Springer Nature
World Journal of Microbiology and Biotechnology
,  том 39 ,  издание 9 ,  номер публикации 229

The effect of metabarcoding 18S rRNA region choice on diversity of microeukaryotes including phytoplankton

Тип публикации: Journal Article
Дата публикации: 2023-06-21
Springer Nature
scimago Q2
wos Q2
БС2
SJR: 0.892
CiteScore: 6.7
Impact factor: 4.2
ISSN: 09593993, 15730972
General Medicine
Applied Microbiology and Biotechnology
Biotechnology
Physiology
Краткое описание
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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BUKIN Y. S. et al. The effect of metabarcoding 18S rRNA region choice on diversity of microeukaryotes including phytoplankton // World Journal of Microbiology and Biotechnology. 2023. Vol. 39. No. 9. 229
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BUKIN Y. S., Mikhailov I. S., Petrova D. P., Galachyants Y. P., Zakharova Y. R., Likhoshway Y. V. The effect of metabarcoding 18S rRNA region choice on diversity of microeukaryotes including phytoplankton // World Journal of Microbiology and Biotechnology. 2023. Vol. 39. No. 9. 229
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TY - JOUR
DO - 10.1007/s11274-023-03678-1
UR - https://doi.org/10.1007/s11274-023-03678-1
TI - The effect of metabarcoding 18S rRNA region choice on diversity of microeukaryotes including phytoplankton
T2 - World Journal of Microbiology and Biotechnology
AU - BUKIN, YURI S.
AU - Mikhailov, Ivan S
AU - Petrova, Darya P
AU - Galachyants, Yuri P
AU - Zakharova, Yulia R
AU - Likhoshway, Yelena V
PY - 2023
DA - 2023/06/21
PB - Springer Nature
IS - 9
VL - 39
PMID - 37341802
SN - 0959-3993
SN - 1573-0972
ER -
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@article{2023_BUKIN,
author = {YURI S. BUKIN and Ivan S Mikhailov and Darya P Petrova and Yuri P Galachyants and Yulia R Zakharova and Yelena V Likhoshway},
title = {The effect of metabarcoding 18S rRNA region choice on diversity of microeukaryotes including phytoplankton},
journal = {World Journal of Microbiology and Biotechnology},
year = {2023},
volume = {39},
publisher = {Springer Nature},
month = {jun},
url = {https://doi.org/10.1007/s11274-023-03678-1},
number = {9},
pages = {229},
doi = {10.1007/s11274-023-03678-1}
}