate molecular genetic identification of species. An exhaustive checklist of parasitoids accounting for 93 species associated with D. sibirisus in northern Asia was compiled. Finally, the literature and original data on parasitism in D. sibiricus populations for the last 83 years (1940-2022) were analysed taking into account the pest population dynamics (i.e., growth, outbreak, decline, and depression phases). A gradual time-lagged increase in egg and pupal parasitism in D. sibiricus populations was detected, with a peak in the pest decline phase. According to long-term observations, the following species are able to cause significant mortality of D. sibiricus in Northern Asia: the hymenopteran egg parasitoids Telenomus tetratomus and Ooencyrtus pinicolus; the larval parasitoids Aleiodes esenbeckii sp. dendrolimi, Cotesia spp., and Glyptapanteles liparidis; and the dipteran pupal parasitoids Masicera sphingivora, Tachina sp., and Blepharipa sp. Their potential should be further explored in order to develop biocontrol programs for this important forest pest.
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Affiliation(s)
- Natalia I. Kirichenko
- Federal Research Center, Sukachev Institute of Forest, Siberian Branch of the Russian Academy of Sciences, Akademgorodok 50/28, 660036 Krasnoyarsk, Russia
- Institute of Ecology and Geography, Siberian Federal University, Svobodny pr. 79, 660041 Krasnoyarsk, Russia
- All-Russian Plant Quarantine Center (FGBU VNIIKR), Krasnoyarsk Branch, Zhelyabova Str., 6/6, 660020 Krasnoyarsk, Russia
| | - Alexander A. Ageev
- All-Russian Research Institute of Forestry and Forestry Mechanization (VNIILM), “Forest Pyrology Center”, Krasnoyarsk Branch, Krupskoy St., 42, 660062 Krasnoyarsk, Russia; (A.A.A.); (S.A.A.); (A.N.G.)
| | - Sergey A. Astapenko
- All-Russian Research Institute of Forestry and Forestry Mechanization (VNIILM), “Forest Pyrology Center”, Krasnoyarsk Branch, Krupskoy St., 42, 660062 Krasnoyarsk, Russia; (A.A.A.); (S.A.A.); (A.N.G.)
- Federal Budgetary Institution “Russian Forest Protection Center”, Akademgorodok 50/2, 660036 Krasnoyarsk, Russia
| | - Anna N. Golovina
- All-Russian Research Institute of Forestry and Forestry Mechanization (VNIILM), “Forest Pyrology Center”, Krasnoyarsk Branch, Krupskoy St., 42, 660062 Krasnoyarsk, Russia; (A.A.A.); (S.A.A.); (A.N.G.)
| | - Dmitry R. Kasparyan
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia; (D.R.K.); (E.V.T.)
| | - Oksana V. Kosheleva
- All-Russian Institute of Plant Protection (FSBSI VIZR), Podbelskogo 3, 196608 Saint Petersburg, Russia;
| | - Alexander V. Timokhov
- Department of Entomology, Lomonosov Moscow State University, Leninskie Gory, 119234 Moscow, Russia;
| | - Ekaterina V. Tselikh
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia; (D.R.K.); (E.V.T.)
| | - Evgeny V. Zakharov
- Canadian Center for DNA Barcoding, Centre for Biodiversity Genomics, College of Biological Sciences, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada;
| | - Dmitrii L. Musolin
- European and Mediterranean Plant Protection Organization, 21 Boulevard Richard Lenoir, 75011 Paris, France;
| | - Sergey A. Belokobylskij
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia; (D.R.K.); (E.V.T.)
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3
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Noll NW, Scherber C, Schäffler L. taxalogue: a toolkit to create comprehensive CO1 reference databases. PeerJ 2023; 11:e16253. [PMID: 38077427 PMCID: PMC10702336 DOI: 10.7717/peerj.16253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/18/2023] [Indexed: 12/18/2023] Open
Abstract
Background Taxonomic identification through DNA barcodes gained considerable traction through the invention of next-generation sequencing and DNA metabarcoding. Metabarcoding allows for the simultaneous identification of thousands of organisms from bulk samples with high taxonomic resolution. However, reliable identifications can only be achieved with comprehensive and curated reference databases. Therefore, custom reference databases are often created to meet the needs of specific research questions. Due to taxonomic inconsistencies, formatting issues, and technical difficulties, building a custom reference database requires tremendous effort. Here, we present taxalogue, an easy-to-use software for creating comprehensive and customized reference databases that provide clean and taxonomically harmonized records. In combination with extensive geographical filtering options, taxalogue opens up new possibilities for generating and testing evolutionary hypotheses. Methods taxalogue collects DNA sequences from several online sources and combines them into a reference database. Taxonomic incongruencies between the different data sources can be harmonized according to available taxonomies. Dereplication and various filtering options are available regarding sequence quality or metadata information. taxalogue is implemented in the open-source Ruby programming language, and the source code is available at https://github.com/nwnoll/taxalogue. We benchmark four reference databases by sequence identity against eight queries from different localities and trapping devices. Subsamples from each reference database were used to compare how well another one is covered. Results taxalogue produces reference databases with the best coverage at high identities for most tested queries, enabling more accurate, reliable predictions with higher certainty than the other benchmarked reference databases. Additionally, the performance of taxalogue is more consistent while providing good coverage for a variety of habitats, regions, and sampling methods. taxalogue simplifies the creation of reference databases and makes the process reproducible and transparent. Multiple available output formats for commonly used downstream applications facilitate the easy adoption of taxalogue in many different software pipelines. The resulting reference databases improve the taxonomic classification accuracy through high coverage of the query sequences at high identities.
