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Lu C, Hao SD, Ha PZ, Huang LB, Dai LZ, Wang JW, Wang L, Zhang ZY, Ren ZG, Wang JZ. A multiplex direct PCR method for the rapid and accurate discrimination of three species of spider mites (Acari: Tetranychidae) in fruit orchards in Beijing. EXPERIMENTAL & APPLIED ACAROLOGY 2024; 92:403-421. [PMID: 38489086 DOI: 10.1007/s10493-023-00900-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 12/30/2023] [Indexed: 03/17/2024]
Abstract
Spider mites (Acari: Tetranychidae) are polyphagous pests of economic importance in agriculture, among which the two-spotted spider mite Tetranychus urticae Koch has spread widely worldwide as an invasive species, posing a serious threat to fruit tree production in China, including Beijing. The hawthorn spider mite, Amphitetranychus viennensis Zacher, is also a worldwide pest of fruit trees and woody ornamental plants. The cassava mite, Tetranychus truncatus Ehara, is mainly found in Asian countries, including China, Korea and Japan, and mainly affects fruit trees and agricultural crops. These three species of spider mites are widespread and serious fruit tree pests in Beijing. Rapid and accurate identification of spider mites is essential for effective pest and plant quarantine in Beijing orchard fields. The identification of spider mite species is difficult due to their limited morphological characteristics. Although the identification of insect and mite species based on PCR and real-time polymerase chain reaction TaqMan is becoming increasingly common, DNA extraction is difficult, expensive and time-consuming due to the minute size of spider mites. Therefore, the objective of this study was to establish a direct multiplex PCR method for the simultaneous identification of three common species of spider mites in orchards, A. viennensis, T. truncatus and T. urticae, to provide technical support for the differentiation of spider mite species and phytosanitary measures in orchards in Beijing. Based on the mitochondrial cytochrome c oxidase subunit I (COI) of the two-spotted spider mite and the cassava mite and the 18S gene sequence of the hawthorn spider mite as the amplification target, three pairs of specific primers were designed, and the primer concentrations were optimized to establish a direct multiplex PCR system for the rapid and accurate discrimination of the three spider mites without the need for DNA extraction and purification. The method showed a high sensitivity of 0.047 ng for T. truncatus and T. urticae DNA and 0.0002 ng for A. viennensis. This method eliminates the DNA extraction and sequencing procedures of spider mite samples, offers a possibility for rapid monitoring of multiple spider mites in an integrated microarray laboratory system, reducing the time and cost of leaf mite identification and quarantine monitoring in the field.
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Affiliation(s)
- Can Lu
- Key Laboratory of Urban Agriculture, Ministry of Agriculture, College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, North China, China
| | - Shao-Dong Hao
- Key Laboratory of Urban Agriculture, Ministry of Agriculture, College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, North China, China
| | - Pa-Zi Ha
- Agriculture Promotion Center of Qinghe County, Xinjiang, 836200, China
| | - Li-Bin Huang
- Key Laboratory of Urban Agriculture, Ministry of Agriculture, College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, North China, China
| | - Li-Zhen Dai
- Key Laboratory of Urban Agriculture, Ministry of Agriculture, College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, North China, China
| | - Jian-Wen Wang
- Key Laboratory of Urban Agriculture, Ministry of Agriculture, College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, North China, China
| | - Long Wang
- Key Laboratory of Urban Agriculture, Ministry of Agriculture, College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, North China, China
| | - Zhi-Yong Zhang
- Key Laboratory of Urban Agriculture, Ministry of Agriculture, College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, North China, China
| | - Zheng-Guang Ren
- Key Laboratory of Urban Agriculture, Ministry of Agriculture, College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, North China, China
| | - Jin-Zhong Wang
- Key Laboratory of Urban Agriculture, Ministry of Agriculture, College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, North China, China.
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Röder N, Stoll VS, Jupke JF, Kolbenschlag S, Bundschuh M, Theißinger K, Schwenk K. How non-target chironomid communities respond to mosquito control: Integrating DNA metabarcoding and joint species distribution modelling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169735. [PMID: 38163597 DOI: 10.1016/j.scitotenv.2023.169735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/26/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
The conservation and management of riparian ecosystems rely on understanding the ecological consequences of anthropogenic stressors that impact natural communities. In this context, studies investigating the effects of anthropogenic stressors require reliable methods capable of mapping the relationships between taxa occurrence or abundance and environmental predictors within a spatio-temporal framework. Here, we present an integrative approach using DNA metabarcoding and Hierarchical Modelling of Species Communities (HMSC) to unravel the intricate dynamics and resilience of chironomid communities exposed to Bacillus thuringiensis var. israelensis (Bti). Chironomid emergence was sampled from a total of 12 floodplain pond mesocosms, half of which received Bti treatment, during a 16-week period spanning spring and summer of 2020. Subsequently, we determined the community compositions of chironomids and examined their genus-specific responses to the Bti treatment, considering their phylogenetic affiliations and ecological traits of the larvae. Additionally, we investigated the impact of the Bti treatment on the body size distribution of emerging chironomids. Our study revealed consistent responses to Bti among different chironomid genera, indicating that neither phylogenetic affiliations nor larval feeding strategies significantly contributed to the observed patterns. Both taxonomic and genetic diversity were positively correlated with the number of emerged individuals. Furthermore, our findings demonstrated Bti-related effects on chironomid body size distribution, which could have relevant implications for size-selective terrestrial predators. Hence, our study highlights the value of employing a combination of DNA metabarcoding and HMSC to unravel the complex dynamics of Bti-related non-target effects on chironomid communities. The insights gained from this integrated framework contribute to our understanding of the ecological consequences of anthropogenic stressors and provide a foundation for informed decision-making regarding the conservation and management of riparian ecosystems.
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Affiliation(s)
- Nina Röder
- iES - Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Landau, Germany.
| | - V Sophie Stoll
- iES - Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Landau, Germany
| | - Jonathan F Jupke
- iES - Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Landau, Germany
| | - Sara Kolbenschlag
- iES - Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Landau, Germany
| | - Mirco Bundschuh
- iES - Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Landau, Germany; Department of Aquatic Science and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Kathrin Theißinger
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Klaus Schwenk
- iES - Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Landau, Germany; LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
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3
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Scriver M, von Ammon U, Youngbull C, Pochon X, Stanton JAL, Gemmell NJ, Zaiko A. Drop it all: extraction-free detection of targeted marine species through optimized direct droplet digital PCR. PeerJ 2024; 12:e16969. [PMID: 38410796 PMCID: PMC10896080 DOI: 10.7717/peerj.16969] [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: 12/01/2023] [Accepted: 01/29/2024] [Indexed: 02/28/2024] Open
Abstract
Molecular biomonitoring programs increasingly use environmental DNA (eDNA) for detecting targeted species such as marine non-indigenous species (NIS) or endangered species. However, the current molecular detection workflow is cumbersome and time-demanding, and thereby can hinder management efforts and restrict the "opportunity window" for rapid management responses. Here, we describe a direct droplet digital PCR (direct-ddPCR) approach to detect species-specific free-floating extra-cellular eDNA (free-eDNA) signals, i.e., detection of species-specific eDNA without the need for filtration or DNA extraction, with seawater samples. This first proof-of-concept aquarium study was conducted with three distinct marine species: the Mediterranean fanworm Sabella spallanzanii, the ascidian clubbed tunicate Styela clava, and the brown bryozoan Bugula neritina to evaluate the detectability of free-eDNA in seawater. The detectability of targeted free-eDNA was assessed by directly analysing aquarium marine water samples using an optimized species-specific ddPCR assay. The results demonstrated the consistent detection of S. spallanzanii and B. neritina free-eDNA when these organisms were present in high abundance. Once organisms were removed, the free-eDNA signal exponentially declined, noting that free-eDNA persisted between 24-72 h. Results indicate that organism biomass, specimen characteristics (e.g., stress and viability), and species-specific biological differences may influence free-eDNA detectability. This study represents the first step in assessing the feasibility of direct-ddPCR technology for the detection of marine species. Our results provide information that could aid in the development of new technology, such as a field development of ddPCR systems, which could allow for automated continuous monitoring of targeted marine species, enabling point-of-need detection and rapid management responses.
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Affiliation(s)
- Michelle Scriver
- Biosecurity Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Ulla von Ammon
- Biosecurity Group, Cawthron Institute, Nelson, New Zealand
| | - Cody Youngbull
- Nucleic Sensing Systems, LCC, Saint Paul, Minnesota, United States
| | - Xavier Pochon
- Biosecurity Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Jo-Ann L Stanton
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Anastasija Zaiko
- Biosecurity Group, Cawthron Institute, Nelson, New Zealand
- Sequench Ltd, Nelson, New Zealand
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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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Stein F, Wagner S, Bräsicke N, Gailing O, Moura CCM, Götz M. A Non-Destructive High-Speed Procedure to Obtain DNA Barcodes from Soft-Bodied Insect Samples with a Focus on the Dipteran Section of Schizophora. INSECTS 2022; 13:insects13080679. [PMID: 36005305 PMCID: PMC9409269 DOI: 10.3390/insects13080679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 02/04/2023]
Abstract
While the need for biodiversity research is growing, paradoxically, global taxonomical expertise is decreasing as a result of the neglected funding for young academics in taxonomy. Non-destructive approaches for DNA barcoding are necessary for a more efficient use of this dwindling expertise to fill gaps, and identify incorrect entries in sequence databases like BOLD or GenBank. They are efficient because morphological re-examination of species vouchers is still possible post-DNA barcoding. Non-destructive approaches for Diptera with a comprehensive species representation or the consideration of diagnostic fragile morphological characters are missing. Additionally, most non-destructive approaches combine a time intensive and non-destructive digestion step with common DNA extraction methods, such as commercial kits or CTAB DNA isolation. We circumvented those approaches and combined a modified non-destructive TE buffer high-speed DNA extraction, with a PCR inhibitor-resistant PCR reaction system, to a non-destructive DNA barcoding procedure for fresh and frozen samples of the Schizophora (Diptera). This method avoids morphological impairment and the application of harmful chemicals, is cost and time effective, restricts the need for laboratory equipment to a minimum, and prevents cross-contamination risk during DNA isolation. Moreover, the study indicates that the presented non-destructive DNA barcoding procedure is transferable to other soft-bodied insects. We suggest that PCR inhibitor-resistant master mixes enable the development of new—and the modification of existing—non-destructive approaches with the avoidance of further DNA template cleaning.
