V9 Hypervariable Region Metabarcoding Primers for Euglenozoa and Metamonada

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60077344%3A_____%2F24%3A00599967" target="_blank" >RIV/60077344:_____/24:00599967 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/60076658:12310/24:43908777 RIV/00216208:11310/24:10487026

Výsledek na webu

<a href="https://doi.org/10.1002/edn3.70022" target="_blank" >https://doi.org/10.1002/edn3.70022</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1002/edn3.70022" target="_blank" >10.1002/edn3.70022</a>

Jazyk výsledku

angličtina

Název v původním jazyce

V9 Hypervariable Region Metabarcoding Primers for Euglenozoa and Metamonada

Popis výsledku v původním jazyce

Short amplicon sequencing is a commonly used method to study the diversity of organisms in various habitats. The hypervariable regions of the small subunit rRNA gene (18S rDNA) are the most general barcodes for eukaryotes, which can provide detailed taxonomic information across a wide range of eukaryotic diversity. However, some organisms are often missed by universal primers, which have difficulty amplifying their barcodes. In this study, specific primers were designed for the amplification of the highly diverse 18S-V9 region of the Euglenozoa and Metamonada groups. The performance of the newly designed primers-V9Eug and V9Meta-was compared with the universal V9 primer on cultured communities derived from a range of freshwater environments of the Soos Natural Reserve and the Slavkov Forest in the Czech Republic. The V9Eug primer was more specific with Euglenozoa representing 91.8% of reads and 57.0% of OTUs, while the V9Meta primer showed lower specificity with only 48.4% of reads and 19.7% of OTUs assigned to Metamonada. Both the Euglenozoa and Metamonada primer pairs significantly improved recovery of their target groups compared to the universal V9 primer pair, detecting 2.7 and 1.8 times more OTUs, respectively. These results provide a more sensitive protocol for studying the diversity of these eukaryotic taxa.

Název v anglickém jazyce

V9 Hypervariable Region Metabarcoding Primers for Euglenozoa and Metamonada

Popis výsledku anglicky

Short amplicon sequencing is a commonly used method to study the diversity of organisms in various habitats. The hypervariable regions of the small subunit rRNA gene (18S rDNA) are the most general barcodes for eukaryotes, which can provide detailed taxonomic information across a wide range of eukaryotic diversity. However, some organisms are often missed by universal primers, which have difficulty amplifying their barcodes. In this study, specific primers were designed for the amplification of the highly diverse 18S-V9 region of the Euglenozoa and Metamonada groups. The performance of the newly designed primers-V9Eug and V9Meta-was compared with the universal V9 primer on cultured communities derived from a range of freshwater environments of the Soos Natural Reserve and the Slavkov Forest in the Czech Republic. The V9Eug primer was more specific with Euglenozoa representing 91.8% of reads and 57.0% of OTUs, while the V9Meta primer showed lower specificity with only 48.4% of reads and 19.7% of OTUs assigned to Metamonada. Both the Euglenozoa and Metamonada primer pairs significantly improved recovery of their target groups compared to the universal V9 primer pair, detecting 2.7 and 1.8 times more OTUs, respectively. These results provide a more sensitive protocol for studying the diversity of these eukaryotic taxa.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10601 - Cell biology

Projekt

—

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2024

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Environmental DNA

ISSN

2637-4943

e-ISSN

2637-4943

Svazek periodika

6

Číslo periodika v rámci svazku

5

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

11

Strana od-do

e70022

Kód UT WoS článku

001335902500001

EID výsledku v databázi Scopus

2-s2.0-85206369137