A multi-marker fish eDNA metabarcoding study comparing Illumina and Nanopore high-throughput sequencing platforms

A multi-marker fish eDNA metabarcoding study comparing Illumina and Nanopore high-throughput sequencing platforms | Authorea try { document.documentElement.classList.add('js'); } catch (e) { } var _gaq = _gaq || []; _gaq.push(['_setAccount', 'G-8VDV14Y67G']); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); Skip to main content Preprints Collections Wiley Open Research IET Open Research Ecological Society of Japan All Collections About About Authorea FAQs Contact Us Quick Search anywhere Search for preprint articles, keywords, etc. Search Search ADVANCED SEARCH SCROLL This is a preprint and has not been peer reviewed. Data may be preliminary. 27 January 2025 V1 Latest version Share on A multi-marker fish eDNA metabarcoding study comparing Illumina and Nanopore high-throughput sequencing platforms Authors : Maddalena Tibone 0009-0002-0915-0761 [email protected] , Sergio Stefanni , Jacopo Aguzzi , Bernadette O'Neill , and Luca Mirimin 0000-0001-9601-1457 Authors Info & Affiliations https://doi.org/10.22541/au.173797976.60860858/v1 764 views 306 downloads Contents Abstract Supplementary Material Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract Technological developments are a great advantage for biodiversity monitoring, if they are cross-validated with established protocols before their routine application. In the context of fish communities’ characterization, portable sequencers such as Oxford Nanopore Technology (ONT)’s MinION devices have the power to revolutionise field surveys through eDNA metabarcoding. However, Nanopore’s raw reads high error rates can disincentivise its use when compared to Illumina sequencers. Here, three sequencing protocols (two for Nanopore and one for Illumina) targeting short and long regions of two mitochondrial genes (12S and COI) were compared using fish mock communities and environmental DNA samples from mesocosm and field environments. Raw read quality, species richness detected, and taxonomic resolution of the platforms and genes were assessed. The latest Nanopore chemistry was comparable to Illumina for number of species retrieved, however discrepancies in species detected were observed between platforms and genes. Long amplicons provided higher taxonomic resolution compared to the short fragments. The 12S markers outperformed COI by detecting a higher number of species, while a multi-marker approach increased overall species richness in most cases. Sequencing technologies and primer selection can have significant impacts on fish eDNA metabarcoding results. Given its high specificity and taxonomic resolution, the long 12S region is presented as a promising marker for long-read metabarcoding. The latest Nanopore sequencing technology successfully profiled fish communities from mock and eDNA samples and due to its portability, quick turn-around time and reduced costs provides an innovative tool to conduct field-base studies. Supplementary Material File (tibone_et_al_mer_24.01.2025.docx) Download 1.44 MB Information & Authors Information Version history V1 Version 1 27 January 2025 Copyright This work is licensed under a Non Exclusive No Reuse License. Keywords 12s coi environmental dna illumina metabarcoding nanopore Authors Affiliations Maddalena Tibone 0009-0002-0915-0761 [email protected] Atlantic Technological University - Galway City View all articles by this author Sergio Stefanni Stazione Zoologica Anton Dohrn Napoli View all articles by this author Jacopo Aguzzi Instituto de Ciencias del Mar View all articles by this author Bernadette O'Neill Atlantic Technological University - Galway City View all articles by this author Luca Mirimin 0000-0001-9601-1457 Atlantic Technological University - Galway City View all articles by this author Metrics & Citations Metrics Article Usage 764 views 306 downloads .FvxKWukQNSOunydq8rnd { width: 100px; } Citations Download citation Maddalena Tibone, Sergio Stefanni, Jacopo Aguzzi, et al. A multi-marker fish eDNA metabarcoding study comparing Illumina and Nanopore high-throughput sequencing platforms. Authorea . 27 January 2025. 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Kelly, Fast, Flexible, Feasible: A Transparent Framework for Evaluating eDNA Workflow Trade‐Offs in Resource‐Limited Settings , Molecular Ecology Resources, 26 , 1, (2026). https://doi.org/10.1111/1755-0998.70091 Crossref Loading... View Options View options PDF View PDF Figures Tables Media Share Share Share article link Copy Link Copied! Copying failed. 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