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Lu S, Zeng H, Xiong F, Yao M, He S. Advances in environmental DNA monitoring: standardization, automation, and emerging technologies in aquatic ecosystems. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1368-1384. [PMID: 38512561 DOI: 10.1007/s11427-023-2493-5] [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: 09/07/2023] [Accepted: 10/30/2023] [Indexed: 03/23/2024]
Abstract
Environmental DNA (eDNA) monitoring, a rapidly advancing technique for assessing biodiversity and ecosystem health, offers a noninvasive approach for detecting and quantifying species from various environmental samples. In this review, a comprehensive overview of current eDNA collection and detection technologies is provided, emphasizing the necessity for standardization and automation in aquatic ecological monitoring. Furthermore, the intricacies of water bodies, from streams to the deep sea, and the associated challenges they pose for eDNA capture and analysis are explored. The paper delineates three primary eDNA survey methods, namely, bringing back water, bringing back filters, and bringing back data, each with specific advantages and constraints in terms of labor, transport, and data acquisition. Additionally, innovations in eDNA sampling equipment, including autonomous drones, subsurface samplers, and in-situ filtration devices, and their applications in monitoring diverse taxa are discussed. Moreover, recent advancements in species-specific detection and eDNA metabarcoding are addressed, highlighting the integration of novel techniques such as CRISPR-Cas and nanopore sequencing that enable precise and rapid detection of biodiversity. The implications of environmental RNA and epigenetic modifications are considered for future applications in providing nuanced ecological data. Lastly, the review stresses the critical role of standardization and automation in enhancing data consistency and comparability for robust long-term biomonitoring. We propose that the amalgamation of these technologies represents a paradigm shift in ecological monitoring, aligning with the urgent call for biodiversity conservation and sustainable management of aquatic ecosystems.
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Affiliation(s)
- Suxiang Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Honghui Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fan Xiong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
- School of Life Sciences, Peking University, Beijing, 100871, China.
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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2
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Vasilita C, Feng V, Hansen AK, Hartop E, Srivathsan A, Struijk R, Meier R. Express barcoding with NextGenPCR and MinION for species-level sorting of ecological samples. Mol Ecol Resour 2024; 24:e13922. [PMID: 38240168 DOI: 10.1111/1755-0998.13922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 03/06/2024]
Abstract
The use of DNA barcoding is well established for specimen identification and large-scale biodiversity discovery, but remains underutilized for time-sensitive applications such as rapid species discovery in field stations, identifying pests, citizen science projects, and authenticating food. The main reason is that existing express barcoding workflows are either too expensive or can only be used in very well-equipped laboratories by highly-trained staff. We here show an alternative workflow combining rapid DNA extraction with HotSHOT, amplicon production with NextGenPCR thermocyclers, and sequencing with low-cost MinION sequencers. We demonstrate the power of the approach by generating 250 barcodes for 285 specimens within 6 h including specimen identification through BLAST. The workflow required only the following major equipment that easily fits onto a lab bench: Thermocycler, NextGenPCR, microplate sealer, Qubit, and MinION. Based on our results, we argue that simplified barcoding workflows for species-level sorting are now faster, more accurate, and sufficiently cost-effective to replace traditional morpho-species sorting in many projects.
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Affiliation(s)
| | - Vivian Feng
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
- Humboldt-Universität zu Berlin, Institut für Biologie, Berlin, Germany
| | - Aslak Kappel Hansen
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
| | - Emily Hartop
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
| | - Amrita Srivathsan
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
| | - Robin Struijk
- Molecular Biology Systems B.V., Goes, The Netherlands
| | - Rudolf Meier
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
- Humboldt-Universität zu Berlin, Institut für Biologie, Berlin, Germany
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3
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Srivathsan A, Feng V, Suárez D, Emerson B, Meier R. ONTbarcoder 2.0: rapid species discovery and identification with real-time barcoding facilitated by Oxford Nanopore R10.4. Cladistics 2024; 40:192-203. [PMID: 38041646 DOI: 10.1111/cla.12566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 12/03/2023] Open
Abstract
Most arthropod species are undescribed and hidden in specimen-rich samples that are difficult to sort to species using morphological characters. For such samples, sorting to putative species with DNA barcodes is an attractive alternative, but needs cost-effective techniques that are suitable for use in many laboratories around the world. Barcoding using the portable and inexpensive MinION sequencer produced by Oxford Nanopore Technologies (ONT) could be useful for presorting specimen-rich samples with DNA barcodes because it requires little space and is inexpensive. However, similarly important is user-friendly and reliable software for analysis of the ONT data. It is here provided in the form of ONTbarcoder 2.0 that is suitable for all commonly used operating systems and includes a Graphical User Interface (GUI). Compared with an earlier version, ONTbarcoder 2.0 has three key improvements related to the higher read quality obtained with ONT's latest flow cells (R10.4), chemistry (V14 kits) and basecalling model (super-accuracy model). First, the improved read quality of ONT's latest flow cells (R10.4) allows for the use of primers with shorter indices than those previously needed (9 bp vs. 12-13 bp). This decreases the primer cost and can potentially improve PCR success rates. Second, ONTbarcoder now delivers real-time barcoding to complement ONT's real-time sequencing. This means that the first barcodes are obtained within minutes of starting a sequencing run; i.e. flow cell use can be optimized by terminating sequencing runs when most barcodes have already been obtained. The only input needed by ONTbarcoder 2.0 is a demultiplexing sheet and sequencing data (raw or basecalled) generated by either a Mk1B or a Mk1C. Thirdly, we demonstrate that the availability of R10.4 chemistry for the low-cost Flongle flow cell is an attractive option for users who require only 200-250 barcodes at a time.