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Affiliation(s)
- Frederik Stein
- Institute for Plant Protection in Horticulture and Forests, Julius Kühn Institute, 38014 Braunschweig, Germany; (S.W.); (N.B.); (M.G.)
- Correspondence: ; Tel.: +49-(0)-3946-47-4010
| | - Stefan Wagner
- Institute for Plant Protection in Horticulture and Forests, Julius Kühn Institute, 38014 Braunschweig, Germany; (S.W.); (N.B.); (M.G.)
| | - Nadine Bräsicke
- Institute for Plant Protection in Horticulture and Forests, Julius Kühn Institute, 38014 Braunschweig, Germany; (S.W.); (N.B.); (M.G.)
| | - Oliver Gailing
- Büsgen Institute, Forest Genetics and Forest Tree Breeding, University of Göttingen, 37073 Göttingen, Germany; (O.G.); (C.C.M.M.)
| | - Carina C. M. Moura
- Büsgen Institute, Forest Genetics and Forest Tree Breeding, University of Göttingen, 37073 Göttingen, Germany; (O.G.); (C.C.M.M.)
| | - Monika Götz
- Institute for Plant Protection in Horticulture and Forests, Julius Kühn Institute, 38014 Braunschweig, Germany; (S.W.); (N.B.); (M.G.)
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Gadawski P, Montagna M, Rossaro B, Giłka W, Pešić V, Grabowski M, Magoga G. DNA barcoding of Chironomidae from the Lake Skadar region: Reference library and a comparative analysis of the European fauna. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13504] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022] Open
Affiliation(s)
- Piotr Gadawski
- Department of Invertebrate Zoology and Hydrobiology University of Lodz Lodz Poland
| | - Matteo Montagna
- Department of Agricultural Sciences University of Naples Federico II Portici Italy
- BAT Center ‐ Interuniversity Center for Studies on Bioinspired Agro‐environmental Technology University of Napoli Federico II Portici Italy
| | - Bruno Rossaro
- Department of Agricultural and Environmental Sciences – Production, Landscape, Agroenergy University of Milan Milan Italy
| | - Wojciech Giłka
- Laboratory of Systematic Zoology Department of Invertebrate Zoology and Parasitology Faculty of Biology University of Gdańsk Gdańsk Poland
| | - Vladimir Pešić
- Department of Biology Faculty of Science University of Montenegro Podgorica Montenegro
| | - Michał Grabowski
- Department of Invertebrate Zoology and Hydrobiology University of Lodz Lodz Poland
| | - Giulia Magoga
- Department of Agricultural and Environmental Sciences – Production, Landscape, Agroenergy University of Milan Milan Italy
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Competitiveness of Quantitative Polymerase Chain Reaction (qPCR) and Droplet Digital Polymerase Chain Reaction (ddPCR) Technologies, with a Particular Focus on Detection of Antibiotic Resistance Genes (ARGs). Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1030028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
With fast-growing polymerase chain reaction (PCR) technologies and various application methods, the technique has benefited science and medical fields. While having strengths and limitations on each technology, there are not many studies comparing the efficiency and specificity of PCR technologies. The objective of this review is to summarize a large amount of scattered information on PCR technologies focused on the two majorly used technologies: qPCR (quantitative polymerase chain reaction) and ddPCR (droplet-digital polymerase chain reaction). Here we analyze and compare the two methods for (1) efficiency, (2) range of detection and limitations under different disciplines and gene targets, (3) optimization, and (4) status on antibiotic resistance genes (ARGs) analysis. It has been identified that the range of detection and quantification limit varies depending on the PCR method and the type of sample. Careful optimization of target gene analysis is essential for building robust analysis for both qPCR and ddPCR. In our era where mutation of genes may lead to a pandemic of viral infectious disease or antibiotic resistance-induced health threats, this study hopes to set guidelines for meticulous detection, quantification, and analysis to help future prevention and protection of global health, the economy, and ecosystems.
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Yeo D, Srivathsan A, Puniamoorthy J, Maosheng F, Grootaert P, Chan L, Guénard B, Damken C, Wahab RA, Yuchen A, Meier R. Mangroves are an overlooked hotspot of insect diversity despite low plant diversity. BMC Biol 2021; 19:202. [PMID: 34521395 PMCID: PMC8442405 DOI: 10.1186/s12915-021-01088-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 07/08/2021] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The world's fast disappearing mangrove forests have low plant diversity and are often assumed to also have a species-poor insect fauna. We here compare the tropical arthropod fauna across a freshwater swamp and six different forest types (rain-, swamp, dry-coastal, urban, freshwater swamp, mangroves) based on 140,000 barcoded specimens belonging to ca. 8500 species. RESULTS We find that the globally imperiled habitat "mangroves" is an overlooked hotspot for insect diversity. Our study reveals a species-rich mangrove insect fauna (>3000 species in Singapore alone) that is distinct (>50% of species are mangrove-specific) and has high species turnover across Southeast and East Asia. For most habitats, plant diversity is a good predictor of insect diversity, but mangroves are an exception and compensate for a comparatively low number of phytophagous and fungivorous insect species by supporting an unusually rich community of predators whose larvae feed in the productive mudflats. For the remaining tropical habitats, the insect communities have diversity patterns that are largely congruent across guilds. CONCLUSIONS The discovery of such a sizeable and distinct insect fauna in a globally threatened habitat underlines how little is known about global insect biodiversity. We here show how such knowledge gaps can be closed quickly with new cost-effective NGS barcoding techniques.
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Affiliation(s)
- Darren Yeo
- Department of Biological Sciences, National University of Singapore, 14 Science 8 Drive 4, Singapore, 117543, Singapore.
| | - Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, 14 Science 8 Drive 4, Singapore, 117543, Singapore
| | - Jayanthi Puniamoorthy
- Department of Biological Sciences, National University of Singapore, 14 Science 8 Drive 4, Singapore, 117543, Singapore
| | - Foo Maosheng
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore, 117377, Singapore
| | - Patrick Grootaert
- National Biodiversity Centre, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Lena Chan
- International Biodiversity Conservation Division, National Parks Board, 1 Cluny Road, Singapore, 259569, Singapore
| | - Benoit Guénard
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pok Fu Lam Road, Hong Kong, SAR, China
| | - Claas Damken
- Institute for Biodiversity and Environmental Research, Universiti Brunei Darussalam, Jalan Universiti, BE1410, Gadong, Brunei Darussalam
| | - Rodzay A Wahab
- Institute for Biodiversity and Environmental Research, Universiti Brunei Darussalam, Jalan Universiti, BE1410, Gadong, Brunei Darussalam
| | - Ang Yuchen
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore, 117377, Singapore
| | - Rudolf Meier
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Invalidenstr. 43, Berlin, 10115, Germany.
- Department of Biological Sciences, National University of Singapore, 14 Science 8 Drive 4, Singapore, 117543, Singapore.
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Thongjued K, Chotigeat W, Bumrungsri S, Thanakiatkrai P, Kitpipit T. Direct PCR-DGGE Technique Reveals Wrinkle-Lipped Free-Tailed Bat (Chaerephon plicatus Buchanan, 1800) Predominantly Consume Planthoppers and Mosquitoes in Central Thailand. ACTA CHIROPTEROLOGICA 2021. [DOI: 10.3161/15081109acc2021.23.1.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Kantima Thongjued
- Prince of Songkla University, 15 Karnchanawanich Road, Hat Yai, Songkhla, Thailand 90112
| | - Wilaiwan Chotigeat
- Prince of Songkla University, 15 Karnchanawanich Road, Hat Yai, Songkhla, Thailand 90112
| | - Sara Bumrungsri
- Prince of Songkla University, 15 Karnchanawanich Road, Hat Yai, Songkhla, Thailand 90112
| | - Phuvadol Thanakiatkrai
- Prince of Songkla University, 15 Karnchanawanich Road, Hat Yai, Songkhla, Thailand 90112
| | - Thitika Kitpipit
- Prince of Songkla University, 15 Karnchanawanich Road, Hat Yai, Songkhla, Thailand 90112
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Ge Y, Xia C, Wang J, Zhang X, Ma X, Zhou Q. The efficacy of DNA barcoding in the classification, genetic differentiation, and biodiversity assessment of benthic macroinvertebrates. Ecol Evol 2021; 11:5669-5681. [PMID: 34026038 PMCID: PMC8131818 DOI: 10.1002/ece3.7470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 02/26/2021] [Accepted: 03/05/2021] [Indexed: 11/19/2022] Open
Abstract
Macroinvertebrates have been recognized as key ecological indicators of aquatic environment and are the most commonly used approaches for water quality assessment. However, species identification of macroinvertebrates (especially of aquatic insects) proves to be very difficult due to the lack of taxonomic expertise in some regions and can become time-consuming. In this study, we evaluated the feasibility of DNA barcoding for the classification of benthic macroinvertebrates and investigated the genetic differentiation in seven orders (Insecta: Ephemeroptera, Plecoptera, Trichoptera, Diptera, Hemiptera, Coleoptera, and Odonata) from four large transboundary rivers of northwest China and further explored its potential application to biodiversity assessment. A total of 1,144 COI sequences, belonging to 176 species, 112 genera, and 53 families were obtained and analyzed. The barcoding gap analysis showed that COI gene fragment yielded significant intra- and interspecific divergences and obvious barcoding gaps. NJ phylogenetic trees showed that all species group into monophyletic species clusters whether from the same population or not, except two species (Polypedilum. laetum and Polypedilum. bullum). The distance-based (ABGD) and tree-based (PTP and MPTP) methods were utilized for grouping specimens into Operational Taxonomic Units (OTUs) and delimiting species. The ABGD, PTP, and MPTP analysis were divided into 177 (p = .0599), 197, and 195 OTUs, respectively. The BIN analysis generated 186 different BINs. Overall, our study showed that DNA barcoding offers an effective framework for macroinvertebrate species identification and sheds new light on the biodiversity assessment of local macroinvertebrates. Also, the construction of DNA barcode reference library of benthic macroinvertebrates in Eurasian transboundary rivers provides a solid backup for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future.