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Affiliation(s)
- Niklas W. Noll
- Centre for Biodiversity Monitoring and Conservation Science, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, North Rhine-Westphalia, Germany
| | - Christoph Scherber
- Centre for Biodiversity Monitoring and Conservation Science, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, North Rhine-Westphalia, Germany
| | - Livia Schäffler
- Centre for Biodiversity Monitoring and Conservation Science, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, North Rhine-Westphalia, Germany
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Riza LS, Zain MI, Izzuddin A, Prasetyo Y, Hidayat T, Abu Samah KAF. Implementation of machine learning in DNA barcoding for determining the plant family taxonomy. Heliyon 2023; 9:e20161. [PMID: 37767518 PMCID: PMC10520734 DOI: 10.1016/j.heliyon.2023.e20161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
The DNA barcoding approach has been used extensively in taxonomy and phylogenetics. The differences in certain DNA sequences are able to differentiate and help classify organisms into taxa. It has been used in cases of taxonomic disputes where morphology by itself is insufficient. This research aimed to utilize hierarchical clustering, an unsupervised machine learning method, to determine and resolve disputes in plant family taxonomy. We take a case study of Leguminosae that historically some classify into three families (Fabaceae, Caesalpiniaceae, and Mimosaceae) but others classify into one family (Leguminosae). This study is divided into several phases, which are: (i) data collection, (ii) data preprocessing, (iii) finding the best distance method, and (iv) determining disputed family. The data used are collected from several sources, including National Center for Biotechnology Information (NCBI), journals, and websites. The data for validation of the methods were collected from NCBI. This was used to determine the best distance method for differentiating families or genera. The data for the case study in the Leguminosae group was collected from journals and a website. From the experiment that we have conducted, we found that the Pearson method is the best distance method to do clustering ITS sequence of plants, both in accuracy and computational cost. We use the Pearson method to determine the disputed family between Leguminosae. We found that the case study of Leguminosae should be grouped into one family based on our research.
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Affiliation(s)
- Lala Septem Riza
- Department of Computer Science Education, Universitas Pendidikan Indonesia, Bandung, Indonesia
| | - Muhammad Iqbal Zain
- Department of Computer Science Education, Universitas Pendidikan Indonesia, Bandung, Indonesia
| | - Ahmad Izzuddin
- Department of Computer Science Education, Universitas Pendidikan Indonesia, Bandung, Indonesia
| | - Yudi Prasetyo
- Department of Computer Science Education, Universitas Pendidikan Indonesia, Bandung, Indonesia
| | - Topik Hidayat
- Department of Biology Education, Universitas Pendidikan Indonesia, Bandung, Indonesia
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5
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Hu GL, Brown J, Heikkilä M, Aarvik L, Mutanen M. Molecular phylogeny, divergence time, biogeography and trends in host plant usage in the agriculturally important tortricid tribe Grapholitini (Lepidoptera: Tortricidae: Olethreutinae). Cladistics 2023; 39:359-381. [PMID: 37209356 DOI: 10.1111/cla.12543] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 03/27/2023] [Accepted: 04/25/2023] [Indexed: 05/22/2023] Open
Abstract
The leaf-roller moth tribe Grapholitini comprises about 1200 described species and contains numerous notorious pests of fruits and seeds. The phylogeny of the tribe has been little studied using contemporary methods, and the monophyly of several genera remains questionable. In order to provide a more robust phylogenetic framework for the group, we conducted a multiple-gene phylogenetic analysis of 104 species representing 27 genera of Grapholitini and 29 outgroup species. Divergence time, ancestral area, and host plant usage were also inferred to explore evolutionary trends in the tribe. Our analyses indicate that Larisa and Corticivora, traditionally assigned to Grapholitini, are best excluded from the tribe. After removal of these two genera, the tribe is found to be monophyletic, represented by two major lineages-a Dichrorampha clade and a Cydia clade, the latter of which can be divided into seven generic groups. The genus Grapholita was found to be polyphyletic, comprising three different clades, and we propose three genera to accommodate these groups: Grapholita (sensu stricto), Aspila (formerly a subgenus of Grapholita) and Ephippiphora (formerly considered a synonym of Grapholita). We summarize each generic group, including related genera not included in our analysis, providing morphological, pheromone and food plant characters that support particular branches within the molecular hypotheses. Biogeographical analyses indicate that Grapholitini probably originated in the Nearctic, Afrotropical and Neotropical regions in the Lutetian of the middle Eocene (ca. 44.3 Ma). Our results also indicate that most groups in Grapholitini originated from Fabaceae-feeding monophagous or oligophagous ancestors, and that host plant shifts probably promoted species diversification within the tribe.
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Affiliation(s)
- Gui-Lin Hu
- School of Life Sciences, Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou, China
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - John Brown
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Maria Heikkilä
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Leif Aarvik
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
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6
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Lvarez-Presas M, Littlewood DTJ, Mateos E, Jones HD. Exploring gene sequences and phylogenetic relationships of four terrestrial planarian species (Platyhelminthes; Tricladida; Geoplanidae) in Europe. Zootaxa 2023; 5336:95-112. [PMID: 38221109 DOI: 10.11646/zootaxa.5336.1.4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Indexed: 01/16/2024]
Abstract
Partial mitochondrial cox1 gene sequences from four recently recognised European species of terrestrial planarians, and ribosomal ITS1 sequences for two of them, are presented: Marionfyfea adventor, Artioposthia exulans (both introduced from New Zealand), Australopacifica atrata (from Australia) and specimens putatively identified as Microplana edwardsi, presumed to be native to the UK. The sequences are compared with those from other terrestrial planarian species and analysed phylogenetically. Results indicate that the sister group of M. adventor comprises a clade constituted by at least the genus Arthurdendyus. The phylogenetic position of Ar. exulans remains less certain, Australopacifica atrata might be closely related to the species Parakontikia ventrolineata and Endeavouria septemlineata. The specimens of M. cf. edwardsi are distinct from all other Microplana species for which sequences are available.
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Affiliation(s)
- Marta Lvarez-Presas
- Departament de Gentica; Microbiologia i Estadstica; Facultat de Biologia; Universitat de Barcelona; Barcelona; Spain; Institut de Biologia Evolutiva (UPF-CSIC); Barcelona; Spain.
| | | | - Eduardo Mateos
- Departament de Biologia Evolutiva; Ecologia i Cincies Ambientals; Facultat de Biologia; Universitat de Barcelona; Barcelona; Spain.
