Intragenomic diversity of the V9 hypervariable domain in eukaryotes has little effect on metabarcoding

0575161 - BC 2024 RIV US eng J - Journal Article
Flegontova, Olga - Lukeš, Julius - Horák, Aleš
Intragenomic diversity of the V9 hypervariable domain in eukaryotes has little effect on metabarcoding.
iScience. Roč. 26, č. 8 (2023), č. článku 107291. E-ISSN 2589-0042
R&D Projects: GA ČR(CZ) GA21-26209S; GA ČR(CZ) GX23-06479X
Institutional support: RVO:60077344
Keywords : Intragenomic * eukaryotic * metabarcoding
OECD category: Zoology
Impact factor: 5.8, year: 2022
Method of publishing: Open access
https://www.sciencedirect.com/science/article/pii/S2589004223013688?via%3Dihub

Metabarcoding revolutionized our understanding of diversity and ecology of microorganisms in different habitats. However, it is also associated with several inherent biases, one of which is associated with intragenomic diversity of a molecular barcode. Here, we compare intragenomic variability of the V9 region of the 18S rRNA gene in 19 eukaryotic phyla abundant in marine plankton. The level of intragenomic variability is comparable across all the phyla, and in most genomes and transcriptomes one V9 sequence and one OTU is predominant. However, most of the variability observed at the barcode level is probably caused by sequencing errors and is mitigated by using a denoising tool, DADA2. The SWARM algorithm commonly used in metabarcoding studies is not optimal for collapsing genuine and erroneous sequences into a single OTU, leading to an overestimation of diversity in metabarcoding data. For an unknown reason, SWARM inflates diversity of eupelagonemids more than that of other eukaryotes.
Permanent Link: https://hdl.handle.net/11104/0345275