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Affiliation(s)
- Yihao Ge
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
- The Key Laboratory of Aquatic Biodiversity and ConservationInstitute of HydrobiologyChinese Academy of SciencesWuhanChina
| | - Chengxing Xia
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| | - Jun Wang
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- The Key Laboratory of Aquatic Biodiversity and ConservationInstitute of HydrobiologyChinese Academy of SciencesWuhanChina
| | - Xiujie Zhang
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| | - Xufa Ma
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| | - Qiong Zhou
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
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11
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Rößler DC, Lötters S, Veith M, Fugmann M, Peters C, Künzel S, Krehenwinkel H. An amplicon sequencing protocol for attacker identification from DNA traces left on artificial prey. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniela C. Rößler
- FAS Center for Systems Biology Harvard University Cambridge MA USA
- Department of Biogeography Trier University Trier Germany
| | - Stefan Lötters
- Department of Biogeography Trier University Trier Germany
| | - Michael Veith
- Department of Biogeography Trier University Trier Germany
| | | | | | - Sven Künzel
- Max Planck Institute for Evolutionary Biology Plön Germany
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12
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Ståhls G, Meier R, Sandrock C, Hauser M, Šašić Zorić L, Laiho E, Aracil A, Doderović J, Badenhorst R, Unadirekkul P, Mohd Adom NAB, Wein L, Richards C, Tomberlin JK, Rojo S, Veselić S, Parviainen T. The puzzling mitochondrial phylogeography of the black soldier fly (Hermetia illucens), the commercially most important insect protein species. BMC Evol Biol 2020; 20:60. [PMID: 32448128 PMCID: PMC7247124 DOI: 10.1186/s12862-020-01627-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 05/13/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The black soldier fly (Diptera: Stratiomyidae, Hermetia illucens) is renowned for its bioconversion ability of organic matter, and is the worldwide most widely used source of insect protein. Despite varying extensively in morphology, it is widely assumed that all black soldier flies belong to the same species, Hermetia illucens. We here screened about 600 field-collected and cultured flies from 39 countries and six biogeographic regions to test this assumption based on data for three genes (mitochondrial COI, nuclear ITS2 & 28S rDNA) and in order to gain insights into the phylogeography of the species. RESULTS Our study reveals a surprisingly high level of intraspecific genetic diversity for the mitochondrial barcoding gene COI (divergences up to 4.9%). This level of variability is often associated with the presence of multiple species, but tested nuclear markers (ITS2 and 28S rDNA) were invariant and fly strain hybridization experiments under laboratory conditions revealed reproductive compatibility. COI haplotype diversity is not only very high in all biogeographic regions (56 distinct haplotypes in total), but also in breeding facilities and research centers from six continents (10 haplotypes: divergences up to 4.3%). The high genetic diversity in fly-breeding facilities is mostly likely due to many independent acquisitions of cultures via sharing and/or establishing new colonies from field-collected flies. However, explaining some of the observed diversity in several biogeographic regions is difficult given that the origin of the species is considered to be New World (32 distinct haplotypes) and one would expect severely reduced genetic diversity in the putatively non-native populations in the remaining biogeographic regions. However, distinct, private haplotypes are known from the Australasian (N = 1), Oriental (N = 4), and the Eastern Palearctic (N = 4) populations. We reviewed museum specimen records and conclude that the evidence for introductions is strong for the Western Palearctic and Afrotropical regions which lack distinct, private haplotypes. CONCLUSIONS Based on the results of this paper, we urge the black soldier fly community to apply molecular characterization (genotyping) of the fly strains used in artificial fly-breeding and share these data in research publications as well as when sharing cultures. In addition, fast-evolving nuclear markers should be used to reconstruct the recent invasion history of the species.
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Affiliation(s)
- Gunilla Ståhls
- Finnish Museum of Natural History Luomus, Zoology unit, University of Helsinki, PO Box 17, FI-00014, Helsinki, Finland.
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Block S3 #05-01, 14 Science Dr 4, Singapore, 117543, Singapore
| | - Christoph Sandrock
- Department of Livestock Sciences, Research Institute of Organic Agriculture (FiBL), Ackerstrasse 113, 5070, Frick, Switzerland
| | - Martin Hauser
- California Department of Food and Agriculture, Plant Pest Diagnostics Branch, 3294 Meadowview Road, Sacramento, California, 95832-1448, USA
| | | | - Elina Laiho
- Finnish Museum of Natural History Luomus, Zoology unit, University of Helsinki, PO Box 17, FI-00014, Helsinki, Finland
| | - Andrea Aracil
- Department of Environmental Sciences & Natural Resources, University of Alicante, PO Box 99, E-03080, Alicante, Spain
| | - Jovana Doderović
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, 2100, Serbia
| | | | - Phira Unadirekkul
- Department of Biological Sciences, National University of Singapore, Block S3 #05-01, 14 Science Dr 4, Singapore, 117543, Singapore
| | - Nur Arina Binte Mohd Adom
- Department of Biological Sciences, National University of Singapore, Block S3 #05-01, 14 Science Dr 4, Singapore, 117543, Singapore
| | - Leo Wein
- Protenga, 302 Ang Mo Kio Ave 3, #01-1840 560302, Singapore, Singapore
| | | | - Jeffery K Tomberlin
- Department of Entomology, Texas A&M University, TAMU 2475, College Station, TX, 77843-2475, USA
| | - Santos Rojo
- Department of Environmental Sciences & Natural Resources, University of Alicante, PO Box 99, E-03080, Alicante, Spain
| | - Sanja Veselić
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, 2100, Serbia
| | - Tuure Parviainen
- VTT Technical Research Centre of Finland Ltd, TT2 Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
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13
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Kennedy SR, Prost S, Overcast I, Rominger AJ, Gillespie RG, Krehenwinkel H. High-throughput sequencing for community analysis: the promise of DNA barcoding to uncover diversity, relatedness, abundances and interactions in spider communities. Dev Genes Evol 2020; 230:185-201. [PMID: 32040713 PMCID: PMC7127999 DOI: 10.1007/s00427-020-00652-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 01/29/2020] [Indexed: 12/19/2022]
Abstract
Large-scale studies on community ecology are highly desirable but often difficult to accomplish due to the considerable investment of time, labor and, money required to characterize richness, abundance, relatedness, and interactions. Nonetheless, such large-scale perspectives are necessary for understanding the composition, dynamics, and resilience of biological communities. Small invertebrates play a central role in ecosystems, occupying critical positions in the food web and performing a broad variety of ecological functions. However, it has been particularly difficult to adequately characterize communities of these animals because of their exceptionally high diversity and abundance. Spiders in particular fulfill key roles as both predator and prey in terrestrial food webs and are hence an important focus of ecological studies. In recent years, large-scale community analyses have benefitted tremendously from advances in DNA barcoding technology. High-throughput sequencing (HTS), particularly DNA metabarcoding, enables community-wide analyses of diversity and interactions at unprecedented scales and at a fraction of the cost that was previously possible. Here, we review the current state of the application of these technologies to the analysis of spider communities. We discuss amplicon-based DNA barcoding and metabarcoding for the analysis of community diversity and molecular gut content analysis for assessing predator-prey relationships. We also highlight applications of the third generation sequencing technology for long read and portable DNA barcoding. We then address the development of theoretical frameworks for community-level studies, and finally highlight critical gaps and future directions for DNA analysis of spider communities.
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Affiliation(s)
- Susan R Kennedy
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg Museum, Frankfurt, Germany
- National Zoological Garden, South African National Biodiversity Institute, Pretoria, South Africa
| | - Isaac Overcast
- Graduate Center of the City University New York, New York, NY, USA
- Ecole Normale Supérieure, Paris, France
| | | | - Rosemary G Gillespie
- Environmental Sciences Policy and Management, University of California Berkeley, Berkeley, CA, USA
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14
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Janik P, Ronikier M, Ronikier A. New protocol for successful isolation and amplification of DNA from exiguous fractions of specimens: a tool to overcome the basic obstacle in molecular analyses of myxomycetes. PeerJ 2020; 8:e8406. [PMID: 32002333 PMCID: PMC6984339 DOI: 10.7717/peerj.8406] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/16/2019] [Indexed: 11/23/2022] Open
Abstract
Herbarium collections provide an essential basis for a wide array of biological research and, with development of DNA-based methods, they have become an invaluable material for genetic analyses. Yet, the use of such material is hindered by technical limitations related to DNA degradation and to quantity of biological material. The latter is inherent for some biological groups, as best exemplified by myxomycetes which form minute sporophores. It is estimated that ca. two-thirds of myxomycete taxa are represented by extremely scanty material. As DNA isolation methods applied so far in myxomycete studies require destructive sampling of many sporophores, a large part of described diversity of the group remains unavailable for phylogenetic studies or barcoding. Here, we tested several procedures of DNA isolation and amplification to seek for an efficient and possibly non-destructive method of sampling. Tests were based on herbarium specimens of 19 species representing different taxonomic orders. We assayed several variants of isolation based on silica gel membrane columns, and a newly designed procedure using highly reduced amount of biological material (small portion of spores), based on fine disruption of spores and direct PCR. While the most frequently used column-based method led to PCR success in 89.5% of samples when a large amount of material was used, its performance dropped to 52% when based on single sporophores. Single sporophores provided amplicons in 89.5% of samples when using a kit dedicated to low-amount DNA samples. Our new procedure appeared the most effective (94.7%) while it used only a small fraction of spores, being nearly non-destructive; it was also the most cost-effective. We thus demonstrate that combination of adequate handling of spore micro-disruption coupled with application of direct PCR can be an efficient way to circumvent technical limitations for genetic studies in myxomycetes and thus can substantially improve taxon sampling for phylogeny and barcoding. Additionally, this approach gives a unique possibility to apply both molecular and morphological assays to the same structure (sporophore), which then can be further stored as documentation.