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7
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Zink FA, Tembrock LR, Timm AE, Gilligan TM. Ultra-deep sequencing of 45S rDNA to discern intragenomic diversity in three Chrysodeixis species for molecular identification. Sci Rep 2023; 13:13017. [PMID: 37563256 PMCID: PMC10415407 DOI: 10.1038/s41598-023-39673-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/28/2023] [Indexed: 08/12/2023] Open
Abstract
Species identification is necessary to prevent introductions of exotic plant pests through global trade. Many of these pests are understudied and lack publicly available DNA sequence data on which rapid molecular identification methods can be based. One such lineage is the genus Chrysodeixis, which includes three species of potential concern for United States trade initiatives: C. includens, C. chalcites, and C. eriosoma. Here we describe a method to generate robust 45S rDNA profiles using long read sequencing in order to clarify evolutionary relationships and develop a real-time PCR identification technique. Such an identification tool will be useful in rapidly differentiating between Chrysodeixis species of quarantine concern where traditional morphological identification methods are insufficient. Molecular methods such as this greatly reduce the time spent identifying each specimen, allow for detection of eDNA, vastly increase throughput, and increase the probability of detection. The methods presented here will be generally adaptable to any understudied lepidopteran taxa that necessitates a molecular diagnostic assay and, with adjustment or testing of the primers, could be applied to any group for which development of rDNA profiles in a benchtop setting would prove useful.
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Affiliation(s)
- Frida A Zink
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA.
| | - Alicia E Timm
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Todd M Gilligan
- Pest Identification Technology Laboratory, USDA-APHIS-PPQ-Science and Technology, Fort Collins, CO, USA
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8
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The global spread and invasion capacities of alien ants. Curr Biol 2023; 33:566-571.e3. [PMID: 36610395 DOI: 10.1016/j.cub.2022.12.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/20/2022] [Accepted: 12/08/2022] [Indexed: 01/09/2023]
Abstract
Many alien species are neither cultivated nor traded but spread unintentionally, and their global movements, capacities to invade ecosystems, and susceptibility to detection by biosecurity measures are poorly known.1,2,3,4 We addressed these key knowledge gaps for ants, a ubiquitous group of stowaway and contaminant organisms that include some of the world's most damaging invasive species.5,6,7,8,9,10 We assembled a dataset of over 146,000 occurrence records to comprehensively map the human-mediated spread of 520 alien ant species across 525 regions globally. From descriptions of the environments in which species were collected within individual regions-such as in imported cargoes, buildings, and outdoor settings-we determined whether different barriers to invasion had been overcome11 and classified alien ant species under three levels of invasion capacity corresponding to increasing biosecurity threat. We found that alien species of different invasion capacities had different sources and sinks globally. For instance, although the diversity of indoor-confined species peaked in the Palearctic realm, that of species able to establish outdoors peaked in the Nearctic and Oceanian realms, and these mainly originated from the Neotropical and Oriental realms. We also found that border interceptions worldwide missed two-thirds of alien species with naturalization capacity, many associated with litter and soil. Our study documents the vast spread of alien ants globally while highlighting avenues for more targeted biosecurity responses, such as prioritizing the screening of imports from regions that are diversity hotspots for species of high invasion capacity and improving the detection of cryptic alien invertebrates dwelling in substrates.
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9
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Nahrung HF, Liebhold AM, Brockerhoff EG, Rassati D. Forest Insect Biosecurity: Processes, Patterns, Predictions, Pitfalls. ANNUAL REVIEW OF ENTOMOLOGY 2023; 68:211-229. [PMID: 36198403 DOI: 10.1146/annurev-ento-120220-010854] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The economic and environmental threats posed by non-native forest insects are ever increasing with the continuing globalization of trade and travel; thus, the need for mitigation through effective biosecurity is greater than ever. However, despite decades of research and implementation of preborder, border, and postborder preventative measures, insect invasions continue to occur, with no evidence of saturation, and are even predicted to accelerate. In this article, we review biosecurity measures used to mitigate the arrival, establishment, spread, and impacts of non-native forest insects and possible impediments to the successful implementation of these measures. Biosecurity successes are likely under-recognized because they are difficult to detect and quantify, whereas failures are more evident in the continued establishment of additional non-native species. There are limitations in existing biosecurity systems at global and country scales (for example, inspecting all imports is impossible, no phytosanitary measures are perfect, knownunknowns cannot be regulated against, and noncompliance is an ongoing problem). Biosecurity should be a shared responsibility across countries, governments, stakeholders, and individuals.
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Affiliation(s)
- Helen F Nahrung
- Forest Research Institute, University of the Sunshine Coast, Sippy Downs, Queensland, Australia;
| | - Andrew M Liebhold
- US Forest Service Northern Research Station, Morgantown, West Virginia, USA;
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Czech Republic
| | - Eckehard G Brockerhoff
- Forest Health and Biotic Interactions, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland;
| | - Davide Rassati
- Department of Agronomy, Food, Natural Resources, Animals and the Environment, University of Padova, Italy;
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10
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Baena-Bejarano N, Reina C, Martínez-Revelo DE, Medina CA, Tovar E, Uribe-Soto S, Neita-Moreno JC, Gonzalez MA. Taxonomic identification accuracy from BOLD and GenBank databases using over a thousand insect DNA barcodes from Colombia. PLoS One 2023; 18:e0277379. [PMID: 37093820 PMCID: PMC10124890 DOI: 10.1371/journal.pone.0277379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/10/2023] [Indexed: 04/25/2023] Open
Abstract
Recent declines of insect populations at high rates have resulted in the need to develop a quick method to determine their diversity and to process massive data for the identification of species of highly diverse groups. A short sequence of DNA from COI is widely used for insect identification by comparing it against sequences of known species. Repositories of sequences are available online with tools that facilitate matching of the sequences of interest to a known individual. However, the performance of these tools can differ. Here we aim to assess the accuracy in identification of insect taxonomic categories from two repositories, BOLD Systems and GenBank. This was done by comparing the sequence matches between the taxonomist identification and the suggested identification from the platforms. We used 1,160 COI sequences representing eight orders of insects from Colombia. After the comparison, we reanalyzed the results from a representative subset of the data from the subfamily Scarabaeinae (Coleoptera). Overall, BOLD systems outperformed GenBank, and the performance of both engines differed by orders and other taxonomic categories (species, genus and family). Higher rates of accurate identification were obtained at family and genus levels. The accuracy was higher in BOLD for the order Coleoptera at family level, for Coleoptera and Lepidoptera at genus and species level. Other orders performed similarly in both repositories. Moreover, the Scarabaeinae subset showed that species were correctly identified only when BOLD match percentage was above 93.4% and a total of 85% of the samples were correctly assigned to a taxonomic category. These results accentuate the great potential of the identification engines to place insects accurately into their respective taxonomic categories based on DNA barcodes and highlight the reliability of BOLD Systems for insect identification in the absence of a large reference database for a highly diverse country.