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Affiliation(s)
- Amrita Srivathsan
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Invalidenstraße 43, 10115, Berlin, Germany
| | - Vivian Feng
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Invalidenstraße 43, 10115, Berlin, Germany
| | - Daniel Suárez
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), C/Astrofísico Francisco Sánchez 3, La Laguna, Tenerife, Canary Islands, 38206, Spain
- School of Doctoral and Postgraduate Studies, University of La Laguna, 38200 La Laguna, Tenerife, Canary Islands, 38200, Spain
| | - Brent Emerson
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), C/Astrofísico Francisco Sánchez 3, La Laguna, Tenerife, Canary Islands, 38206, Spain
| | - Rudolf Meier
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Invalidenstraße 43, 10115, Berlin, Germany
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
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4
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Shideler SM, Goff K, Gauthier J, Levesque RC, Lewenza S. Complete genome sequence of Pseudomonas veronii strain OST1911 isolated from oil sand tailing pond water in Alberta, Canada. Microbiol Resour Announc 2023; 12:e0064623. [PMID: 37966238 PMCID: PMC10720577 DOI: 10.1128/mra.00646-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/07/2023] [Indexed: 11/16/2023] Open
Abstract
Here, we report the complete genome sequence of Pseudomonas veronii strain OST1911, recovered from oil sand process-affected water accumulated in tailing ponds. This water contains numerous organic and inorganic compounds of environmental significance. The genome size is 6,435,955 bp with a G+C content of 61.21%.
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Affiliation(s)
- Steven M. Shideler
- Department of Immunology and Infectious Diseases, University of Calgary, Alberta, Canada
| | - Kira Goff
- Department of Immunology and Infectious Diseases, University of Calgary, Alberta, Canada
- Faculty of Science and Technology, Athabasca University, Athabasca, Alberta, Canada
| | - Jeff Gauthier
- Institute of Integrative and Systems Biology, Laval University, Quebec, Canada
| | - Roger C. Levesque
- Institute of Integrative and Systems Biology, Laval University, Quebec, Canada
| | - Shawn Lewenza
- Department of Immunology and Infectious Diseases, University of Calgary, Alberta, Canada
- Faculty of Science and Technology, Athabasca University, Athabasca, Alberta, Canada
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5
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Boehm JT, Bovee E, Harris SE, Eddins K, Akahoho I, Foster M, Pell SK, Hickerson MJ, Amato G, DeSalle R, Waldman J. The United States dried seahorse trade: A comparison of traditional Chinese medicine and ecommerce-curio markets using molecular identification. PLoS One 2023; 18:e0291874. [PMID: 37788253 PMCID: PMC10547177 DOI: 10.1371/journal.pone.0291874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/07/2023] [Indexed: 10/05/2023] Open
Abstract
Tens of millions of dried seahorses (genus Hippocampus) are traded annually, and the pressure from this trade along with their life history traits (involved parental care and small migration distances and home ranges) has led to near global population declines. This and other forms of overexploitation have led to all seahorse species being listed in Appendix II under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). The signatory nations of CITES recommended a 10-cm size limit of seahorses to ensure harvested individuals have reached reproductive maturity, and have thus had the chance to produce offspring, to maintain a more sustainable global seahorse fishery. We assessed adherence to CITES recommendations using DNA barcoding and size measurements to compare two prominent U.S. dried seahorse markets: (1) traditional Chinese medicine (TCM), and (2) non-medicinal ecommerce and coastal curio (ECC). We also estimated U.S. import abundance from CITES records. Of the nine species identified among all samples (n = 532), eight were found in the TCM trade (n = 168); composed mostly (75%) of the Indo-Pacific species Hippocampus trimaculatus, and Hippocampus spinosissimus, and the Latin American Hippocampus ingens. In contrast, ECC samples (n = 344) included 5 species, primarily juvenile Indo-Pacific Hippocampus kuda (51.5%) and the western Atlantic Hippocampus zosterae (40.7). The majority of TCM samples (85.7%) met the CITES size recommendation, in contrast to 4.8% of ECC samples. These results suggest non-size discriminatory bycatch is the most likely source of imported ECC specimens. In addition, CITES records indicate that approximately 602,275 dried specimens were imported into the U.S. from 2004-2020, but the exact species composition remains unknown as many U.S. imports records list one species or Hippocampus spp. from confiscated shipments due to difficulties in morphological identification and large numbers of individuals per shipment. Molecular identification was used to identify the species composition of confiscated shipment imports containing undesignated species, and similar to TCM, found H. trimaculatus and H. spinosissimus the most abundant. By combining DNA barcoding, size comparisons, and CITES database records, these results provide an important glimpse into the two primary dried U.S. seahorse end-markets, and may further inform the conservation status of several Hippocampus species.