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Affiliation(s)
- Paulina Janik
- W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
| | - Michał Ronikier
- W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
| | - Anna Ronikier
- W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
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15
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de Kerdrel GA, Andersen JC, Kennedy SR, Gillespie R, Krehenwinkel H. Rapid and cost-effective generation of single specimen multilocus barcoding data from whole arthropod communities by multiple levels of multiplexing. Sci Rep 2020; 10:78. [PMID: 31919378 PMCID: PMC6952404 DOI: 10.1038/s41598-019-54927-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/19/2019] [Indexed: 11/23/2022] Open
Abstract
In light of the current biodiversity crisis, molecular barcoding has developed into an irreplaceable tool. Barcoding has been considerably simplified by developments in high throughput sequencing technology, but still can be prohibitively expensive and laborious when community samples of thousands of specimens need to be processed. Here, we outline an Illumina amplicon sequencing approach to generate multilocus data from large collections of arthropods. We reduce cost and effort up to 50-fold, by combining multiplex PCRs and DNA extractions from pools of presorted and morphotyped specimens and using two levels of sample indexing. We test our protocol by generating a comprehensive, community wide dataset of barcode sequences for several thousand Hawaiian arthropods from 14 orders, which were collected across the archipelago using various trapping methods. We explore patterns of diversity across the Archipelago and compare the utility of different arthropod trapping methods for biodiversity explorations on Hawaii, highlighting undergrowth beating as highly efficient method. Moreover, we show the effects of barcode marker, taxonomy and relative biomass of the targeted specimens and sequencing coverage on taxon recovery. Our protocol enables rapid and inexpensive explorations of diversity patterns and the generation of multilocus barcode reference libraries across whole ecosystems.
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Affiliation(s)
- Guillemette A de Kerdrel
- Department of Environmental Sciences, Policy and Management, University of California Berkeley, Mulford Hall, Berkeley, California, USA
| | - Jeremy C Andersen
- Department of Environmental Sciences, Policy and Management, University of California Berkeley, Mulford Hall, Berkeley, California, USA
| | - Susan R Kennedy
- Department of Biogeography, Trier University, Trier, Germany
- Okinawa Institute of Science and Technology, Onna, Japan
| | - Rosemary Gillespie
- Department of Environmental Sciences, Policy and Management, University of California Berkeley, Mulford Hall, Berkeley, California, USA
| | - Henrik Krehenwinkel
- Department of Environmental Sciences, Policy and Management, University of California Berkeley, Mulford Hall, Berkeley, California, USA.
- Department of Biogeography, Trier University, Trier, Germany.
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16
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Ip YCA, Tay YC, Gan SX, Ang HP, Tun K, Chou LM, Huang D, Meier R. From marine park to future genomic observatory? Enhancing marine biodiversity assessments using a biocode approach. Biodivers Data J 2019; 7:e46833. [PMID: 31866739 PMCID: PMC6917626 DOI: 10.3897/bdj.7.e46833] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/21/2019] [Indexed: 12/27/2022] Open
Abstract
Few tropical marine sites have been thoroughly characterised for their animal species, even though they constitute the largest proportion of multicellular diversity. A number of focused biodiversity sampling programmes have amassed immense collections to address this shortfall, but obstacles remain due to the lack of identification tools and large proportion of undescribed species globally. These problems can be partially addressed with DNA barcodes ("biocodes"), which have the potential to facilitate the estimation of species diversity and identify animals to named species via barcode databases. Here, we present the first results of what is intended to be a sustained, systematic study of the marine fauna of Singapore's first marine park, reporting more than 365 animal species, determined based on DNA barcodes and/or morphology represented by 931 specimens (367 zooplankton, 564 macrofauna including 36 fish). Due to the lack of morphological and molecular identification tools, only a small proportion could be identified to species solely based on either morphology (24.5%) or barcodes (24.6%). Estimation of species numbers for some taxa was difficult because of the lack of sufficiently clear barcoding gaps. The specimens were imaged and added to "Biodiversity of Singapore" (http://singapore.biodiversity.online), which now contains images for > 13,000 species occurring in the country.
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Affiliation(s)
- Yin Cheong Aden Ip
- Department of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Ywee Chieh Tay
- National University of Singapore, Singapore, SingaporeNational University of SingaporeSingaporeSingapore
- Temasek Life Sciences Laboratory, Singapore, SingaporeTemasek Life Sciences LaboratorySingaporeSingapore
| | - Su Xuan Gan
- Department of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Hui Ping Ang
- National Parks Board, Singapore, SingaporeNational Parks BoardSingaporeSingapore
| | - Karenne Tun
- National Parks Board, Singapore, SingaporeNational Parks BoardSingaporeSingapore
| | - Loke Ming Chou
- Department of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of SingaporeSingaporeSingapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, SingaporeTropical Marine Science Institute, National University of SingaporeSingaporeSingapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of SingaporeSingaporeSingapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, SingaporeTropical Marine Science Institute, National University of SingaporeSingaporeSingapore
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of SingaporeSingaporeSingapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, SingaporeTropical Marine Science Institute, National University of SingaporeSingaporeSingapore
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17
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Srivathsan A, Hartop E, Puniamoorthy J, Lee WT, Kutty SN, Kurina O, Meier R. Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing. BMC Biol 2019; 17:96. [PMID: 31783752 PMCID: PMC6884855 DOI: 10.1186/s12915-019-0706-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/09/2019] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND More than 80% of all animal species remain unknown to science. Most of these species live in the tropics and belong to animal taxa that combine small body size with high specimen abundance and large species richness. For such clades, using morphology for species discovery is slow because large numbers of specimens must be sorted based on detailed microscopic investigations. Fortunately, species discovery could be greatly accelerated if DNA sequences could be used for sorting specimens to species. Morphological verification of such "molecular operational taxonomic units" (mOTUs) could then be based on dissection of a small subset of specimens. However, this approach requires cost-effective and low-tech DNA barcoding techniques because well-equipped, well-funded molecular laboratories are not readily available in many biodiverse countries. RESULTS We here document how MinION sequencing can be used for large-scale species discovery in a specimen- and species-rich taxon like the hyperdiverse fly family Phoridae (Diptera). We sequenced 7059 specimens collected in a single Malaise trap in Kibale National Park, Uganda, over the short period of 8 weeks. We discovered > 650 species which exceeds the number of phorid species currently described for the entire Afrotropical region. The barcodes were obtained using an improved low-cost MinION pipeline that increased the barcoding capacity sevenfold from 500 to 3500 barcodes per flowcell. This was achieved by adopting 1D sequencing, resequencing weak amplicons on a used flowcell, and improving demultiplexing. Comparison with Illumina data revealed that the MinION barcodes were very accurate (99.99% accuracy, 0.46% Ns) and thus yielded very similar species units (match ratio 0.991). Morphological examination of 100 mOTUs also confirmed good congruence with morphology (93% of mOTUs; > 99% of specimens) and revealed that 90% of the putative species belong to the neglected, megadiverse genus Megaselia. We demonstrate for one Megaselia species how the molecular data can guide the description of a new species (Megaselia sepsioides sp. nov.). CONCLUSIONS We document that one field site in Africa can be home to an estimated 1000 species of phorids and speculate that the Afrotropical diversity could exceed 200,000 species. We furthermore conclude that low-cost MinION sequencers are very suitable for reliable, rapid, and large-scale species discovery in hyperdiverse taxa. MinION sequencing could quickly reveal the extent of the unknown diversity and is especially suitable for biodiverse countries with limited access to capital-intensive sequencing facilities.
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Affiliation(s)
- Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, Singapore
| | - Emily Hartop
- Zoology Department, Stockholms Universitet, Stockholm, Sweden
- Station Linné, Öland, Sweden
| | - Jayanthi Puniamoorthy
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, Singapore
| | - Wan Ting Lee
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, Singapore
| | - Sujatha Narayanan Kutty
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Olavi Kurina
- Estonian University of Life Sciences, Kreutzwaldi 5D, Tartu, Estonia
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, Singapore.
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore.
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18
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Krehenwinkel H, Pomerantz A, Prost S. Genetic Biomonitoring and Biodiversity Assessment Using Portable Sequencing Technologies: Current Uses and Future Directions. Genes (Basel) 2019; 10:E858. [PMID: 31671909 PMCID: PMC6895800 DOI: 10.3390/genes10110858] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/18/2019] [Accepted: 10/25/2019] [Indexed: 12/12/2022] Open
Abstract
We live in an era of unprecedented biodiversity loss, affecting the taxonomic composition of ecosystems worldwide. The immense task of quantifying human imprints on global ecosystems has been greatly simplified by developments in high-throughput DNA sequencing technology (HTS). Approaches like DNA metabarcoding enable the study of biological communities at unparalleled detail. However, current protocols for HTS-based biodiversity exploration have several drawbacks. They are usually based on short sequences, with limited taxonomic and phylogenetic information content. Access to expensive HTS technology is often restricted in developing countries. Ecosystems of particular conservation priority are often remote and hard to access, requiring extensive time from field collection to laboratory processing of specimens. The advent of inexpensive mobile laboratory and DNA sequencing technologies show great promise to facilitate monitoring projects in biodiversity hot-spots around the world. Recent attention has been given to portable DNA sequencing studies related to infectious organisms, such as bacteria and viruses, yet relatively few studies have focused on applying these tools to Eukaryotes, such as plants and animals. Here, we outline the current state of genetic biodiversity monitoring of higher Eukaryotes using Oxford Nanopore Technology's MinION portable sequencing platform, as well as summarize areas of recent development.