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Affiliation(s)
| | - Catalina Reina
- ICA-Instituto Colombiano Agropecuario, Soledad, Atlántico, Colombia
| | - Diego Esteban Martínez-Revelo
- Asociación GAICA, Pasto, Nariño, Colombia
- Grupo de Investigación en Sistemática Molecular, Universidad Nacional de Colombia, Sede Medellín, Medellín, Antioquia, Colombia
| | - Claudia A Medina
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá, Colombia
| | - Eduardo Tovar
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá, Colombia
| | - Sandra Uribe-Soto
- Grupo de Investigación en Sistemática Molecular, Universidad Nacional de Colombia, Sede Medellín, Medellín, Antioquia, Colombia
| | | | - Mailyn A Gonzalez
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá, Colombia
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11
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DNA Barcoding of Lepidoptera Species from the Maltese Islands: New and Additional Records, with an Insight into Endemic Diversity. DIVERSITY 2022. [DOI: 10.3390/d14121090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This work presents the first outcomes resulting from a DNA barcode reference library of lepidopteran species from Malta. The library presented here was constructed from the specimens collected between 2015 and 2019 and covers the genetic barcodes of 146 species (ca. 25% of lepidopterous Maltese fauna), including four newly recorded Lepidoptera species from the Maltese islands: Apatema baixerasi, Bostra dipectinialis, Oiketicoides lutea, and Phereoeca praecox. The DNA reference barcode library constructed during this study was analyzed in conjunction with publicly available DNA barcodes and used to assess the ability of the local DNA barcodes to discriminate species. Results showed that each species occupies a different BOLD BIN; therefore, DNA barcoding was able to discriminate between the studied species. Our data led to the formation of 12 new BOLD BINs—that is, OTUs that were identified during this work—while nearly 46% of the barcodes generated during this study were never recorded on conspecifics, further indicating the uniqueness of genetic diversity on these central Mediterranean islands. The outcomes of this study highlight the integrative taxonomic approach, where molecular taxonomy plays an important role for biodiversity investigation in its entirety.
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12
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Rapid and zero-cost DNA extraction from soft-bodied insects for routine PCR-based applications. PLoS One 2022; 17:e0271312. [PMID: 35839213 PMCID: PMC9286237 DOI: 10.1371/journal.pone.0271312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 06/28/2022] [Indexed: 11/30/2022] Open
Abstract
Nucleic acid extraction is the first and foremost step in molecular biology studies. Extraction of DNA from small, soft-bodied insects is often time-consuming and costly. A fast, easy, and cost-effective DNA extraction method with greater yield and purity of DNA would aid in the rapid diagnostics, screening of large populations, and other routine PCR-based applications. The present study evaluated and standardized a rapid and zero-cost DNA extraction from soft-bodied small insects for routine molecular studies. Five rapid DNA extraction methods viz. extraction in sterile distilled water (SDW), 1X phosphate-buffered saline (PBS, pH 7.4), 1.4 M sodium chloride (NaCl), 20 mM ethylenediaminetetraacetic acid (EDTA, pH 8.0), and elution from blotted nitrocellulose membrane (NCM) were compared with standard CTAB extraction buffer and DNeasy® Blood and Tissue Kit methods. The average yield, purity, storage stability, time, and cost of extraction were assessed for all the methods and compared. A method of DNA extraction by simply crushing the soft-bodied insects in SDW was ideal in terms of yield, purity, storability, and performing routine PCR-based applications including detection of pathogens from vector species. The extraction could be accomplished in 2.5 min only with zero-reagent cost. The method would be useful in rapid molecular diagnostics and screening large populations of soft-bodied insects.
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Misbah S, Low VL, Mohd Rahim NF, Jaba R, Basari N, Ya'cob Z, Abu Bakar S. Mitochondrial Diversity of the Asian Tiger Mosquito Aedes albopictus (Diptera: Culicidae) in Peninsular Malaysia. JOURNAL OF MEDICAL ENTOMOLOGY 2022; 59:865-873. [PMID: 35178576 DOI: 10.1093/jme/tjac014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Indexed: 06/14/2023]
Abstract
Aedes albopictus is one of the main mosquito vectors responsible for transmitting arboviruses to humans and animals. The ability of this mosquito to support virus transmission has been linked to vector competence, which is partly attributed to the genetic disparities in Ae. albopictus population. At present, little is known about the biologically important traits of Ae. albopictus in Malaysia. Thus, the study aims to determine the genetic variation of Ae. albopictus based on the mitochondria-encoded sequences of cytochrome oxidase subunit I (COI). A statistical parsimony network of 253 taxa aligned as 321 characters of the COI gene revealed 42 haplotypes (H1-H42), of which H1 was the most widespread haplotype in Peninsular Malaysia. Three highly divergent haplotypes (H21, H30, and H31) were detected from the northern population. Overall, haplotype and nucleotide diversities were 0.576 and 0.003, respectively, with low genetic differentiation (FST = 0.039) and high gene flow (Nm = 12.21) across all populations.
