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
| Autor: | Manuela Krüger, Zuzana Kolaříková, Petr Kohout, Claudia Krüger, Renata Slavíková |
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| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
0301 basic medicine Physiology Plant Science Computational biology 01 natural sciences DNA Ribosomal Glomeromycota 03 medical and health sciences Mycorrhizae Environmental DNA Internal transcribed spacer DNA Fungal Gene Phylogeny biology Phylogenetic tree fungi Fungi Sequence Analysis DNA Ribosomal RNA Amplicon biology.organism_classification 030104 developmental biology Nested polymerase chain reaction 010606 plant biology & botany |
| Zdroj: | The New phytologistReferences. 231(1) |
| ISSN: | 1469-8137 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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