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Affiliation(s)
| | - Aaron Pomerantz
- Department of Integrative Biology, University of California, Berkeley, CA-94720, USA.
- Marine Biology Laboratory, Woods Hole, MA-02543, USA.
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg Museum, 60325 Frankfurt, Germany.
- South African National Biodiversity Institute, National Zoological Garden, Pretoria 0002, South Africa.
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19
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Thongjued K, Chotigeat W, Bumrungsri S, Thanakiatkrai P, Kitpipit T. A new cost-effective and fast direct PCR protocol for insects based on PBS buffer. Mol Ecol Resour 2019; 19:691-701. [PMID: 30758899 DOI: 10.1111/1755-0998.13005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 02/06/2019] [Accepted: 02/08/2019] [Indexed: 01/26/2023]
Abstract
Insect DNA barcoding is a species identification technique used in biodiversity assessment and ecological studies. However, DNA extraction can result in the loss of up to 70% of DNA. Recent research has reported that direct PCR can overcome this issue. However, the success rates could still be improved, and tissues used for direct PCR could not be reused for further genetic studies. Here, we developed a direct PCR workflow that incorporates a 2-min sample preparation in PBS-buffer step for fast and effective universal insect species identification. The developed protocol achieved 100% success rates for amplification in six orders: Mantodea, Phasmatodea, Neuroptera, Odonata, Blattodea and Orthoptera. High and moderate success rates were obtained for five other species: Lepidoptera (97.3%), Coleoptera (93.8%), Diptera (90.5%), Hemiptera (81.8%) and Hymenoptera (75.0%). High-quality sequencing data were also obtained from these amplifiable products, allowing confidence in species identification. The method was sensitive down to 1/4th of a 1-mm fragment of leg or body and its success rates with oven-dried, ethanol-preserved, food, bat guano and museum specimens were 100%, 98.6%, 90.0%, 84.0% and 30.0%, respectively. In addition, the pre-PCR solution (PBS with insect tissues) could be used for further DNA extraction if needed. The workflow will be beneficial in the fields of insect taxonomy and ecological studies due to its low cost, simplicity and applicability to highly degraded specimens.
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Affiliation(s)
- Kantima Thongjued
- Department of Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Wilaiwan Chotigeat
- Department of Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.,Center for Genomics and Bioinformatics Research, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Sara Bumrungsri
- Department of Biology, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Phuvadol Thanakiatkrai
- Forensic Science Program, Department of Applied Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Thitika Kitpipit
- Forensic Science Program, Department of Applied Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
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20
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Gueuning M, Ganser D, Blaser S, Albrecht M, Knop E, Praz C, Frey JE. Evaluating next-generation sequencing (NGS) methods for routine monitoring of wild bees: Metabarcoding, mitogenomics or NGS barcoding. Mol Ecol Resour 2019; 19:847-862. [PMID: 30912868 PMCID: PMC6850489 DOI: 10.1111/1755-0998.13013] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 03/15/2019] [Indexed: 12/26/2022]
Abstract
Implementing cost‐effective monitoring programs for wild bees remains challenging due to the high costs of sampling and specimen identification. To reduce costs, next‐generation sequencing (NGS)‐based methods have lately been suggested as alternatives to morphology‐based identifications. To provide a comprehensive presentation of the advantages and weaknesses of different NGS‐based identification methods, we assessed three of the most promising ones, namely metabarcoding, mitogenomics and NGS barcoding. Using a regular monitoring data set (723 specimens identified using morphology), we found that NGS barcoding performed best for both species presence/absence and abundance data, producing only few false positives (3.4%) and no false negatives. In contrast, the proportion of false positives and false negatives was higher using metabarcoding and mitogenomics. Although strong correlations were found between biomass and read numbers, abundance estimates significantly skewed the communities' composition in these two techniques. NGS barcoding recovered the same ecological patterns as morphology. Ecological conclusions based on metabarcoding and mitogenomics were similar to those based on morphology when using presence/absence data, but different when using abundance data. In terms of workload and cost, we show that metabarcoding and NGS barcoding can compete with morphology, but not mitogenomics which was consistently more expensive. Based on these results, we advocate that NGS barcoding is currently the seemliest NGS method for monitoring of wild bees. Furthermore, this method has the advantage of potentially linking DNA sequences with preserved voucher specimens, which enable morphological re‐examination and will thus produce verifiable records which can be fed into faunistic databases.
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Affiliation(s)
- Morgan Gueuning
- Research Group Molecular Diagnostics, Genomics and Bioinformatics, Agroscope, Wädenswil, Switzerland.,Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
| | - Dominik Ganser
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Agroecology and Environment, Agroscope, Zürich, Switzerland
| | - Simon Blaser
- Research Group Molecular Diagnostics, Genomics and Bioinformatics, Agroscope, Wädenswil, Switzerland.,Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland
| | | | - Eva Knop
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Christophe Praz
- Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
| | - Juerg E Frey
- Research Group Molecular Diagnostics, Genomics and Bioinformatics, Agroscope, Wädenswil, Switzerland
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21
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Guan F, Jin Y, Zhao J, Ai J, Luo Y. A Novel Direct PCR Lysis Buffer Can Improve PCR from Meat Matrices. FOOD ANAL METHOD 2019. [DOI: 10.1007/s12161-018-1342-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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22
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Suchan T, Talavera G, Sáez L, Ronikier M, Vila R. Pollen metabarcoding as a tool for tracking long-distance insect migrations. Mol Ecol Resour 2018; 19:149-162. [PMID: 30267472 DOI: 10.1111/1755-0998.12948] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/11/2018] [Accepted: 07/19/2018] [Indexed: 11/30/2022]
Abstract
Insects account for a large portion of Earth's biodiversity and are key players for ecosystems, notably as pollinators. While insect migration is suspected to represent a natural phenomenon of major importance, remarkably little is known about it, except for a few flagship species. The reason for this situation is mainly due to technical limitations in the study of insect movement. Here, we propose using metabarcoding of pollen carried by insects as a method for tracking their migrations. We developed a flexible and simple protocol allowing efficient multiplexing and not requiring DNA extraction, one of the most time-consuming part of metabarcoding protocols, and apply this method to the study of the long-distance migration of the butterfly Vanessa cardui, an emerging model for insect migration. We collected 47 butterfly samples along the Mediterranean coast of Spain in spring and performed metabarcoding of pollen collected from their bodies to test for potential arrivals from the African continent. In total, we detected 157 plant species from 23 orders, most of which (82.8%) were insect-pollinated. Taxa present in Africa-Arabia represented 73.2% of our data set, and 19.1% were endemic to this region, strongly supporting the hypothesis that migratory butterflies colonize southern Europe from Africa in spring. Moreover, our data suggest that a northwards trans-Saharan migration in spring is plausible for early arrivals (February) into Europe, as shown by the presence of Saharan floristic elements. Our results demonstrate the possibility of regular insect-mediated transcontinental pollination, with potential implications for ecosystem functioning, agriculture and plant phylogeography.
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Affiliation(s)
- Tomasz Suchan
- W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
| | - Gerard Talavera
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts
| | - Llorenç Sáez
- Systematics and Evolution of Vascular Plants, Associated Unit to CSIC, Unitat de Botànica, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Michał Ronikier
- W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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23
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Baloğlu B, Clews E, Meier R. NGS barcoding reveals high resistance of a hyperdiverse chironomid (Diptera) swamp fauna against invasion from adjacent freshwater reservoirs. Front Zool 2018; 15:31. [PMID: 30127839 PMCID: PMC6092845 DOI: 10.1186/s12983-018-0276-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/23/2018] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Macroinvertebrates such as non-biting midges (Chironomidae: Diptera) are important components of freshwater ecosystems. However, they are often neglected in biodiversity and conservation research because invertebrate species richness is difficult and expensive to quantify with traditional methods. We here demonstrate that Next Generation Sequencing barcodes ("NGS barcodes") can provide relief because they allow for fast and large-scale species-level sorting of large samples at low cost. RESULTS We used NGS barcoding to investigate the midge fauna of Singapore's swamp forest remnant (Nee Soon Swamp Forest). Based on > 14.000 barcoded specimens, we find that the swamp forest maintains an exceptionally rich fauna composed of an observed number of 289 species (estimated 336 species) in a very small area (90 ha). We furthermore barcoded the chironomids from three surrounding reservoirs that are located in close proximity. Although the swamp forest remnant is much smaller than the combined size of the freshwater reservoirs in the study (90 ha vs. > 450 ha), the latter only contains 33 (estimated 61) species. We show that the resistance of the swamp forest species assemblage is high because only 8 of the 314 species are shared despite the close proximity. Moreover, shared species are not very abundant (3% of all specimens). A redundancy analysis revealed that ~ 21% of the compositional variance of midge communities within the swamp forest was explained by a range of variables with conductivity, stream order, stream width, temperature, latitude (flow direction), and year being significant factors influencing community structure. An LME analysis demonstrates that the total species richness decreased with increasing conductivity. CONCLUSION Our study demonstrates that midge diversity of a swamp forest can be so high that it questions global species diversity estimates for Chironomidae, which are an important component of many freshwater ecosystems. We furthermore demonstrate that small and natural habitat remnants can have high species turnover and can be very resistant to the invasion of species from neighboring reservoirs. Lastly, the study shows how NGS barcodes can be used to integrate specimen- and species-rich invertebrate taxa in biodiversity and conservation research.
