PacBio sequencing of Glomeromycota rDNA: a novel amplicon covering all widely used ribosomal barcoding regions and its applicability in taxonomy and ecology of arbuscular mycorrhizal fungi

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F21%3A00546867" target="_blank" >RIV/61388971:_____/21:00546867 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/67985939:_____/21:00545683 RIV/00216208:11310/21:10432693

Výsledek na webu

<a href="https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/nph.17372" target="_blank" >https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/nph.17372</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1111/nph.17372" target="_blank" >10.1111/nph.17372</a>

Jazyk výsledku

angličtina

Název v původním jazyce

PacBio sequencing of Glomeromycota rDNA: a novel amplicon covering all widely used ribosomal barcoding regions and its applicability in taxonomy and ecology of arbuscular mycorrhizal fungi

Popis výsledku v původním jazyce

There is no consensus barcoding region for determination of arbuscular mycorrhizal fungal (AMF) taxa. To overcome this obstacle, we have developed an approach to sequence an AMF marker within the ribosome-encoding operon (rDNA) that covers all three widely applied variable molecular markers.nUsing a nested PCR approach specific to AMF, we amplified a part (c. 2.5 kb) of the rDNA spanning the majority of the small subunit rRNA (SSU) gene, the complete internal transcribed spacer (ITS) region and a part of the large subunit (LSU) rRNA gene. The PCR products were sequenced on the PacBio platform utilizing Single Molecule Real Time (SMRT) sequencing.nEmploying this method for selected environmental DNA samples, we were able to describe complex AMF communities consisting of various glomeromycotan lineages.nWe demonstrate the applicability of this new 2.5 kb approach to provide robust phylogenetic assignment of AMF lineages without known sequences from pure cultures and to consolidate information about AMF taxon distributions coming from three widely used barcoding regions into one integrative dataset.

Název v anglickém jazyce

PacBio sequencing of Glomeromycota rDNA: a novel amplicon covering all widely used ribosomal barcoding regions and its applicability in taxonomy and ecology of arbuscular mycorrhizal fungi

Popis výsledku anglicky

There is no consensus barcoding region for determination of arbuscular mycorrhizal fungal (AMF) taxa. To overcome this obstacle, we have developed an approach to sequence an AMF marker within the ribosome-encoding operon (rDNA) that covers all three widely applied variable molecular markers.nUsing a nested PCR approach specific to AMF, we amplified a part (c. 2.5 kb) of the rDNA spanning the majority of the small subunit rRNA (SSU) gene, the complete internal transcribed spacer (ITS) region and a part of the large subunit (LSU) rRNA gene. The PCR products were sequenced on the PacBio platform utilizing Single Molecule Real Time (SMRT) sequencing.nEmploying this method for selected environmental DNA samples, we were able to describe complex AMF communities consisting of various glomeromycotan lineages.nWe demonstrate the applicability of this new 2.5 kb approach to provide robust phylogenetic assignment of AMF lineages without known sequences from pure cultures and to consolidate information about AMF taxon distributions coming from three widely used barcoding regions into one integrative dataset.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10606 - Microbiology

Projekt

<a href="/cs/project/GA17-03921S" target="_blank" >GA17-03921S: Molekulární fylogeneze Glomeromycota: od virtuálních taxonů k fylogeneticky vymezeným druhům a globální ekologii a biogeografii</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2021

Kód důvěrnosti údajů

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

Název periodika

New Phytologist

ISSN

0028-646X

e-ISSN

1469-8137

Svazek periodika

231

Číslo periodika v rámci svazku

1

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

10

Strana od-do

490-499

Kód UT WoS článku

000645953600001

EID výsledku v databázi Scopus

2-s2.0-85105234417