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Intragenomic diversity of the V9 hypervariable domain in eukaryotes has little effect on metabarcoding
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 th...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10404988/ https://www.ncbi.nlm.nih.gov/pubmed/37554448 http://dx.doi.org/10.1016/j.isci.2023.107291 |
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author | Flegontova, Olga Lukeš, Julius Horák, Aleš |
author_facet | Flegontova, Olga Lukeš, Julius Horák, Aleš |
author_sort | Flegontova, Olga |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-10404988 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-104049882023-08-08 Intragenomic diversity of the V9 hypervariable domain in eukaryotes has little effect on metabarcoding Flegontova, Olga Lukeš, Julius Horák, Aleš iScience Article 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. Elsevier 2023-07-12 /pmc/articles/PMC10404988/ /pubmed/37554448 http://dx.doi.org/10.1016/j.isci.2023.107291 Text en © 2023 The Authors https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Flegontova, Olga Lukeš, Julius Horák, Aleš Intragenomic diversity of the V9 hypervariable domain in eukaryotes has little effect on metabarcoding |
title | Intragenomic diversity of the V9 hypervariable domain in eukaryotes has little effect on metabarcoding |
title_full | Intragenomic diversity of the V9 hypervariable domain in eukaryotes has little effect on metabarcoding |
title_fullStr | Intragenomic diversity of the V9 hypervariable domain in eukaryotes has little effect on metabarcoding |
title_full_unstemmed | Intragenomic diversity of the V9 hypervariable domain in eukaryotes has little effect on metabarcoding |
title_short | Intragenomic diversity of the V9 hypervariable domain in eukaryotes has little effect on metabarcoding |
title_sort | intragenomic diversity of the v9 hypervariable domain in eukaryotes has little effect on metabarcoding |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10404988/ https://www.ncbi.nlm.nih.gov/pubmed/37554448 http://dx.doi.org/10.1016/j.isci.2023.107291 |
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