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Affiliation(s)
- Bilgenur Baloğlu
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road E, Guelph, Ontario N1G2W1 Canada
| | - Esther Clews
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Block S2S, Singapore, 119222 Singapore
| | - Rudolf Meier
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road E, Guelph, Ontario N1G2W1 Canada
- Lee Kong Chian Natural History Museum, 2 Conservatory Drive, Singapore, 117377 Singapore
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24
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Carew ME, Coleman RA, Hoffmann AA. Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding? PeerJ 2018; 6:e4980. [PMID: 29915700 PMCID: PMC6004113 DOI: 10.7717/peerj.4980] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/25/2018] [Indexed: 11/20/2022] Open
Abstract
Background High throughput DNA sequencing of bulk invertebrate samples or metabarcoding is becoming increasingly used to provide profiles of biological communities for environmental monitoring. As metabarcoding becomes more widely applied, new reference DNA barcodes linked to individual specimens identified by taxonomists are needed. This can be achieved through using DNA extraction methods that are not only suitable for metabarcoding but also for building reference DNA barcode libraries. Methods In this study, we test the suitability of a rapid non-destructive DNA extraction method for metabarcoding of freshwater invertebrate samples. Results This method resulted in detection of taxa from many taxonomic groups, comparable to results obtained with two other tissue-based extraction methods. Most taxa could also be successfully used for subsequent individual-based DNA barcoding and taxonomic identification. The method was successfully applied to field-collected invertebrate samples stored for taxonomic studies in 70% ethanol at room temperature, a commonly used storage method for freshwater samples. Discussion With further refinement and testing, non-destructive extraction has the potential to rapidly characterise species biodiversity in invertebrate samples, while preserving specimens for taxonomic investigation.
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Affiliation(s)
- Melissa E Carew
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Rhys A Coleman
- Applied Research, Melbourne Water Corporation, Melbourne, Victoria, Australia
| | - Ary A Hoffmann
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
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25
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Srivathsan A, Baloğlu B, Wang W, Tan WX, Bertrand D, Ng AHQ, Boey EJH, Koh JJY, Nagarajan N, Meier R. A MinION™-based pipeline for fast and cost-effective DNA barcoding. Mol Ecol Resour 2018; 18:1035-1049. [PMID: 29673082 DOI: 10.1111/1755-0998.12890] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/09/2018] [Accepted: 03/13/2018] [Indexed: 01/01/2023]
Abstract
DNA barcodes are useful for species discovery and species identification, but obtaining barcodes currently requires a well-equipped molecular laboratory and is time-consuming, and/or expensive. We here address these issues by developing a barcoding pipeline for Oxford Nanopore MinION™ and demonstrating that one flow cell can generate barcodes for ~500 specimens despite the high basecall error rates of MinION™ reads. The pipeline overcomes these errors by first summarizing all reads for the same tagged amplicon as a consensus barcode. Consensus barcodes are overall mismatch-free but retain indel errors that are concentrated in homopolymeric regions. They are addressed with an optional error correction pipeline that is based on conserved amino acid motifs from publicly available barcodes. The effectiveness of this pipeline is documented by analysing reads from three MinION™ runs that represent three different stages of MinION™ development. They generated data for (i) 511 specimens of a mixed Diptera sample, (ii) 575 specimens of ants and (iii) 50 specimens of Chironomidae. The run based on the latest chemistry yielded MinION™ barcodes for 490 of the 511 specimens which were assessed against reference Sanger barcodes (N = 471). Overall, the MinION™ barcodes have an accuracy of 99.3%-100% with the number of ambiguous bases after correction ranging from <0.01% to 1.5% depending on which correction pipeline is used. We demonstrate that it requires ~2 hr of sequencing to gather all information needed for obtaining reliable barcodes for most specimens (>90%). We estimate that up to 1,000 barcodes can be generated in one flow cell and that the cost per barcode can be
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Affiliation(s)
- Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Bilgenur Baloğlu
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Wendy Wang
- Lee Kong Chian Natural History Museum, Singapore
| | - Wei X Tan
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Denis Bertrand
- Computational & Systems Biology, Genome Institute of Singapore, Singapore
| | - Amanda H Q Ng
- Computational & Systems Biology, Genome Institute of Singapore, Singapore
| | - Esther J H Boey
- Computational & Systems Biology, Genome Institute of Singapore, Singapore
| | - Jayce J Y Koh
- Computational & Systems Biology, Genome Institute of Singapore, Singapore
| | - Niranjan Nagarajan
- Computational & Systems Biology, Genome Institute of Singapore, Singapore
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore
- Lee Kong Chian Natural History Museum, Singapore
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26
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Wang WY, Srivathsan A, Foo M, Yamane SK, Meier R. Sorting specimen-rich invertebrate samples with cost-effective NGS barcodes: Validating a reverse workflow for specimen processing. Mol Ecol Resour 2018; 18:490-501. [PMID: 29314756 DOI: 10.1111/1755-0998.12751] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 12/20/2017] [Accepted: 12/20/2017] [Indexed: 11/28/2022]
Abstract
Biologists frequently sort specimen-rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative is barcoding every specimen in a bulk sample and then presorting the specimens using DNA barcodes, thus mitigating downstream morphological work on presorted units. Such a "reverse workflow" is too expensive using Sanger sequencing, but we here demonstrate that is feasible with an next-generation sequencing (NGS) barcoding pipeline that allows for cost-effective high-throughput generation of short specimen-specific barcodes (313 bp of COI; laboratory cost <$0.50 per specimen) through next-generation sequencing of tagged amplicons. We applied our approach to a large sample of tropical ants, obtaining barcodes for 3,290 of 4,032 specimens (82%). NGS barcodes and their corresponding specimens were then sorted into molecular operational taxonomic units (mOTUs) based on objective clustering and Automated Barcode Gap Discovery (ABGD). High diversity of 88-90 mOTUs (4% clustering) was found and morphologically validated based on preserved vouchers. The mOTUs were overwhelmingly in agreement with morphospecies (match ratio 0.95 at 4% clustering). Because of lack of coverage in existing barcode databases, only 18 could be accurately identified to named species, but our study yielded new barcodes for 48 species, including 28 that are potentially new to science. With its low cost and technical simplicity, the NGS barcoding pipeline can be implemented by a large range of laboratories. It accelerates invertebrate species discovery, facilitates downstream taxonomic work, helps with building comprehensive barcode databases and yields precise abundance information.
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Affiliation(s)
- Wendy Y Wang
- Lee Kong Chian Natural History Museum, Faculty of Science, National University of Singapore, Singapore
| | - Amrita Srivathsan
- Evolutionary Biology Laboratory, Department of Biological Sciences, National University of Singapore, Singapore
| | - Maosheng Foo
- Lee Kong Chian Natural History Museum, Faculty of Science, National University of Singapore, Singapore
| | | | - Rudolf Meier
- Lee Kong Chian Natural History Museum, Faculty of Science, National University of Singapore, Singapore.,Evolutionary Biology Laboratory, Department of Biological Sciences, National University of Singapore, Singapore
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27
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Cavanaugh SE, Bathrick AS. Direct PCR amplification of forensic touch and other challenging DNA samples: A review. Forensic Sci Int Genet 2018; 32:40-49. [DOI: 10.1016/j.fsigen.2017.10.005] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/11/2017] [Accepted: 10/16/2017] [Indexed: 01/08/2023]
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28
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Jinfa W, Maosheng F, Tan HTW, Meier R. Whitefly predation and extensive mesonotum color polymorphism in an Acletoxenus population from Singapore (Diptera, Drosophilidae). Zookeys 2017; 725:49-69. [PMID: 29430204 PMCID: PMC5806509 DOI: 10.3897/zookeys.725.13675] [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] [Received: 05/14/2017] [Accepted: 09/12/2017] [Indexed: 11/26/2022] Open
Abstract
Acletoxenus is a small genus of Drosophilidae with only four described species that are closely associated with whiteflies (adults and larvae). Here, the first video recordings of larvae feeding on whiteflies (Aleurotrachelus trachoides) are presented. Typical morphological adaptations for predation by schizophoran larvae are also described: the larval pseudocephalon lacks a facial mask and the cephaloskeleton is devoid of cibarial ridges that could be used for saprophagy via filtration. Despite being a predator, Acletoxenus is unlikely to be a good candidate for biological control of whiteflies because the life cycle is fairly long (24 days), lab cultures could not be established, and the puparia have high parasitization rates by a pteromalid wasp (Pachyneuron leucopiscida). Unfortunately, a confident identification of the Singapore Acletoxenus population to species was not possible because species identification and description in the genus overemphasize coloration characters of the mesonotum which are shown to be unsuitable because the Singapore population has flies with coloration patterns matching three of the four described species. Based on morphology and DNA sequences, the population from Singapore is tentatively assigned to Acletoxenus indicus or a closely related species.