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Affiliation(s)
- Suzana Misbah
- Biological Security and Sustainability (BioSES) Research Interest Group, Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Van Lun Low
- Higher Institution Centre of Excellence (HICoE), Tropical Infectious Diseases Research & Education Centre (TIDREC), Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nurul Farhana Mohd Rahim
- Higher Institution Centre of Excellence (HICoE), Tropical Infectious Diseases Research & Education Centre (TIDREC), Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Rizzuaeammie Jaba
- Biological Security and Sustainability (BioSES) Research Interest Group, Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Norasmah Basari
- Biological Security and Sustainability (BioSES) Research Interest Group, Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Zubaidah Ya'cob
- Higher Institution Centre of Excellence (HICoE), Tropical Infectious Diseases Research & Education Centre (TIDREC), Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sazaly Abu Bakar
- Higher Institution Centre of Excellence (HICoE), Tropical Infectious Diseases Research & Education Centre (TIDREC), Universiti Malaya, 50603, Kuala Lumpur, Malaysia
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Universal Mitochondrial Multi-Locus Sequence Analysis (mtMLSA) to Characterise Populations of Unanticipated Plant Pest Biosecurity Detections. BIOLOGY 2022; 11:biology11050654. [PMID: 35625382 PMCID: PMC9138331 DOI: 10.3390/biology11050654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/11/2022] [Accepted: 04/21/2022] [Indexed: 12/02/2022]
Abstract
Simple Summary Agricultural and environmental sustainability requires effective biosecurity responses that prevent the establishment or spread of exotic insect pests. Understanding where new detections may have come from or if recurrent detections are connected contributes to this. Suitable population genetic markers use relatively rapidly evolving gene regions which render the PCR method species-specific at best. Because resource limitations mean these are pre-emptively developed for the highest risk species, populations of other exotic pests are unable to be characterised at the time. Here we have developed a generic method that is useful across species within the same taxonomic Order, including where there is little or no prior knowledge of their gene sequences. Markers are formed by concomitant sequencing of four gene regions. Sequence concatenation was shown to retrieve higher resolution signatures than standard DNA barcoding. The method is encouragingly universal, as illustrated across species in ten fly and 11 moth superfamilies. Although as-yet untested in a biosecurity situation, this relatively low-tech, off-the-shelf method makes a proactive contribution to the toolbox of quarantine agencies at the time of detection without the need for impromptu species-specific research and development. Abstract Biosecurity responses to post-border exotic pest detections are more effective with knowledge of where the species may have originated from or if recurrent detections are connected. Population genetic markers for this are typically species-specific and not available in advance for any but the highest risk species, leaving other less anticipated species difficult to assess at the time. Here, new degenerate PCR primer sets are designed for within the Lepidoptera and Diptera for the 3′ COI, ND3, ND6, and 3′ plus 5′ 16S gene regions. These are shown to be universal at the ordinal level amongst species of 14 and 15 families across 10 and 11 dipteran and lepidopteran superfamilies, respectively. Sequencing the ND3 amplicons as an example of all the loci confirmed detection of population-level variation. This supported finding multiple population haplotypes from the publicly available sequences. Concatenation of the sequences also confirmed that higher population resolution is achieved than for the individual genes. Although as-yet untested in a biosecurity situation, this method is a relatively simple, off-the-shelf means to characterise populations. This makes a proactive contribution to the toolbox of quarantine agencies at the time of detection without the need for unprepared species-specific research and development.
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Phillips JD, Gillis DJ, Hanner RH. Lack of Statistical Rigor in DNA Barcoding Likely Invalidates the Presence of a True Species' Barcode Gap. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.859099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA barcoding has been largely successful in satisfactorily exposing levels of standing genetic diversity for a wide range of taxonomic groups through the employment of only one or a few universal gene markers. However, sufficient coverage of geographically-broad intra-specific haplotype variation within genomic databases like the Barcode of Life Data Systems (BOLD) and GenBank remains relatively sparse. As reference sequence libraries continue to grow exponentially in size, there is now the need to identify novel ways of meaningfully analyzing vast amounts of available DNA barcode data. This is an important issue to address promptly for the routine tasks of specimen identification and species discovery, which have seen broad adoption in areas as diverse as regulatory forensics and resource conservation. Here, it is demonstrated that the interpretation of DNA barcoding data is lacking in statistical rigor. To highlight this, focus is set specifically on one key concept that has become a household name in the field: the DNA barcode gap. Arguments outlined herein specifically center on DNA barcoding in animal taxa and stem from three angles: (1) the improper allocation of specimen sampling effort necessary to capture adequate levels of within-species genetic variation, (2) failing to properly visualize intra-specific and interspecific genetic distances, and (3) the inconsistent, inappropriate use, or absence of statistical inferential procedures in DNA barcoding gap analyses. Furthermore, simple statistical solutions are outlined which can greatly propel the use of DNA barcoding as a tool to irrefutably match unknowns to knowns on the basis of the barcoding gap with a high degree of confidence. Proposed methods examined herein are illustrated through application to DNA barcode sequence data from Canadian Pacific fish species as a case study.
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DNA barcoding of insects from India: Current status and future perspectives. Mol Biol Rep 2022; 49:10617-10626. [PMID: 35716293 PMCID: PMC9206398 DOI: 10.1007/s11033-022-07628-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/01/2022]
Abstract
Insect fauna occupy the largest proportion of animal biodiversity on earth, but the assessment or quantification in terms of species diversity is far from complete. Several recent studies have demonstrated the rapid pace at which insect population decline is occurring. There is an urgent need to document and quantify the diversity of insect fauna for a proper understanding of terrestrial ecosystems. This can be achieved by using modern technology to identify species much faster than relying on traditional methods alone. In line with this, the molecular approach through DNA barcoding coupled with morphological identification needs to be focused and accelerated. The present paper describes the current status of barcoding of insect species in India along with the gaps that need to be remedied. This analysis shows that barcoded specimens cover a very meagre proportion of less than 3.73% of the known taxa/described species and the most represented orders are Lepidoptera and Hemiptera followed by Diptera and Coleoptera. There is a need to expedite insect species discovery and documentation in a collaborative mode between traditional taxonomists and molecular biologists, to accomplish the DNA barcoding of all known insect taxa from India.
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Hu JL, Ci XQ, Liu ZF, Dormontt EE, Conran JG, Lowe AJ, Li J. Assessing candidate DNA barcodes for Chinese and internationally traded timber species. Mol Ecol Resour 2021; 22:1478-1492. [PMID: 34752673 DOI: 10.1111/1755-0998.13546] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 10/22/2021] [Accepted: 11/01/2021] [Indexed: 11/27/2022]
Abstract
Accurate identification of species from timber is an essential step to help control illegal logging and forest loss. However, current approaches to timber identification based on morphological and anatomical characteristics have limited species resolution. DNA barcoding is a proven tool for plant species identification, but there is a need to build reliable reference data across broad taxonomic and spatial scales. Here, we construct a species barcoding library consisting of 1550 taxonomically diverse timber species from 656 genera and 124 families, representing a comprehensive genetic reference data set for Chinese timber species and international commercial traded timber species, using four barcodes (rbcL, matK, trnH-psbA, and ITS2). The ITS2 fragment was found to be the most efficient locus for Chinese timber species identification among the four barcodes tested, both at the species and genus level, despite its low recovery rate. Nevertheless, the barcode combination matK+trnH-psbA+ITS2 was required as a complementary barcode to distinguish closely related species in complex data sets involving internationally traded timber species. Comparative analyses of family-level discrimination and species/genus ratios indicated that the inclusion of closely related species is an important factor affecting the resolution ability of barcodes for timber species verification. Our study indicates that although nuclear ITS2 is the most efficient single barcode for timber species authentication in China, complementary combinations like matK+trnH-psbA+ITS2 are required to provide broader discrimination power. These newly-generated sequences enrich the existing publicly available databases, especially for tropical and subtropical evergreen timber trees and this current timber species barcode reference library can serve as an important genetic resource for forestry monitoring, illegal logging prosecution and biodiversity projects.
