Filling reference libraries with diatom environmental sequences: strengths and weaknesses

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11310%2F23%3A10478976" target="_blank" >RIV/00216208:11310/23:10478976 - isvavai.cz</a>

Výsledek na webu

<a href="https://verso.is.cuni.cz/pub/verso.fpl?fname=obd_publikace_handle&handle=xqiACkd91B" target="_blank" >https://verso.is.cuni.cz/pub/verso.fpl?fname=obd_publikace_handle&handle=xqiACkd91B</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1080/0269249X.2023.2237977" target="_blank" >10.1080/0269249X.2023.2237977</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Filling reference libraries with diatom environmental sequences: strengths and weaknesses

Popis výsledku v původním jazyce

Diatom species identification with DNA metabarcoding is an economical, fast and reliable alternative to identification via light microscopy for river quality monitoring. Using a short DNA sequence of the rbcL gene and &apos;Diat.barcode&apos;, a reference barcode library, enables the identification of more than 90% of the environmental sequences to species level in French rivers. But the completeness of this library is much lower in other regions, such as the tropical French overseas departments. A barcode library completion method using high-throughput sequencing data combined with microscopy count data from natural samples (Rimet et al. 2018) was applied and tested in rivers of Martinique and Guadeloupe (West Indies), for which only 45% of the environmental sequences could be identified to species level using Diat.barcode v9. Assigning barcodes to the most abundant species in the islands by this method is illustrated with Ulnaria goulardii and two new species belonging to Nupela and Epithemia, which are also described in this paper. The more complex situation of morphologically similar species is illustrated by reference to Gomphonema designatum and G. bourbonense. Using a combination of molecular and morphological data, their conspecificity, as G. bourbonense, is demonstrated with their reference barcodes. However, when several morphologically similar species and several environmental sequences belonging to the same clade are present, it is not possible to relate the barcodes to corresponding morphological species. Applying this method enabled the Diat.barcode library (v.10) to be updated, with 84% of the environmental sequences from the West Indies now identifiable at the species level. However, many morphological species still lack barcodes. In these cases, more classical methods, such as cell isolation, Sanger sequencing and morphological observations of cultures, must be applied.

Název v anglickém jazyce

Filling reference libraries with diatom environmental sequences: strengths and weaknesses

Popis výsledku anglicky

Diatom species identification with DNA metabarcoding is an economical, fast and reliable alternative to identification via light microscopy for river quality monitoring. Using a short DNA sequence of the rbcL gene and &apos;Diat.barcode&apos;, a reference barcode library, enables the identification of more than 90% of the environmental sequences to species level in French rivers. But the completeness of this library is much lower in other regions, such as the tropical French overseas departments. A barcode library completion method using high-throughput sequencing data combined with microscopy count data from natural samples (Rimet et al. 2018) was applied and tested in rivers of Martinique and Guadeloupe (West Indies), for which only 45% of the environmental sequences could be identified to species level using Diat.barcode v9. Assigning barcodes to the most abundant species in the islands by this method is illustrated with Ulnaria goulardii and two new species belonging to Nupela and Epithemia, which are also described in this paper. The more complex situation of morphologically similar species is illustrated by reference to Gomphonema designatum and G. bourbonense. Using a combination of molecular and morphological data, their conspecificity, as G. bourbonense, is demonstrated with their reference barcodes. However, when several morphologically similar species and several environmental sequences belonging to the same clade are present, it is not possible to relate the barcodes to corresponding morphological species. Applying this method enabled the Diat.barcode library (v.10) to be updated, with 84% of the environmental sequences from the West Indies now identifiable at the species level. However, many morphological species still lack barcodes. In these cases, more classical methods, such as cell isolation, Sanger sequencing and morphological observations of cultures, must be applied.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10618 - Ecology

Projekt

—

Návaznosti

S - Specificky vyzkum na vysokych skolach<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2023

Kód důvěrnosti údajů

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

Název periodika

Diatom Research

ISSN

0269-249X

e-ISSN

2159-8347

Svazek periodika

38

Číslo periodika v rámci svazku

2

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

25

Strana od-do

103-127

Kód UT WoS článku

001076352000001

EID výsledku v databázi Scopus

2-s2.0-85170713386