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Affiliation(s)
- J T Boehm
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- Department of Biology, City College of New York, New York, New York, United States of America
- Subprogram in Ecology, Evolution Biology and Behavior, The Graduate Center of the City University of New York, New York, New York, United States of America
| | - Eric Bovee
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Stephen E Harris
- Subprogram in Ecology, Evolution Biology and Behavior, The Graduate Center of the City University of New York, New York, New York, United States of America
- School of Natural and Social Science, SUNY Purchase College, Purchase, New York, United States of America
| | - Kathryn Eddins
- The New School, New York, New York, United States of America
| | - Ishmael Akahoho
- Brooklyn Academy of Science and the Environment High School, Brooklyn, New York, United States of America
| | - Marcia Foster
- Brooklyn Academy of Science and the Environment High School, Brooklyn, New York, United States of America
| | - Susan K Pell
- Brooklyn Botanic Garden, Brooklyn, New York, United States of America
| | - Michael J Hickerson
- Department of Biology, City College of New York, New York, New York, United States of America
- Subprogram in Ecology, Evolution Biology and Behavior, The Graduate Center of the City University of New York, New York, New York, United States of America
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
| | - George Amato
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
| | - John Waldman
- Subprogram in Ecology, Evolution Biology and Behavior, The Graduate Center of the City University of New York, New York, New York, United States of America
- Biology Department, Queens College, City University of New York, New York, United States of America
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6
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Seeber PA, Epp LS. Environmental
DNA
and metagenomics of terrestrial mammals as keystone taxa of recent and past ecosystems. Mamm Rev 2022. [DOI: 10.1111/mam.12302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Peter A. Seeber
- Limnological Institute University of Konstanz Konstanz Germany
| | - Laura S. Epp
- Limnological Institute University of Konstanz Konstanz Germany
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7
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Rapid in situ identification of biological specimens via DNA amplicon sequencing using miniaturized laboratory equipment. Nat Protoc 2022; 17:1415-1443. [DOI: 10.1038/s41596-022-00682-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 01/04/2022] [Indexed: 12/24/2022]
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8
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Egeter B, Veríssimo J, Lopes-Lima M, Chaves C, Pinto J, Riccardi N, Beja P, Fonseca NA. Speeding up the detection of invasive bivalve species using environmental DNA: a Nanopore and Illumina sequencing comparison. Mol Ecol Resour 2022; 22:2232-2247. [PMID: 35305077 DOI: 10.1111/1755-0998.13610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 02/09/2022] [Accepted: 03/02/2022] [Indexed: 11/30/2022]
Abstract
Traditional detection of aquatic invasive species via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindrances, but sample processing is often lengthy. More recently, portable nanopore sequencing technology has become available, which has the potential to make molecular detection of invasive species more widely accessible and substantially decrease sample turnaround times. However, nanopore-sequenced reads have a much higher error rate than those produced by Illumina platforms, which has so far hindered the adoption of this technology. We provide a detailed laboratory protocol and bioinformatic tools (msi package) to increase the reliability of nanopore sequencing to detect invasive species, and we test its application using invasive bivalves while comparing it with Illumina-based sequencing. We sampled water from sites with pre-existing bivalve occurrence and abundance data, and contrasting bivalve communities, in Italy and Portugal. Samples were extracted, amplified, and sequenced by the two platforms. The mean agreement between sequencing methods was 69% and the difference between methods was non-significant. The lack of detections of some species at some sites could be explained by their known low abundances. This is the first reported use of MinION to detect aquatic invasive species from eDNA samples.
