From short to long reads: enhanced protist diversity profiling via Nanopore metabarcoding

Résumé fourni par la source

In the last decades, environmental metabarcoding has revolutionised biodiversity research, particularly for microbial organisms such as protists, enabling large-scale assessments of diversity and ecological patterns across time and space. With the advent of long-read sequencing, Nanopore-based metabarcoding represents a promising alternative to short-read approaches. Due to the limited number of available studies, the effectiveness of Nanopore sequencing - alone or in combination with short-read data - for assessing the biodiversity and ecological patterns of protists in different ecosystems is not yet sufficiently explored. Here, we present BaNaNA (Barcoding Nanopore Neat Annotator), a pipeline designed to generate high-quality OTUs and abundance estimates from Nanopore sequencing data. The performance of the pipeline was evaluated using a mock community as well as on marine and freshwater environmental samples to demonstrate its relevance for protist biodiversity and ecological studies. Our results show that BaNaNA generates high-quality full-length 18S rDNAOTUs from Nanopore long reads that are directly comparable to short-read V4-18S rDNAASVs, supporting their synergistic use in long-term biodiversity studies. While both approaches reveal similar overall community diversity, long-read OTUs provide greater taxonomic resolution, richer phylogenetic information enabling the discovery of new clades and yield fewer false positives. These advantages make long-read Nanopore metabarcoding not only a powerful cost effective complement, but also a reliable replacement to short-read methods. By providing a pipeline for processing Nanopore data, BaNaNA paves the way for a broader application of long-read Nanopore sequencing in protist ecology and biodiversity research.

Ce résumé expose les affirmations des auteurs. BNTIC ne l’interprète pas comme une validation indépendante des résultats.