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Affiliation(s)
- Wong Jinfa
- Department of Biological Sciences, National University of Singapore, Singapore
117543
| | - Foo Maosheng
- Lee Kong Chian Natural History Museum, National University of Singapore,
Singapore 117377
| | - Hugh T. W. Tan
- Department of Biological Sciences, National University of Singapore, Singapore
117543
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore
117543
- Lee Kong Chian Natural History Museum, National University of Singapore,
Singapore 117377
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29
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Reproductive interference and fecundity affect competitive interactions of sibling species with low mating barriers: experimental and theoretical evidence. Heredity (Edinb) 2017; 119:438-446. [PMID: 28902188 DOI: 10.1038/hdy.2017.56] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 11/09/2022] Open
Abstract
When allopatric species with incomplete prezygotic isolation come into secondary contact, the outcome of their interaction is not easily predicted. The parasitoid wasp Encarsia suzannae (iES), infected by Cardinium inducing cytoplasmic incompatibility (CI), and its sibling species E. gennaroi (EG), not infected by bacterial endosymbionts, may have diverged because of the complementary action of CI and asymmetric hybrid incompatibilities. Whereas postzygotic isolation is now complete because of sterility of F1 hybrid progeny, prezygotic isolation is still incipient. We set up laboratory population cage experiments to evaluate the outcome of the interaction between ES and EG in two pairwise combinations: iES vs EG and cured ES (cES, where Cardinium was removed with antibiotics) vs EG. We also built a theoretical model aimed at exploring the role of life-history differences and asymmetric mating on competitive outcomes. In three of four cages in each treatment, ES dominated the interaction. We found evidence for reproductive interference, driven by asymmetric mating preferences, that gave a competitive edge to ES, the species that better discriminated against heterospecifics. However, we did not find the fecundity cost previously shown to be associated with Cardinium infection in iES. The model largely supported the experimental results. The finding of only a slight competitive edge of ES over EG in population cages suggests that in a more heterogeneous environment the species could coexist. This is supported by evidence that the two species coexist in sympatry, where preliminary data suggest reproductive character displacement may have reinforced postzygotic isolation.
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30
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Giantsis IA, Chaskopoulou A, Claude Bon M. Direct Multiplex PCR (dmPCR) for the Identification of Six Phlebotomine Sand Fly Species (Diptera: Psychodidae), Including Major Leishmania Vectors of the Mediterranean. JOURNAL OF ECONOMIC ENTOMOLOGY 2017; 110:245-249. [PMID: 28025389 DOI: 10.1093/jee/tow269] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Sand flies (Diptera: Psychodidae, subfamily Phlebotominae) are hematophagous insects that are known to transmit several anthroponotic and zoonotic diseases. Reliable identification of sand flies at species level is crucial for their surveillance, the detection and spread of their pathogens, and the implementation of targeted pest control strategies. Here, we designed a novel, time-saving, cost-effective and easy-to-apply molecular methodology, which avoids sequencing, for the identification of the following six Eastern Mediterranean sand fly species: Phebotomus perfiliewi Parrot, Phebotomus simici Theodor, Phebotomus tobbi Adler and Theodor, Phebotomus papatasi Scopoli, Sergentomyia dentata Sinton, and Sergentomyia minuta Theodor. This methodology, which is a multiplex PCR assay using one common and six diagnostic primers, is based on species-specific single-nucleotide polymorphisms of the nuclear 18S rRNA gene. Amplification products were easily and reliably separated in agarose gel yielding one single clear band of diagnostic size for each species. Further, we verified its successful application on tissue samples that were immersed directly to the PCR mix, skipping DNA extraction. The direct multiplex PCR can be completed in < 3 h, including all operating procedures, and costing no more than a simple PCR. The applicability of this methodology in the detection of hybrids is an additional considerable benefit.
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Affiliation(s)
- Ioannis A Giantsis
- USDA - ARS, European Biological Control Laboratory, Tsimiski, Thessaloniki, Greece
- Perrotis College, American Farm School, Marinou Antipa, Thessaloniki, Greece
- Corresponding author
| | - Alexandra Chaskopoulou
- USDA - ARS, European Biological Control Laboratory, Tsimiski, Thessaloniki, Greece
- Perrotis College, American Farm School, Marinou Antipa, Thessaloniki, Greece
| | - Marie Claude Bon
- USDA - ARS, European Biological Control Laboratory, Campus International de Baillarguet, Montferrier-sur-Lez, France
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31
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Rugman-Jones PF, Stouthamer R. High-resolution melt analysis without DNA extraction affords rapid genotype resolution and species identification. Mol Ecol Resour 2016; 17:598-607. [PMID: 27658237 DOI: 10.1111/1755-0998.12599] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/08/2016] [Accepted: 09/16/2016] [Indexed: 11/28/2022]
Abstract
Extracting and sequencing DNA from specimens can impose major time and monetary costs to studies requiring genotyping, or identification to species, of large numbers of individuals. As such, so-called direct PCR methods have been developed enabling significant savings at the DNA extraction step. Similarly, real-time quantitative PCR techniques (qPCR) offer very cost-effective alternatives to sequencing. High-resolution melt analysis (HRM) is a qPCR method that incorporates an intercalating dye into a double-stranded PCR amplicon. The dye fluoresces brightly, but only when it is bound. Thus, after PCR, raising the temperature of the amplicon while measuring the fluorescence of the reaction results in the generation of a sequence-specific melt curve, allowing discrimination of genotypes. Methods combining HRM (or other qPCR methods) and direct PCR have not previously been reported, most likely due to concerns that any tissue in the reaction tube would interfere with detection of the fluorescent signal. Here, we couple direct PCR with HRM and, by way of three examples, demonstrate a very quick and cost-effective method for genotyping large numbers of specimens, using Rotor-Gene HRM instruments (QIAGEN). In contrast to the heated-block design of most qPCR/HRM instruments, the Rotor-Gene's centrifugal rotor and air-based temperature-regulation system facilitate our method by depositing tissues away from the pathway of the machine's fluorescence detection optics.
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Affiliation(s)
- Paul F Rugman-Jones
- Department of Entomology, University of California, Riverside, CA, 92521, USA
| | - Richard Stouthamer
- Department of Entomology, University of California, Riverside, CA, 92521, USA
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32
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Wilson JJ, Sing KW, Lee PS, Wee AKS. Application of DNA barcodes in wildlife conservation in Tropical East Asia. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2016; 30:982-9. [PMID: 27341687 DOI: 10.1111/cobi.12787] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 02/12/2016] [Indexed: 05/24/2023]
Abstract
Over the past 50 years, Tropical East Asia has lost more biodiversity than any tropical region. Tropical East Asia is a megadiverse region with an acute taxonomic impediment. DNA barcodes are short standardized DNA sequences used for taxonomic purposes and have the potential to lessen the challenges of biodiversity inventory and assessments in regions where they are most needed. We reviewed DNA barcoding efforts in Tropical East Asia relative to other tropical regions. We suggest DNA barcodes (or metabarcodes from next-generation sequencers) may be especially useful for characterizing and connecting species-level biodiversity units in inventories encompassing taxa lacking formal description (particularly arthropods) and in large-scale, minimal-impact approaches to vertebrate monitoring and population assessments through secondary sources of DNA (invertebrate derived DNA and environmental DNA). We suggest interest and capacity for DNA barcoding are slowly growing in Tropical East Asia, particularly among the younger generation of researchers who can connect with the barcoding analogy and understand the need for new approaches to the conservation challenges being faced.
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Affiliation(s)
- John-James Wilson
- Ecology and Biodiversity Program, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- Museum of Zoology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Kong-Wah Sing
- Ecology and Biodiversity Program, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Museum of Zoology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Ping-Shin Lee
- Ecology and Biodiversity Program, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Museum of Zoology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Alison K S Wee
- Centre for Integrative Conservation, Xisshangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun Township, Mengla County, Yunnan Province, 666303, China
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33
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Ng TH, Tan SK, Wong WH, Meier R, Chan SY, Tan HH, Yeo DCJ. Molluscs for Sale: Assessment of Freshwater Gastropods and Bivalves in the Ornamental Pet Trade. PLoS One 2016; 11:e0161130. [PMID: 27525660 PMCID: PMC4985174 DOI: 10.1371/journal.pone.0161130] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 07/29/2016] [Indexed: 01/24/2023] Open
Abstract
The ornamental pet trade is often considered a key culprit for conservation problems such as the introduction of invasive species (including infectious diseases) and overharvesting of rare species. Here, we present the first assessment of the biodiversity of freshwater molluscs in the ornamental pet trade in Singapore, one of the most important global hubs of the ornamental aquarium trade, and discuss associated conservation concerns. We recorded freshwater molluscs from ornamental pet shops and major exporters including non-ornamental species (e.g., hitchhikers, molluscs sold as fish feed). We recorded an unexpectedly high diversity-59 species-of freshwater bivalves and gastropods, with the majority (38 species or 64%) being from the Oriental region. In addition to morphological examination, we sequenced the DNA barcode region of mitochondrial CO1 and 16S genes to provide molecular data for the confirmation of the identification and for future re-identification. DNA barcodes were obtained for 50 species, and all but four were separated by > 3% uncorrected pairwise distances. The trade has been considered a main introduction pathway for non-native species to Singapore, and we found that out of 15 species in the trade as well as in the wild in Singapore, 12 are either introduced or of unknown origin, representing almost half of the known non-native freshwater molluscs in Singapore. Particularly prevalent are non-ornamental species: six hitchhikers on aquarium plants and six species sold as fish feed. We found that a quarter of the trade species have a history of introduction, which includes 11 known or potentially invasive species. We conclude that potential overharvesting is difficult to assess because only half of the trade species have been treated by IUCN. Of these, 21 species are of Least Concern and three are Data Deficient. Our checklist, with accompanying DNA barcodes, images, and museum vouchers, provides an important reference library for future monitoring, and constitutes a step toward creating a more sustainable ornamental pet trade.