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Affiliation(s)
- Bastian Egeter
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,NatureMetrics, Bakeham Lane, Egham, Surrey, TW20 9TY, U.K
| | - Joana Veríssimo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Manuel Lopes-Lima
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,IUCN SSC Mollusc Specialist Group, c/o 219 Huntingdon Road, Cambridge, CB3 0DL, U.K
| | - Cátia Chaves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Joana Pinto
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | | | - Pedro Beja
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,CIBIO/InBIO, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Nuno A Fonseca
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
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9
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Vierstraete AR, Braeckman BP. Amplicon_sorter: A tool for reference‐free amplicon sorting based on sequence similarity and for building consensus sequences. Ecol Evol 2022; 12:e8603. [PMID: 35261737 PMCID: PMC8888255 DOI: 10.1002/ece3.8603] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/12/2022] [Accepted: 01/18/2022] [Indexed: 11/23/2022] Open
Abstract
Oxford Nanopore Technologies (ONT) is a third‐generation sequencing technology that is gaining popularity in ecological research for its portable and low‐cost sequencing possibilities. Although the technology excels at long‐read sequencing, it can also be applied to sequence amplicons. The downside of ONT is the low quality of the raw reads. Hence, generating a high‐quality consensus sequence is still a challenge. We present Amplicon_sorter, a tool for reference‐free sorting of ONT sequenced amplicons based on their similarity in sequence and length and for building solid consensus sequences.
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Affiliation(s)
- Andy R. Vierstraete
- Laboratory of aging physiology and Molecular Evolution University of Gent Gent Belgium
| | - Bart P. Braeckman
- Laboratory of aging physiology and Molecular Evolution University of Gent Gent Belgium
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10
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Linchangco GV, Foley B, Leitner T. Updated HIV-1 Consensus Sequences Change but Stay Within Similar Distance From Worldwide Samples. Front Microbiol 2022; 12:828765. [PMID: 35178042 PMCID: PMC8843389 DOI: 10.3389/fmicb.2021.828765] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/20/2021] [Indexed: 12/15/2022] Open
Abstract
HIV consensus sequences are used in various bioinformatic, evolutionary, and vaccine related research. Since the previous HIV-1 subtype and CRF consensus sequences were constructed in 2002, the number of publicly available HIV-1 sequences have grown exponentially, especially from non-EU and US countries. Here, we reconstruct 90 new HIV-1 subtype and CRF consensus sequences from 3,470 high-quality, representative, full genome sequences in the LANL HIV database. While subtypes and CRFs are unevenly spread across the world, in total 89 countries were represented. For consensus sequences that were based on at least 20 genomes, we found that on average 2.3% (range 0.8–10%) of the consensus genome site states changed from 2002 to 2021, of which about half were nucleotide state differences and the rest insertions and deletions. Interestingly, the 2021 consensus sequences were shorter than in 2002, and compared to 4,674 HIV-1 worldwide genome sequences, the 2021 consensuses were somewhat closer to the worldwide genome sequences, i.e., showing on average fewer nucleotide state differences. Some subtypes/CRFs have had limited geographical spread, and thus sampling of subtypes/CRFs is uneven, at least in part, due to the epidemiological dynamics. Thus, taken as a whole, the 2021 consensus sequences likely are good representations of the typical subtype/CRF genome nucleotide states. The new consensus sequences are available at the LANL HIV database.
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Affiliation(s)
- Gregorio V Linchangco
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Brian Foley
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, United States
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11
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Dudenhoeffer M, Roth JD, Johnson LK, Petersen SD. Arctic fox winter dietary response to damped lemming cycles estimated from fecal DNA. J Mammal 2021. [DOI: 10.1093/jmammal/gyab115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Climate-caused changes in prey abundance may alter predator–prey dynamics in the Arctic food web. Lemmings (Dicrostonyx spp.) are important prey for Arctic foxes (Vulpes lagopus) and their annual population fluctuations drive fox reproduction, creating strongly linked predator–prey population cycles. Winter diet directly impacts Arctic fox reproductive success, but winter prey diversity on the tundra is low. Strategies such as using the marine environment to scavenge seals have allowed Arctic foxes to persist during years of low lemming abundance. However, warming winters have decreased snowpack quality, preventing lemmings from reaching their previous high abundances, which may reduce their impact on predator dynamics. We investigated Arctic fox dietary response to lemming abundance by reconstructing Arctic fox winter diet in the low Arctic. Next-generation sequencing of fecal DNA, from samples (n = 627) collected at dens in winters of 2011–2018, identified prey both from terrestrial and marine environments. Despite lemming cycle damping, Arctic foxes still increased lemming consumption during years of higher lemming abundance. Alternative prey such as marine resources were consumed more during years of low lemming abundance, with up to 45% of samples containing marine resources in low lemming years. In addition, Arctic foxes consumed high proportions of meadow voles (Microtus pennsylvanicus), which may represent a new alternative prey, suggesting climate change may be creating new foraging opportunities. Changes in prey abundance illustrate how climate-caused disturbances are altering Arctic food-web dynamics. Dietary flexibility and availability of alternative prey may become increasingly important for Arctic predators as the Arctic continues to change.
