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Short- and long-read metabarcoding of the eukaryotic rRNA operon: Evaluation of primers and comparison to shotgun metagenomics sequencing
Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden; Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark.
Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. (EcoChange; UMFpub)ORCID iD: 0000-0002-1298-3839
Oceanographic Research, Swedish Meteorological and Hydrological Institute, Gothenburg, Sweden.
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2022 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 22, no 6, p. 2304-2318Article in journal (Refereed) Published
Abstract [en]

High-throughput sequencing-based analysis of microbial diversity has evolved vastly over the last decade. Currently, the go-to method for studying microbial eukaryotes is short-read metabarcoding of variable regions of the 18S rRNA gene with <500 bp amplicons. However, there is a growing interest in applying long-read sequencing of amplicons covering the rRNA operon for improving taxonomic resolution. For both methods, the choice of primers is crucial. It determines if community members are covered, if they can be identified at a satisfactory taxonomic level, and if the obtained community profile is representative. Here, we designed new primers targeting 18S and 28S rRNA based on 177,934 and 21,072 database sequences, respectively. The primers were evaluated in silico along with published primers on reference sequence databases and marine metagenomics data sets. We further evaluated a subset of the primers for short- and long-read sequencing on environmental samples in vitro and compared the obtained community profile with primer-unbiased metagenomic sequencing. Of the short-read pairs, a new V6-V8 pair and the V4_Balzano pair used with a simplified PCR protocol provided good results in silico and in vitro. Fewer differences were observed between the long-read primer pairs. The long-read amplicons and ITS1 alone provided higher taxonomic resolution than V4. Together, our results represent a reference and guide for selection of robust primers for research on and environmental monitoring of microbial eukaryotes.

Place, publisher, year, edition, pages
John Wiley & Sons, 2022. Vol. 22, no 6, p. 2304-2318
Keywords [en]
marine plankton, metabarcoding, microbial eukaryotes, PacBio long-read sequencing, primer design, rRNA operon
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:umu:diva-194894DOI: 10.1111/1755-0998.13623ISI: 000791463400001PubMedID: 35437888Scopus ID: 2-s2.0-85129364555OAI: oai:DiVA.org:umu-194894DiVA, id: diva2:1665132
Funder
Swedish Agency for Marine and Water ManagementSwedish Environmental Protection Agency, NV-03728-17Swedish Research Council Formas, 2017-00694Available from: 2022-06-07 Created: 2022-06-07 Last updated: 2022-12-06Bibliographically approved

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Brugel, SoniaAndersson, Agneta

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