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Affiliation(s)
- Ting Hui Ng
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Siong Kiat Tan
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore
| | - Wing Hing Wong
- The Division of Biology and Biomedical Sciences, Washington University in St. Louis, United States of America
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore
| | | | - Heok Hui Tan
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore
| | - Darren C. J. Yeo
- Department of Biological Sciences, National University of Singapore, Singapore
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34
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Tay YC, Chng MWP, Sew WWG, Rheindt FE, Tun KPP, Meier R. Beyond the Coral Triangle: high genetic diversity and near panmixia in Singapore's populations of the broadcast spawning sea star Protoreaster nodosus. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160253. [PMID: 27853600 PMCID: PMC5108950 DOI: 10.1098/rsos.160253] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/19/2016] [Indexed: 06/06/2023]
Abstract
The Coral Triangle is widely considered the most important centre of marine biodiversity in Asia while areas on its periphery such as the South China Sea, have received much less interest. Here, we demonstrate that a small population of the knobbly sea star Protoreaster nodosus in Singapore has similarly high levels of genetic diversity as comparable Indonesian populations from the Coral Triangle. The high genetic diversity of this population is remarkable because it is maintained despite decades of continued anthropogenic disturbance. We postulate that it is probably due to broadcast spawning which is likely to maintain high levels of population connectivity. To test this, we analysed 6140 genome-wide single nucleotide polymorphism (SNP) loci for Singapore's populations and demonstrate a pattern of near panmixia. We here document a second case of high genetic diversity and low genetic structure for a broadcast spawner in Singapore, which suggests that such species have high resilience against anthropogenic disturbances. The study demonstrates the feasibility and power of using genome-wide SNPs for connectivity studies of marine invertebrates without a sequenced genome.
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Affiliation(s)
- Y. C. Tay
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Republic of Singapore
| | - M. W. P. Chng
- Centre for Liveable Cities, Ministry of National Development, The URA Centre, 45 Maxwell Road no. 07-01, Singapore 069118, Republic of Singapore
| | - W. W. G. Sew
- DHI Water and Environment (S) Pte Ltd, 1 Cleantech Loop, Cleantech One, no. 03-05, Singapore 637141, Republic of Singapore
| | - F. E. Rheindt
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Republic of Singapore
| | - K. P. P. Tun
- National Parks Board, 1 Cluny Road, Singapore 259569, Republic of Singapore
| | - R. Meier
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Republic of Singapore
- Lee Kong Chian Natural History Museum, Department of Biological Sciences, National University of Singapore, Singapore, Republic of Singapore
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Colony-PCR Is a Rapid Method for DNA Amplification of Hyphomycetes. J Fungi (Basel) 2016; 2:jof2020012. [PMID: 29376929 PMCID: PMC5753074 DOI: 10.3390/jof2020012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 11/23/2022] Open
Abstract
Fungal pure cultures identified with both classical morphological methods and through barcoding sequences are a basic requirement for reliable reference sequences in public databases. Improved techniques for an accelerated DNA barcode reference library construction will result in considerably improved sequence databases covering a wider taxonomic range. Fast, cheap, and reliable methods for obtaining DNA sequences from fungal isolates are, therefore, a valuable tool for the scientific community. Direct colony PCR was already successfully established for yeasts, but has not been evaluated for a wide range of anamorphic soil fungi up to now, and a direct amplification protocol for hyphomycetes without tissue pre-treatment has not been published so far. Here, we present a colony PCR technique directly from fungal hyphae without previous DNA extraction or other prior manipulation. Seven hundred eighty-eight fungal strains from 48 genera were tested with a success rate of 86%. PCR success varied considerably: DNA of fungi belonging to the genera Cladosporium, Geomyces, Fusarium, and Mortierella could be amplified with high success. DNA of soil-borne yeasts was always successfully amplified. Absidia, Mucor, Trichoderma, and Penicillium isolates had noticeably lower PCR success.
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Werblow A, Flechl E, Klimpel S, Zittra C, Lebl K, Kieser K, Laciny A, Silbermayr K, Melaun C, Fuehrer HP. Direct PCR of indigenous and invasive mosquito species: a time- and cost-effective technique of mosquito barcoding. MEDICAL AND VETERINARY ENTOMOLOGY 2016; 30:8-13. [PMID: 26663040 PMCID: PMC4982094 DOI: 10.1111/mve.12154] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 12/29/2014] [Accepted: 02/17/2015] [Indexed: 06/05/2023]
Abstract
Millions of people die each year as a result of pathogens transmitted by mosquitoes. However, the morphological identification of mosquito species can be difficult even for experts. The identification of morphologically indistinguishable species, such as members of the Anopheles maculipennis complex (Diptera: Culicidae), and possible hybrids, such as Culex pipiens pipiens/Culex pipiens molestus (Diptera: Culicidae), presents a major problem. In addition, the detection and discrimination of newly introduced species can be challenging, particularly to researchers without previous experience. Because of their medical importance, the clear identification of all relevant mosquito species is essential. Using the direct polymerase chain reaction (PCR) method described here, DNA amplification without prior DNA extraction is possible and thus species identification after sequencing can be achieved. Different amounts of tissue (leg, head; larvae or adult) as well as different storage conditions (dry, ethanol, -20 and -80 °C) and storage times were successfully applied and showed positive results after amplification and gel electrophoresis. Overall, 28 different indigenous and non-indigenous mosquito species were analysed using a gene fragment of the COX1 gene for species differentiation and identification by sequencing this 658-bp fragment. Compared with standard PCR, this method is time- and cost-effective and could thus improve existing surveillance and control programmes.
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Affiliation(s)
- A Werblow
- Institute for Ecology, Evolution and Diversity, Goethe University (GU); Senckenberg Biodiversity and Climate Research Centre (BiK-F); Senckenberg Gesellschaft für Naturforschung (SGN), Frankfurt am Main, Germany
| | - E Flechl
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - S Klimpel
- Institute for Ecology, Evolution and Diversity, Goethe University (GU); Senckenberg Biodiversity and Climate Research Centre (BiK-F); Senckenberg Gesellschaft für Naturforschung (SGN), Frankfurt am Main, Germany
| | - C Zittra
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - K Lebl
- Institute for Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - K Kieser
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - A Laciny
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - K Silbermayr
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - C Melaun
- Institute for Ecology, Evolution and Diversity, Goethe University (GU); Senckenberg Biodiversity and Climate Research Centre (BiK-F); Senckenberg Gesellschaft für Naturforschung (SGN), Frankfurt am Main, Germany
| | - H-P Fuehrer
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
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Anglès d'Auriac MB, Norling P, Rinde E. A rapid and inexpensive DNA extraction protocol for oysters. Anim Genet 2016; 47:389-90. [PMID: 26857622 DOI: 10.1111/age.12417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2015] [Indexed: 11/26/2022]
Affiliation(s)
| | - Pia Norling
- Norwegian Institute of Water Research, Gaustadalléen 21, N-0349, Oslo, Norway.,Swedish Agency for Marine and Water Management (SwAM), P.O. Box 11 930, SE-404 39, Gothenburg, Sweden (former employee at NIVA)
| | - Eli Rinde
- Norwegian Institute of Water Research, Gaustadalléen 21, N-0349, Oslo, Norway
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39
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Kranzfelder P, Ekrem T, Stur E. Trace DNA from insect skins: a comparison of five extraction protocols and direct PCR on chironomid pupal exuviae. Mol Ecol Resour 2015; 16:353-63. [PMID: 26186122 DOI: 10.1111/1755-0998.12446] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/06/2015] [Accepted: 07/13/2015] [Indexed: 11/30/2022]
Abstract
Insect skins (exuviae) are of extracellular origin and shed during moulting. The skins do not contain cells or DNA themselves, but epithelial cells and other cell-based structures might accidentally attach as they are shed. This source of trace DNA can be sufficient for PCR amplification and sequencing of target genes and aid in species identification through DNA barcoding or association of unknown life stages. Species identification is essential for biomonitoring programs, as species vary in sensitivities to environmental factors. However, it requires a DNA isolation protocol that optimizes the output of target DNA. Here, we compare the relative effectiveness of five different DNA extraction protocols and direct PCR in isolation of DNA from chironomid pupal exuviae. Chironomidae (Diptera) is a species-rich group of aquatic macroinvertebrates widely distributed in freshwater environments and considered a valuable bioindicator of water quality. Genomic DNA was extracted from 61.2% of 570 sampled pupal exuviae. There were significant differences in the methods with regard to cost, handling time, DNA quantity, PCR success, sequence success and the ability to sequence target taxa. The NucleoSpin(®) Tissue XS Kit, DNeasy(®) Blood and Tissue kit, and QuickExtract(™) DNA Extraction Solution provided the best results in isolating DNA from single pupal exuviae. Direct PCR and DTAB/CTAB methods gave poor results. While the observed differences in DNA isolation methods on trace DNA will be relevant to research that focuses on aquatic macroinvertebrate ecology, taxonomy and systematics, they should also be of interest for studies using environmental barcoding and metabarcoding of aquatic environments.
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Affiliation(s)
- Petra Kranzfelder
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway.,Department of Entomology, University of Minnesota, 1980 Folwell Avenue, Saint Paul, MN, 55108, USA
| | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway
| | - Elisabeth Stur
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway
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Meier R, Wong W, Srivathsan A, Foo M. $1 DNA barcodes for reconstructing complex phenomes and finding rare species in specimen-rich samples. Cladistics 2015; 32:100-110. [DOI: 10.1111/cla.12115] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2015] [Indexed: 12/01/2022] Open
Affiliation(s)
- Rudolf Meier
- Lee Kong Chian Natural History Museum; National University of Singapore; 6 Science Drive 2 Singapore 117546 Singapore
- Department of Biological Sciences; National University of Singapore; 14 Science Drive 4 Singapore 117543 Singapore
- University Scholars Programme; National University of Singapore, University Town; 18 College Avenue East Singapore 138593 Singapore
| | - Winghing Wong
- Department of Biological Sciences; National University of Singapore; 14 Science Drive 4 Singapore 117543 Singapore
| | - Amrita Srivathsan
- Department of Biological Sciences; National University of Singapore; 14 Science Drive 4 Singapore 117543 Singapore
| | - Maosheng Foo
- Lee Kong Chian Natural History Museum; National University of Singapore; 6 Science Drive 2 Singapore 117546 Singapore
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