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Affiliation(s)
- Megan Dudenhoeffer
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - James D Roth
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Lucy K Johnson
- Fisheries and Oceans Canada, 501 University Crescent, Winnipeg, Manitoba R3T 2N6, Canada
| | - Stephen D Petersen
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, Manitoba R3T 2N2, Canada
- Conservation and Research Department, Assiniboine Park Zoo, 2595 Roblin Boulevard, Winnipeg, Manitoba R3R 2N7, Canada
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12
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Abstract
AbstractObserving and quantifying primate behavior in the wild is challenging. Human presence affects primate behavior and habituation of new, especially terrestrial, individuals is a time-intensive process that carries with it ethical and health concerns, especially during the recent pandemic when primates are at even greater risk than usual. As a result, wildlife researchers, including primatologists, have increasingly turned to new technologies to answer questions and provide important data related to primate conservation. Tools and methods should be chosen carefully to maximize and improve the data that will be used to answer the research questions. We review here the role of four indirect methods—camera traps, acoustic monitoring, drones, and portable field labs—and improvements in machine learning that offer rapid, reliable means of combing through large datasets that these methods generate. We describe key applications and limitations of each tool in primate conservation, and where we anticipate primate conservation technology moving forward in the coming years.
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13
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Srivathsan A, Lee L, Katoh K, Hartop E, Kutty SN, Wong J, Yeo D, Meier R. ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone. BMC Biol 2021; 19:217. [PMID: 34587965 PMCID: PMC8479912 DOI: 10.1186/s12915-021-01141-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/03/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND DNA barcodes are a useful tool for discovering, understanding, and monitoring biodiversity which are critical tasks at a time of rapid biodiversity loss. However, widespread adoption of barcodes requires cost-effective and simple barcoding methods. We here present a workflow that satisfies these conditions. It was developed via "innovation through subtraction" and thus requires minimal lab equipment, can be learned within days, reduces the barcode sequencing cost to < 10 cents, and allows fast turnaround from specimen to sequence by using the portable MinION sequencer. RESULTS We describe how tagged amplicons can be obtained and sequenced with the real-time MinION sequencer in many settings (field stations, biodiversity labs, citizen science labs, schools). We also provide amplicon coverage recommendations that are based on several runs of the latest generation of MinION flow cells ("R10.3") which suggest that each run can generate barcodes for > 10,000 specimens. Next, we present a novel software, ONTbarcoder, which overcomes the bioinformatics challenges posed by MinION reads. The software is compatible with Windows 10, Macintosh, and Linux, has a graphical user interface (GUI), and can generate thousands of barcodes on a standard laptop within hours based on only two input files (FASTQ, demultiplexing file). We document that MinION barcodes are virtually identical to Sanger and Illumina barcodes for the same specimens (> 99.99%) and provide evidence that MinION flow cells and reads have improved rapidly since 2018. CONCLUSIONS We propose that barcoding with MinION is the way forward for government agencies, universities, museums, and schools because it combines low consumable and capital cost with scalability. Small projects can use the flow cell dongle ("Flongle") while large projects can rely on MinION flow cells that can be stopped and re-used after collecting sufficient data for a given project.
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Affiliation(s)
- Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Leshon Lee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Kazutaka Katoh
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Artificial Intelligence Research Center, AIST, Tokyo, Japan
| | - Emily Hartop
- Zoology Department, Stockholms Universitet, Stockholm, Sweden
- Station Linné, Öland, Sweden
| | - Sujatha Narayanan Kutty
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Johnathan Wong
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Darren Yeo
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Berlin, Germany.
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A Rapid and Cost-Effective Identification of Invertebrate Pests at the Borders Using MinION Sequencing of DNA Barcodes. Genes (Basel) 2021; 12:genes12081138. [PMID: 34440312 PMCID: PMC8392835 DOI: 10.3390/genes12081138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 12/12/2022] Open
Abstract
The rapid and accurate identification of invertebrate pests detected at the border is a challenging task. Current diagnostic methods used at the borders are mainly based on time consuming visual and microscopic examinations. Here, we demonstrate a rapid in-house workflow for DNA extraction, PCR amplification of the barcode region of the mitochondrial cytochrome oxidase subunit I (COI) gene and Oxford Nanopore Technologies (ONT) MinION sequencing of amplified products multiplexed after barcoding on ONT Flongle flow cells. A side-by-side comparison was conducted of DNA barcode sequencing-based identification and morphological identification of both large (>0.5 mm in length) and small (<0.5 mm in length) invertebrate specimens intercepted at the Australian border. DNA barcode sequencing results supported the morphological identification in most cases and enabled immature stages of invertebrates and their eggs to be identified more confidently. Results also showed that sequencing the COI barcode region using the ONT rapid sequencing principle is a cost-effective and field-adaptable approach for the rapid and accurate identification of invertebrate pests. Overall, the results suggest that MinION sequencing of DNA barcodes offers a complementary tool to the existing morphological diagnostic approaches and provides rapid, accurate, reliable and defendable evidence for identifying invertebrate pests at the border.
