Comparison of bioinformatic pipelines for eDNA metabarcoding data analysis of fish populations

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60077344%3A_____%2F25%3A00647068" target="_blank" >RIV/60077344:_____/25:00647068 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/60076658:12310/25:43909893

Výsledek na webu

<a href="https://doi.org/10.3390/fishes10050214" target="_blank" >https://doi.org/10.3390/fishes10050214</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.3390/fishes10050214" target="_blank" >10.3390/fishes10050214</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Comparison of bioinformatic pipelines for eDNA metabarcoding data analysis of fish populations

Popis výsledku v původním jazyce

Environmental DNA (eDNA) metabarcoding has gained popularity as a biomonitoring tool, leading to the emergence of various bioinformatic pipelines. However, comparisons are essential to assessing the reliability and similarity of results. In this study, we compared five bioinformatic pipelines (Anacapa, Barque, metaBEAT, MiFish, and SEQme) using samples collected from three reservoirs in the Czech Republic during the autumn and summer seasons. Negative and positive controls were used to monitor potential contamination during sample processing. eDNA was amplified, targeting the 12S fish rRNA gene, sequenced, and analyzed with the selected bioinformatic pipelines. Statistical analyses were applied to assess result similarity, including the number of detected taxa, read count, alpha and beta diversities, and the Mantel test. Our findings showed consistent taxa detection across pipelines, with increased sensitivity compared to traditional methods. Alpha and beta diversities and the Mantel test also exhibited significant similarities between pipelines. Divergences were observed based on the reservoir, season, and their interaction. In conclusion, the choice of bioinformatic pipeline did not significantly affect metabarcoding outcomes or their ecological interpretation.

Název v anglickém jazyce

Comparison of bioinformatic pipelines for eDNA metabarcoding data analysis of fish populations

Popis výsledku anglicky

Environmental DNA (eDNA) metabarcoding has gained popularity as a biomonitoring tool, leading to the emergence of various bioinformatic pipelines. However, comparisons are essential to assessing the reliability and similarity of results. In this study, we compared five bioinformatic pipelines (Anacapa, Barque, metaBEAT, MiFish, and SEQme) using samples collected from three reservoirs in the Czech Republic during the autumn and summer seasons. Negative and positive controls were used to monitor potential contamination during sample processing. eDNA was amplified, targeting the 12S fish rRNA gene, sequenced, and analyzed with the selected bioinformatic pipelines. Statistical analyses were applied to assess result similarity, including the number of detected taxa, read count, alpha and beta diversities, and the Mantel test. Our findings showed consistent taxa detection across pipelines, with increased sensitivity compared to traditional methods. Alpha and beta diversities and the Mantel test also exhibited significant similarities between pipelines. Divergences were observed based on the reservoir, season, and their interaction. In conclusion, the choice of bioinformatic pipeline did not significantly affect metabarcoding outcomes or their ecological interpretation.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Projekt

<a href="/cs/project/QK1920011" target="_blank" >QK1920011: Metodologie kvantifikace dravých druhů ryb ve vodárenských nádržích pro optimalizaci managementu vodních ekosystémů</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2025

Kód důvěrnosti údajů

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

Název periodika

Fishes

ISSN

2410-3888

e-ISSN

2410-3888

Svazek periodika

10

Číslo periodika v rámci svazku

5

Stát vydavatele periodika

CH - Švýcarská konfederace

Počet stran výsledku

24

Strana od-do

214

Kód UT WoS článku

001497109600001

EID výsledku v databázi Scopus

2-s2.0-105006632572