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Affiliation(s)
- Jian-Lin Hu
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiu-Qin Ci
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
| | - Zhi-Fang Liu
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Eleanor E Dormontt
- Advanced DNA, Identification and Forensic Facility, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - John G Conran
- Australian Centre for Evolutionary Biology and Biodiversity (ACEBB) and Sprigg Geobiology Centre (SGC), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Andrew J Lowe
- Advanced DNA, Identification and Forensic Facility, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Jie Li
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
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A Rapid and Cost-Effective Identification of Invertebrate Pests at the Borders Using MinION Sequencing of DNA Barcodes. Genes (Basel) 2021; 12:genes12081138. [PMID: 34440312 PMCID: PMC8392835 DOI: 10.3390/genes12081138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 12/12/2022] Open
Abstract
The rapid and accurate identification of invertebrate pests detected at the border is a challenging task. Current diagnostic methods used at the borders are mainly based on time consuming visual and microscopic examinations. Here, we demonstrate a rapid in-house workflow for DNA extraction, PCR amplification of the barcode region of the mitochondrial cytochrome oxidase subunit I (COI) gene and Oxford Nanopore Technologies (ONT) MinION sequencing of amplified products multiplexed after barcoding on ONT Flongle flow cells. A side-by-side comparison was conducted of DNA barcode sequencing-based identification and morphological identification of both large (>0.5 mm in length) and small (<0.5 mm in length) invertebrate specimens intercepted at the Australian border. DNA barcode sequencing results supported the morphological identification in most cases and enabled immature stages of invertebrates and their eggs to be identified more confidently. Results also showed that sequencing the COI barcode region using the ONT rapid sequencing principle is a cost-effective and field-adaptable approach for the rapid and accurate identification of invertebrate pests. Overall, the results suggest that MinION sequencing of DNA barcodes offers a complementary tool to the existing morphological diagnostic approaches and provides rapid, accurate, reliable and defendable evidence for identifying invertebrate pests at the border.
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Abstract
Over the last two decades, the use of DNA barcodes has transformed our ability to identify and assess life on our planet. Both strengths and weaknesses of the method have been exemplified through thousands of peer-reviewed scientific articles. Given the novel sequencing approaches, currently capable of generating millions of reads at low cost, we reflect on the questions: What will the future bring for DNA barcoding? Will identification of species using short, standardized fragments of DNA stand the test of time? We present reflected opinions of early career biodiversity researchers in the form of a SWOT analysis and discuss answers to these questions.
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20
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Honeycutt RL. Editorial: DNA Barcodes: Controversies, Mechanisms, and Future Applications. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.718865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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21
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Highly diverse and rapidly spreading: Melanagromyza sojae threatens the soybean belt of South America. Biol Invasions 2021. [DOI: 10.1007/s10530-020-02447-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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22
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Karabanov DP, Kodukhova YV, Pashkov AN, Reshetnikov AN, Makhrov AA. “Journey to the West”: Three Phylogenetic Lineages Contributed to the Invasion of Stone Moroko, Pseudorasbora parva (Actinopterygii: Cyprinidae). RUSSIAN JOURNAL OF BIOLOGICAL INVASIONS 2021. [DOI: 10.1134/s2075111721010070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Garcia-Vazquez E, Georges O, Fernandez S, Ardura A. eDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters. Sci Rep 2021; 11:7224. [PMID: 33790382 PMCID: PMC8012656 DOI: 10.1038/s41598-021-86731-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/19/2021] [Indexed: 11/16/2022] Open
Abstract
Zooplankton community inventories are the basis of fisheries management for containing fish larvae and their preys; however, the visual identification of early-stage larvae (the "missing biomass") is difficult and laborious. Here, eDNA metabarcoding was employed to detect zooplankton species of interest for fisheries from open and coastal waters. High-Throughput sequencing (HTS) from environmental samples using small water volumes has been proposed to detect species of interest whose DNA is the most abundant. We analyzed 6-L water samples taken from subtropical and tropical waters using Cytochrome oxidase I (COI) gene as metabarcode. In the open ocean, several commercial fish larvae and invertebrate species important in fish diet were found from metabarcodes and confirmed from individual barcoding. Comparing Atlantic, Mediterranean, Red Sea, and Pacific samples we found a lower taxonomic depth of OTU assignments in samples from tropical waters than in those from temperate ones, suggesting large gaps in reference databases for those areas; thus a higher effort of zooplankton barcoding in tropical oceans is highly recommended. This and similar simplified sampling protocols could be applied in early detection of species important for fisheries.
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Affiliation(s)
- Eva Garcia-Vazquez
- Department of Functional Biology, University of Oviedo, C/Julian Claveria S/N, 33006, Oviedo, Spain
| | - Oriane Georges
- Department of Functional Biology, University of Oviedo, C/Julian Claveria S/N, 33006, Oviedo, Spain
| | - Sara Fernandez
- Department of Natural Sciences, School of Science and Computing, Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Dublin Road, Galway, H91 T8NW, Ireland
| | - Alba Ardura
- Department of Functional Biology, University of Oviedo, C/Julian Claveria S/N, 33006, Oviedo, Spain.