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15
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Nanopore sequencing in non-human forensic genetics. Emerg Top Life Sci 2021; 5:465-473. [PMID: 34002773 PMCID: PMC8457772 DOI: 10.1042/etls20200287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/21/2021] [Accepted: 04/29/2021] [Indexed: 12/28/2022]
Abstract
The past decade has seen a rapid expansion of non-human forensic genetics coinciding with the development of 2nd and 3rd generation DNA sequencing technologies. Nanopore sequencing is one such technology that offers massively parallel sequencing at a fraction of the capital cost of other sequencing platforms. The application of nanopore sequencing to species identification has already been widely demonstrated in biomonitoring studies and has significant potential for non-human forensic casework, particularly in the area of wildlife forensics. This review examines nanopore sequencing technology and assesses its potential applications, advantages and drawbacks for use in non-human forensics, alongside other next-generation sequencing platforms and as a possible replacement to Sanger sequencing. We assess the specific challenges of sequence error rate and the standardisation of consensus sequence production, before discussing recent progress in the validation of nanopore sequencing for use in forensic casework. We conclude that nanopore sequencing may be able to play a considerable role in the future of non-human forensic genetics, especially for applications to wildlife law enforcement within emerging forensic laboratories.
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16
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Ben Chehida S, Filloux D, Fernandez E, Moubset O, Hoareau M, Julian C, Blondin L, Lett JM, Roumagnac P, Lefeuvre P. Nanopore Sequencing Is a Credible Alternative to Recover Complete Genomes of Geminiviruses. Microorganisms 2021; 9:903. [PMID: 33922452 PMCID: PMC8147096 DOI: 10.3390/microorganisms9050903] [Citation(s) in RCA: 9] [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: 03/24/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 01/23/2023] Open
Abstract
Next-generation sequencing (NGS), through the implementation of metagenomic protocols, has led to the discovery of thousands of new viruses in the last decade. Nevertheless, these protocols are still laborious and costly to implement, and the technique has not yet become routine for everyday virus characterization. Within the context of CRESS DNA virus studies, we implemented two alternative long-read NGS protocols, one that is agnostic to the sequence (without a priori knowledge of the viral genome) and the other that use specific primers to target a virus (with a priori). Agnostic and specific long read NGS-based assembled genomes of two capulavirus strains were compared to those obtained using the gold standard technique of Sanger sequencing. Both protocols allowed the detection and accurate full genome characterization of both strains. Globally, the assembled genomes were very similar (99.5-99.7% identity) to the Sanger sequences consensus, but differences in the homopolymeric tracks of these sequences indicated a specific lack of accuracy of the long reads NGS approach that has yet to be improved. Nevertheless, the use of the bench-top sequencer has proven to be a credible alternative in the context of CRESS DNA virus study and could offer a new range of applications not previously accessible.
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Affiliation(s)
- Selim Ben Chehida
- CIRAD, UMR PVBMT, F-97410 St Pierre, La Réunion, France; (S.B.C.); (M.H.); (J.-M.L.)
| | - Denis Filloux
- CIRAD, PHIM, F-34398 Montpellier, France; (D.F.); (E.F.); (O.M.); (C.J.); (L.B.); (P.R.)
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
| | - Emmanuel Fernandez
- CIRAD, PHIM, F-34398 Montpellier, France; (D.F.); (E.F.); (O.M.); (C.J.); (L.B.); (P.R.)
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
| | - Oumaima Moubset
- CIRAD, PHIM, F-34398 Montpellier, France; (D.F.); (E.F.); (O.M.); (C.J.); (L.B.); (P.R.)
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
| | - Murielle Hoareau
- CIRAD, UMR PVBMT, F-97410 St Pierre, La Réunion, France; (S.B.C.); (M.H.); (J.-M.L.)
| | - Charlotte Julian
- CIRAD, PHIM, F-34398 Montpellier, France; (D.F.); (E.F.); (O.M.); (C.J.); (L.B.); (P.R.)
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
| | - Laurence Blondin
- CIRAD, PHIM, F-34398 Montpellier, France; (D.F.); (E.F.); (O.M.); (C.J.); (L.B.); (P.R.)
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
| | - Jean-Michel Lett
- CIRAD, UMR PVBMT, F-97410 St Pierre, La Réunion, France; (S.B.C.); (M.H.); (J.-M.L.)
| | - Philippe Roumagnac
- CIRAD, PHIM, F-34398 Montpellier, France; (D.F.); (E.F.); (O.M.); (C.J.); (L.B.); (P.R.)
