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

0545683 - BÚ 2022 RIV GB eng J - Journal Article
Kolaříková, Zuzana - Slavíková, Renata - Krüger, Claudia - Krüger, Manuela - Kohout, Petr
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.
New Phytologist. Roč. 231, č. 1 (2021), s. 490-499. ISSN 0028-646X. E-ISSN 1469-8137
R&D Projects: GA ČR GA17-03921S
Institutional support: RVO:67985939
Keywords : Archaeosporales * long-read metabarcoding * PacBio
OECD category: Mycology
Impact factor: 10.323, year: 2021
Method of publishing: Limited access
https://doi.org/10.1111/nph.17372

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.
Permanent Link: http://hdl.handle.net/11104/0322357