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Stackhouse T, Martinez-Espinoza AD, Ali ME. Turfgrass Disease Diagnosis: Past, Present, and Future. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1544. [PMID: 33187303 PMCID: PMC7697262 DOI: 10.3390/plants9111544] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/30/2020] [Accepted: 11/09/2020] [Indexed: 01/15/2023]
Abstract
Turfgrass is a multibillion-dollar industry severely affected by plant pathogens including fungi, bacteria, viruses, and nematodes. Many of the diseases in turfgrass have similar signs and symptoms, making it difficult to diagnose the specific problem pathogen. Incorrect diagnosis leads to the delay of treatment and excessive use of chemicals. To effectively control these diseases, it is important to have rapid and accurate detection systems in the early stages of infection that harbor relatively low pathogen populations. There are many methods for diagnosing pathogens on turfgrass. Traditional methods include symptoms, morphology, and microscopy identification. These have been followed by nucleic acid detection and onsite detection techniques. Many of these methods allow for rapid diagnosis, some even within the field without much expertise. There are several methods that have great potential, such as high-throughput sequencing and remote sensing. Utilization of these techniques for disease diagnosis allows for faster and accurate disease diagnosis and a reduction in damage and cost of control. Understanding of each of these techniques can allow researchers to select which method is best suited for their pathogen of interest. The objective of this article is to provide an overview of the turfgrass diagnostics efforts used and highlight prospects for disease detection.
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Affiliation(s)
- Tammy Stackhouse
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA;
| | | | - Md Emran Ali
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA;
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Yu J, Young RG, Deeth LE, Hanner RH. Molecular Detection Mapping and Analysis Platform for R (MDMAPR) facilitating the standardization, analysis, visualization, and sharing of qPCR data and metadata. PeerJ 2020; 8:e9974. [PMID: 33150057 PMCID: PMC7587055 DOI: 10.7717/peerj.9974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/26/2020] [Indexed: 11/30/2022] Open
Abstract
Quantitative polymerase chain reaction (qPCR) has been used as a standard molecular detection tool in many scientific fields. Unfortunately, there is no standard method for managing published qPCR data, and those currently used generally focus on only managing raw fluorescence data. However, associated with qPCR experiments are extensive sample and assay metadata, often under-examined and under-reported. Here, we present the Molecular Detection Mapping and Analysis Platform for R (MDMAPR), an open-source and fully scalable informatics tool for researchers to merge raw qPCR fluorescence data with associated metadata into a standard format, while geospatially visualizing the distribution of the data and relative intensity of the qPCR results. The advance of this approach is in the ability to use MDMAPR to store varied qPCR data. This includes pathogen and environmental qPCR species detection studies ideally suited to geographical visualization. However, it also goes beyond these and can be utilized with other qPCR data including gene expression studies, quantification studies used in identifying health dangers associated with food and water bacteria, and the identification of unknown samples. In addition, MDMAPR’s novel centralized management and geospatial visualization of qPCR data can further enable cross-discipline large-scale qPCR data standardization and accessibility to support research spanning multiple fields of science and qPCR applications.
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Affiliation(s)
- Jiaojia Yu
- Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Robert G Young
- Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Lorna E Deeth
- Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario, Canada
| | - Robert H Hanner
- Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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26
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Garcia-Vazquez E, Ardura A, Planes S. DNA mtCOI Barcodes for Maritime Biosecurity: A Proof of Concept in French Polynesia Ports. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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27
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Young RG, Yu J, Cote MJ, Hanner RH. The Molecular Data Organization for Publication (MDOP) R package to aid the upload of data to shared databases. Biodivers Data J 2020; 8:e50630. [PMID: 32377152 PMCID: PMC7192956 DOI: 10.3897/bdj.8.e50630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/10/2020] [Indexed: 12/19/2022] Open
Abstract
Molecular identification methods, such as DNA barcoding, rely on centralized databases populated with morphologically identified individuals and their referential nucleotide sequence records. As molecular identification approaches have expanded in use to fields such as food fraud, environmental surveys, and border surveillance, there is a need for diverse international data sets. Although central data repositories, like the Barcode of Life Datasystems (BOLD), provided workarounds for formatting data for upload, these workarounds can be taxing on researchers with few resources and limited funding. To address these concerns, we present the Molecular Data Organization for Publication (MDOP) R package to assist researchers in uploading data to public databases. To illustrate the use of these scripts, we use the BOLD system as an example. The main intent of this writing is to assist in the movement of data, from academic, governmental, and other institutional computer systems, to public locations. The movement of these data can then better contribute to the global DNA barcoding initiative and other global molecular data efforts.
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Affiliation(s)
- Robert G Young
- University of Guelph, Guelph, Canada University of Guelph Guelph Canada
| | - Jiaojia Yu
- University of Guelph, Guelph, Canada University of Guelph Guelph Canada
| | - Marie-José Cote
- Canadian Food Inspection Agency, Ottawa, Canada Canadian Food Inspection Agency Ottawa Canada
| | - Robert H Hanner
- University of Guelph, Guelph, Canada University of Guelph Guelph Canada
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28
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Pentinsaari M, Ratnasingham S, Miller SE, Hebert PDN. BOLD and GenBank revisited - Do identification errors arise in the lab or in the sequence libraries? PLoS One 2020; 15:e0231814. [PMID: 32298363 PMCID: PMC7162515 DOI: 10.1371/journal.pone.0231814] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 03/30/2020] [Indexed: 11/23/2022] Open
Abstract
Applications of biological knowledge, such as forensics, often require the determination of biological materials to a species level. As such, DNA-based approaches to identification, particularly DNA barcoding, are attracting increased interest. The capacity of DNA barcodes to assign newly encountered specimens to a species relies upon access to informatics platforms, such as BOLD and GenBank, which host libraries of reference sequences and support the comparison of new sequences to them. As parameterization of these libraries expands, DNA barcoding has the potential to make valuable contributions in diverse applied contexts. However, a recent publication called for caution after finding that both platforms performed poorly in identifying specimens of 17 common insect species. This study follows up on this concern by asking if the misidentifications reflected problems in the reference libraries or in the query sequences used to test them. Because this reanalysis revealed that missteps in acquiring and analyzing the query sequences were responsible for most misidentifications, a workflow is described to minimize such errors in future investigations. The present study also revealed the limitations imposed by the lack of a polished species-level taxonomy for many groups. In such cases, applications can be strengthened by mapping the geographic distributions of sequence-based species proxies rather than waiting for the maturation of formal taxonomic systems based on morphology.