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
| | - Pierre Lefeuvre
- CIRAD, UMR PVBMT, F-97410 St Pierre, La Réunion, France; (S.B.C.); (M.H.); (J.-M.L.)
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17
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Vasiljevic N, Lim M, Humble E, Seah A, Kratzer A, Morf NV, Prost S, Ogden R. Developmental validation of Oxford Nanopore Technology MinION sequence data and the NGSpeciesID bioinformatic pipeline for forensic genetic species identification. Forensic Sci Int Genet 2021; 53:102493. [PMID: 33770699 DOI: 10.1016/j.fsigen.2021.102493] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/09/2021] [Accepted: 03/03/2021] [Indexed: 12/14/2022]
Abstract
Species identification of non-human biological evidence through DNA nucleotide sequencing is routinely used for forensic genetic analysis to support law enforcement. The gold standard for forensic genetics is conventional Sanger sequencing; however, this is gradually being replaced by high-throughput sequencing (HTS) approaches which can generate millions of individual reads in a single experiment. HTS sequencing, which now dominates molecular biology research, has already been demonstrated for use in a number of forensic genetic analysis applications, including species identification. However, the generation of HTS data to date requires expensive equipment and is cost-effective only when large numbers of samples are analysed simultaneously. The Oxford Nanopore Technologies (ONT) MinION™ is an affordable and small footprint DNA sequencing device with the potential to quickly deliver reliable and cost effective data. However, there has been no formal validation of forensic species identification using high-throughput (deep read) sequence data from the MinION making it currently impractical for many wildlife forensic end-users. Here, we present a MinION deep read sequence data validation study for species identification. First, we tested whether the clustering-based bioinformatics pipeline NGSpeciesID can be used to generate an accurate consensus sequence for species identification. Second, we systematically evaluated the read variation distribution around the generated consensus sequences to understand what confidence we have in the accuracy of the resulting consensus sequence and to determine how to interpret individual sample results. Finally, we investigated the impact of differences between the MinION consensus and Sanger control sequences on correct species identification to understand the ability and accuracy of the MinION consensus sequence to differentiate the true species from the next most similar species. This validation study establishes that ONT MinION sequence data used in conjunction with the NGSpeciesID pipeline can produce consensus DNA sequences of sufficient accuracy for forensic genetic species identification.
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Affiliation(s)
- Nina Vasiljevic
- Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland.
| | - Marisa Lim
- Wildlife Conservation Society, Zoological Health Program, Bronx, NY, USA
| | - Emily Humble
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, UK
| | - Adeline Seah
- Wildlife Conservation Society, Zoological Health Program, Bronx, NY, USA
| | - Adelgunde Kratzer
- Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Nadja V Morf
- Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg, Frankfurt, Germany; South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, UK; TRACE Wildlife Forensics Network, Edinburgh, UK
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18
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Complete Genome Sequence of a Pseudomonas Species Isolated from Tailings Pond Water in Alberta, Canada. Microbiol Resour Announc 2021; 10:10/9/e01174-20. [PMID: 33664136 PMCID: PMC7936634 DOI: 10.1128/mra.01174-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
We report the complete genome sequence of strain OST1909, belonging to a Pseudomonas species. The genome size is 6,306,352 bp, with a G+C content of 59.6%. The isolate was recovered from oil sands process-affected water (OSPW), despite the numerous toxic compounds that accumulate in oil sands tailings ponds. We report the complete genome sequence of strain OST1909, belonging to a Pseudomonas species. The genome size is 6,306,352 bp, with a G+C content of 59.6%. The isolate was recovered from oil sands process-affected water (OSPW), despite the numerous toxic compounds that accumulate in oil sands tailings ponds.
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19
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Sahlin K, Lim MCW, Prost S. NGSpeciesID: DNA barcode and amplicon consensus generation from long-read sequencing data. Ecol Evol 2021; 11:1392-1398. [PMID: 33598139 PMCID: PMC7863402 DOI: 10.1002/ece3.7146] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/26/2020] [Accepted: 12/04/2020] [Indexed: 11/10/2022] Open
Abstract
Third-generation sequencing technologies, such as Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), have gained popularity over the last years. These platforms can generate millions of long-read sequences. This is not only advantageous for genome sequencing projects, but also advantageous for amplicon-based high-throughput sequencing experiments, such as DNA barcoding. However, the relatively high error rates associated with these technologies still pose challenges for generating high-quality consensus sequences. Here, we present NGSpeciesID, a program which can generate highly accurate consensus sequences from long-read amplicon sequencing technologies, including ONT and PacBio. The tool includes clustering of the reads to help filter out contaminants or reads with high error rates and employs polishing strategies specific to the appropriate sequencing platform. We show that NGSpeciesID produces consensus sequences with improved usability by minimizing preprocessing and software installation and scalability by enabling rapid processing of hundreds to thousands of samples, while maintaining similar consensus accuracy as current pipelines.
