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

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

© 2021 The Authors New Phytologist © 2021 New Phytologist Foundation.

Bibliographische Detailangaben
Veröffentlicht in:The New phytologist. - 1979. - 231(2021), 1 vom: 28. Juli, Seite 490-499
1. Verfasser: Kolaříková, Zuzana (VerfasserIn)
Weitere Verfasser: Slavíková, Renata, Krüger, Claudia, Krüger, Manuela, Kohout, Petr
Format: Online-Aufsatz
Sprache:English
Veröffentlicht: 2021
Zugriff auf das übergeordnete Werk:The New phytologist
Schlagworte:Journal Article Research Support, Non-U.S. Gov't Archaeosporales Glomeromycota PacBio long-read metabarcoding mycorrhizal fungi distribution third-generation sequencing DNA, Fungal DNA, Ribosomal
Beschreibung
Zusammenfassung:© 2021 The Authors New Phytologist © 2021 New Phytologist Foundation.
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. Using 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. Employing this method for selected environmental DNA samples, we were able to describe complex AMF communities consisting of various glomeromycotan lineages. We 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
Beschreibung:Date Completed 10.06.2021
Date Revised 10.06.2021
published: Print-Electronic
Citation Status MEDLINE
ISSN:1469-8137
DOI:10.1111/nph.17372