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Affiliation(s)
- Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Scott E. Miller
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
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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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Machado DDN, Costa EC, Guedes JVC, Barbosa LR, Martínez G, Mayorga SI, Ramos SO, Branco M, Garcia A, Vanegas-Rico JM, Jiménez-Quiroz E, Laudonia S, Novoselsky T, Hodel DR, Arakelian G, Silva H, Perini CR, Valmorbida I, Ugalde GA, Arnemann JA. One maternal lineage leads the expansion of Thaumastocoris peregrinus (Hemiptera: Thaumastocoridae) in the New and Old Worlds. Sci Rep 2020; 10:3487. [PMID: 32103053 PMCID: PMC7044308 DOI: 10.1038/s41598-020-60236-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 02/05/2020] [Indexed: 11/09/2022] Open
Abstract
The bronze bug, Thaumastocoris peregrinus, an Australian native insect, has become a nearly worldwide invasive pest in the last 16 years and has been causing significant damage to eucalypts (Myrtaceae), including Eucalyptus spp. and Corymbia spp. Its rapid expansion leads to new questions about pathways and routes that T. peregrinus used to invade other continents and countries. We used mtDNA to characterize specimens of T. peregrinus collected from 10 countries where this species has become established, including six recently invaded countries: Chile, Israel, Mexico, Paraguay, Portugal, and the United States of America. We then combined our mtDNA data with previous data available from South Africa, Australia, and Europe to construct a world mtDNA network of haplotypes. Haplotype A was the most common present in all specimens of sites sampled in the New World, Europe, and Israel, however from Australia second more frequently. Haplotype D was the most common one from native populations in Australia. Haplotype A differs from the two major haplotypes found in South Africa (D and G), confirming that at least two independent invasions occurred, one from Australia to South Africa, and the other one from Australia to South America (A). In conclusion, Haplotype A has an invasion success over many countries in the World. Additionally, analyzing data from our work and previous reports, it is possible to suggest some invasive routes of T. peregrinus to predict such events and support preventive control measures.
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Affiliation(s)
- Dayanna do N Machado
- Doutoranda pelo Programa de Pós-Graduação em Engenharia Florestal, Universidade Federal de Santa Maria, Santa Maria, Brasil.
- Departamento de Defesa Fitossanitária, Avenida Roraima n. 1000, prédio 42, sala 3223, 97105-900, Santa Maria, Rio Grande do Sul, Brasil.
| | - Ervandil C Costa
- Departamento de Defesa Fitossanitária, Avenida Roraima n. 1000, prédio 42, sala 3223, 97105-900, Santa Maria, Rio Grande do Sul, Brasil
| | - Jerson V C Guedes
- Departamento de Defesa Fitossanitária, Avenida Roraima n. 1000, prédio 42, sala 3223, 97105-900, Santa Maria, Rio Grande do Sul, Brasil
| | - Leonardo R Barbosa
- Empresa Brasileira de Pesquisa Agropecuária - Embrapa Florestas, Colombo, Paraná, 83411-000, Brazil
| | - Gonzalo Martínez
- Instituto Nacional de Investigación Agropecuaria (INIA), Ruta 5 Km 386, Tacuarembó, Uruguay
| | - Sandra I Mayorga
- Servicio Agrícola y Ganadero (SAG), Av. Presidente Bulnes 140, Santiago, Chile
| | - Sergio O Ramos
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Yuquerí, Ruta Provincial 22 y vías del Ferrocarril 3200, Concordia, Entre Ríos, Argentina
| | - Manuela Branco
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - André Garcia
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Juan Manuel Vanegas-Rico
- Laboratorio de Control de Plagas, Unidad de Morfología y Función (UMF), Facultad de Estudios Superiores Iztacala, UNAM. Av. de los barrios #1. Los Reyes Iztacala, Tlalnepantla de Baz, 54090, Mexico
| | - Eduardo Jiménez-Quiroz
- Laboratorio de Análisis y Referencia en Sanidad Forestal, Av. Progreso 3, 04100, Coyoacán, Ciudad de México, Mexico
| | - Stefania Laudonia
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Portici, Italy
| | - Tania Novoselsky
- The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Donald R Hodel
- University of California, Cooperative Extension, 700 W. Main Street, Alhambra, California, 91801, United States of America
| | - Gevork Arakelian
- Entomologist, Los Angeles County Agricultural Commissioner, 11012 S. Garfield Ave, South Gate, CA, 90280, United States of America
| | - Horacio Silva
- Faculdad de Agronomía Universidad de la República Uruguay, Ruta 3 km 363, 60000, Paysandú, Uruguay
| | - Clérison R Perini
- Departamento de Defesa Fitossanitária, Avenida Roraima n. 1000, prédio 42, sala 3223, 97105-900, Santa Maria, Rio Grande do Sul, Brasil
| | - Ivair Valmorbida
- Department of Entomology, Iowa State University, Ames, Iowa, USA
| | - Gustavo A Ugalde
- Departamento de Defesa Fitossanitária, Avenida Roraima n. 1000, prédio 42, sala 3223, 97105-900, Santa Maria, Rio Grande do Sul, Brasil
| | - Jonas A Arnemann
- Departamento de Defesa Fitossanitária, Avenida Roraima n. 1000, prédio 42, sala 3223, 97105-900, Santa Maria, Rio Grande do Sul, Brasil
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Capacity of United States federal government and its partners to rapidly and accurately report the identity (taxonomy) of non-native organisms intercepted in early detection programs. Biol Invasions 2019. [DOI: 10.1007/s10530-019-02147-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AbstractThe early detection of and rapid response to invasive species (EDRR) depends on accurate and rapid identification of non-native species. The 2016–2018 National Invasive Species Council Management Plan called for an assessment of US government (federal) capacity to report on the identity of non-native organisms intercepted through early detection programs. This paper serves as the response to that action item. Here we summarize survey-based findings and make recommendations for improving the federal government’s capacity to identify non-native species authoritatively in a timely manner. We conclude with recommendations to improve accurate identification within the context of EDRR by increasing coordination, maintaining taxonomic expertise, creating an identification tools clearinghouse, developing and using taxonomic standards for naming and identification protocols, expanding the content of DNA and DNA Barcode libraries, ensuring long-term sustainability of biological collections, and engaging and empowering citizens and citizen science groups.
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