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Affiliation(s)
- Kristoffer Sahlin
- Department of MathematicsScience for Life LaboratoryStockholm UniversityStockholmSweden
| | - Marisa C. W. Lim
- Department of Population Health and ReproductionUniversity of CaliforniaDavisCAUSA
| | - Stefan Prost
- LOEWE‐Centre for Translational Biodiversity GenomicsSenckenbergFrankfurtGermany
- South African National Biodiversity InstituteNational Zoological GardenPretoriaSouth Africa
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20
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Modernizing the Toolkit for Arthropod Bloodmeal Identification. INSECTS 2021; 12:insects12010037. [PMID: 33418885 PMCID: PMC7825046 DOI: 10.3390/insects12010037] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 11/24/2022]
Abstract
Simple Summary The ability to identify the source of vertebrate blood in mosquitoes, ticks, and other blood-feeding arthropod vectors greatly enhances our knowledge of how vector-borne pathogens are spread. The source of the bloodmeal is identified by analyzing the remnants of blood remaining in the arthropod at the time of capture, though this is often fraught with challenges. This review provides a roadmap and guide for those considering modern techniques for arthropod bloodmeal identification with a focus on progress made in the field over the past decade. We highlight genome regions that can be used to identify the vertebrate source of arthropod bloodmeals as well as technological advances made in other fields that have introduced innovative new ways to identify vertebrate meal source based on unique properties of the DNA sequence, protein signatures, or residual molecules present in the blood. Additionally, engineering progress in miniaturization has led to a number of field-deployable technologies that bring the laboratory directly to the arthropods at the site of collection. Although many of these advancements have helped to address the technical challenges of the past, the challenge of successfully analyzing degraded DNA in bloodmeals remains to be solved. Abstract Understanding vertebrate–vector interactions is vitally important for understanding the transmission dynamics of arthropod-vectored pathogens and depends on the ability to accurately identify the vertebrate source of blood-engorged arthropods in field collections using molecular methods. A decade ago, molecular techniques being applied to arthropod blood meal identification were thoroughly reviewed, but there have been significant advancements in the techniques and technologies available since that time. This review highlights the available diagnostic markers in mitochondrial and nuclear DNA and discusses their benefits and shortcomings for use in molecular identification assays. Advances in real-time PCR, high resolution melting analysis, digital PCR, next generation sequencing, microsphere assays, mass spectrometry, and stable isotope analysis each offer novel approaches and advantages to bloodmeal analysis that have gained traction in the field. New, field-forward technologies and platforms have also come into use that offer promising solutions for point-of-care and remote field deployment for rapid bloodmeal source identification. Some of the lessons learned over the last decade, particularly in the fields of DNA barcoding and sequence analysis, are discussed. Though many advancements have been made, technical challenges remain concerning the prevention of sample degradation both by the arthropod before the sample has been obtained and during storage. This review provides a roadmap and guide for those considering modern techniques for arthropod bloodmeal identification and reviews how advances in molecular technology over the past decade have been applied in this unique biomedical context.
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21
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Chang JJM, Ip YCA, Ng CSL, Huang D. Takeaways from Mobile DNA Barcoding with BentoLab and MinION. Genes (Basel) 2020; 11:E1121. [PMID: 32987804 PMCID: PMC7598690 DOI: 10.3390/genes11101121] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/17/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
Since the release of the MinION sequencer in 2014, it has been applied to great effect in the remotest and harshest of environments, and even in space. One of the most common applications of MinION is for nanopore-based DNA barcoding in situ for species identification and discovery, yet the existing sample capability is limited (n ≤ 10). Here, we assembled a portable sequencing setup comprising the BentoLab and MinION and developed a workflow capable of processing 32 samples simultaneously. We demonstrated this enhanced capability out at sea, where we collected samples and barcoded them onboard a dive vessel moored off Sisters' Islands Marine Park, Singapore. In under 9 h, we generated 105 MinION barcodes, of which 19 belonged to fresh metazoans processed immediately after collection. Our setup is thus viable and would greatly fortify existing portable DNA barcoding capabilities. We also tested the performance of the newly released R10.3 nanopore flow cell for DNA barcoding, and showed that the barcodes generated were ~99.9% accurate when compared to Illumina references. A total of 80% of the R10.3 nanopore barcodes also had zero base ambiguities, compared to 50-60% for R9.4.1, suggesting an improved homopolymer resolution and making the use of R10.3 highly recommended.
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Affiliation(s)
- Jia Jin Marc Chang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Y.C.A.I.); (C.S.L.N.)
| | - Yin Cheong Aden Ip
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Y.C.A.I.); (C.S.L.N.)
| | - Chin Soon Lionel Ng
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Y.C.A.I.); (C.S.L.N.)
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Y.C.A.I.); (C.S.L.N.)
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
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