James M. Nolan, Ilze Skujina, Gwenaëlle Hurpy, Andrew J. Tighe, Conor Whelan, Emma C. Teeling
{"title":"利用节肢动物模拟样本和爱尔兰蝙蝠饮食特征评价牛津纳米孔技术MinION测序仪作为一种新型短扩增子元条形码工具","authors":"James M. Nolan, Ilze Skujina, Gwenaëlle Hurpy, Andrew J. Tighe, Conor Whelan, Emma C. Teeling","doi":"10.1002/ece3.71333","DOIUrl":null,"url":null,"abstract":"<p>Biodiversity monitoring using metabarcoding is now widely used as a routine environmental management tool. However, despite the rapid advancement of third-generation high-throughput sequencing platforms, there are limited studies assessing the most suitable tools and approaches for environmental metabarcoding studies. We tested the utility of Oxford Nanopore Technologies MinION sequencing for short-read amplicon sequencing of mitochondrial <i>COI</i> mini-barcodes from a known composition of arthropod species and compared its performance with more commonly used Illumina NovaSeq sequencing. The mock arthropod species assemblage allowed us to optimise a bioinformatic filtering pipeline to identify arthropod species using MinION long reads. Using this pipeline, we identified host species and diet composition by sequencing droppings collected from five individual Irish brown long-eared bats (<i>Plecotus auritus</i>) roosts. We showed that MinION data provided a similar taxonomic assignment to <i>NovaSeq</i> but only if the reference species barcode database was accurate and comprehensive. The <i>P. auritus</i> diet inferred was as expected based on previous morphological and Illumina metabarcoding studies. We showed that less sequencing depth, but a higher number of biological samples were necessary for complete species composition detection by MinION. A relatively simple bioinformatic filtering tool such as NanoPipe could adequately retrieve both host species and diet composition. The biggest standing challenge was the reference database format transferability and comprehensiveness. This pipeline can be used to guide future metabarcoding studies using nanopore sequencing to minimise the cost and effort while optimising results.</p>","PeriodicalId":11467,"journal":{"name":"Ecology and Evolution","volume":"15 5","pages":""},"PeriodicalIF":2.3000,"publicationDate":"2025-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ece3.71333","citationCount":"0","resultStr":"{\"title\":\"Evaluation of Oxford Nanopore Technologies MinION Sequencer as a Novel Short Amplicon Metabarcoding Tool Using Arthropod Mock Sample and Irish Bat Diet Characterisation\",\"authors\":\"James M. Nolan, Ilze Skujina, Gwenaëlle Hurpy, Andrew J. Tighe, Conor Whelan, Emma C. Teeling\",\"doi\":\"10.1002/ece3.71333\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>Biodiversity monitoring using metabarcoding is now widely used as a routine environmental management tool. However, despite the rapid advancement of third-generation high-throughput sequencing platforms, there are limited studies assessing the most suitable tools and approaches for environmental metabarcoding studies. We tested the utility of Oxford Nanopore Technologies MinION sequencing for short-read amplicon sequencing of mitochondrial <i>COI</i> mini-barcodes from a known composition of arthropod species and compared its performance with more commonly used Illumina NovaSeq sequencing. The mock arthropod species assemblage allowed us to optimise a bioinformatic filtering pipeline to identify arthropod species using MinION long reads. Using this pipeline, we identified host species and diet composition by sequencing droppings collected from five individual Irish brown long-eared bats (<i>Plecotus auritus</i>) roosts. We showed that MinION data provided a similar taxonomic assignment to <i>NovaSeq</i> but only if the reference species barcode database was accurate and comprehensive. The <i>P. auritus</i> diet inferred was as expected based on previous morphological and Illumina metabarcoding studies. We showed that less sequencing depth, but a higher number of biological samples were necessary for complete species composition detection by MinION. A relatively simple bioinformatic filtering tool such as NanoPipe could adequately retrieve both host species and diet composition. The biggest standing challenge was the reference database format transferability and comprehensiveness. 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Evaluation of Oxford Nanopore Technologies MinION Sequencer as a Novel Short Amplicon Metabarcoding Tool Using Arthropod Mock Sample and Irish Bat Diet Characterisation
Biodiversity monitoring using metabarcoding is now widely used as a routine environmental management tool. However, despite the rapid advancement of third-generation high-throughput sequencing platforms, there are limited studies assessing the most suitable tools and approaches for environmental metabarcoding studies. We tested the utility of Oxford Nanopore Technologies MinION sequencing for short-read amplicon sequencing of mitochondrial COI mini-barcodes from a known composition of arthropod species and compared its performance with more commonly used Illumina NovaSeq sequencing. The mock arthropod species assemblage allowed us to optimise a bioinformatic filtering pipeline to identify arthropod species using MinION long reads. Using this pipeline, we identified host species and diet composition by sequencing droppings collected from five individual Irish brown long-eared bats (Plecotus auritus) roosts. We showed that MinION data provided a similar taxonomic assignment to NovaSeq but only if the reference species barcode database was accurate and comprehensive. The P. auritus diet inferred was as expected based on previous morphological and Illumina metabarcoding studies. We showed that less sequencing depth, but a higher number of biological samples were necessary for complete species composition detection by MinION. A relatively simple bioinformatic filtering tool such as NanoPipe could adequately retrieve both host species and diet composition. The biggest standing challenge was the reference database format transferability and comprehensiveness. This pipeline can be used to guide future metabarcoding studies using nanopore sequencing to minimise the cost and effort while optimising results.
期刊介绍:
Ecology and Evolution is the peer reviewed journal for rapid dissemination of research in all areas of ecology, evolution and conservation science. The journal gives priority to quality research reports, theoretical or empirical, that develop our understanding of organisms and their diversity, interactions between them, and the natural environment.
Ecology and Evolution gives prompt and equal consideration to papers reporting theoretical, experimental, applied and descriptive work in terrestrial and aquatic environments. The journal will consider submissions across taxa in areas including but not limited to micro and macro ecological and evolutionary processes, characteristics of and interactions between individuals, populations, communities and the environment, physiological responses to environmental change, population genetics and phylogenetics, relatedness and kin selection, life histories, systematics and taxonomy, conservation genetics, extinction, speciation, adaption, behaviour, biodiversity, species abundance, macroecology, population and ecosystem dynamics, and conservation policy.