Abstract
Metabarcoding using high throughput sequencing of amplicons of the 18S rRNA gene is one of the widely used methods for assessing the diversity of microeukaryotes in various ecosystems. We investigated the effectiveness of the V4 and V8-V9 regions of the 18S rRNA gene by comparing the results of metabarcoding microeukaryotic communities using the DADA2 (ASV), USEARCH-UNOISE3 (ZOTU), and USEARCH-UPARSE (OTU with 97% similarity) algorithms. Both regions showed similar levels of genetic variability and taxa identification accuracy. Richness for DADA2 datasets of both regions was lower than for UNOISE3 and UPARSE datasets, which is due to more accurate error correction in amplicons. Microeukaryotic communities (autotrophs and heterotrophs) structure identified using both regions showed a significant relationship with phytoplankton (autotrophs) communities structure based on microscopy in a seasonal freshwater sample series. The strongest relationship was found between the phytoplankton species and V8-V9 ASVs produced by DADA2.
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Anonymous reviewers are acknowledged for their honest and constructive comments which have greatly improved this work.
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This work was supported by the Ministry of Science and Higher Education of Russian Federation project no. 0279–2021-0009 “Study of the role of selected genes and proteins of Baikal diatoms by methods of bioinformatics and physicochemical biology”.
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Yuri Bukin performed methodological planning, statistical analysis, prepared figures, wrote the main text of the manuscript. Ivan Mikhailov performed high-throughput sequencing data analysis, statistical analysis, prepared figures, wrote the main text of the manuscript, organization of expedition work and sampling. Darya Petrova carried out the DNA extraction, quality control of the original DNA preparations. Yuri Galachyants performed methodological planning, performed selection of primers for 18S rRNA. Yulia Zakharova organization of expedition work and sampling. Yelena Likhoshway provided guidance and methodological planning. All authors read and approved the final manuscript.
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Bukin, Y.S., Mikhailov, I.S., Petrova, D.P. et al. The effect of metabarcoding 18S rRNA region choice on diversity of microeukaryotes including phytoplankton. World J Microbiol Biotechnol 39, 229 (2023). https://doi.org/10.1007/s11274-023-03678-1
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DOI: https://doi.org/10.1007/s11274-023-03678-1