The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces
Article
Article Title | The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces |
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ERA Journal ID | 39745 |
Article Category | Article |
Authors | Prahl, Rosa E. (Author), Khan, Shahjahan (Author) and Deo, Ravinesh C. (Author) |
Journal Title | PLoS One |
Journal Citation | 16 (6), pp. 1-28 |
Article Number | e0253772 |
Number of Pages | 28 |
Year | 2021 |
Publisher | Public Library of Science (PLoS) |
Place of Publication | United States |
ISSN | 1932-6203 |
Digital Object Identifier (DOI) | https://doi.org/10.1371/journal.pone.0253772 |
Web Address (URL) | https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0253772 |
Abstract | Many fungi require specific growth conditions before they can be identified. Direct environmental DNA sequencing is advantageous, although for some taxa, specific primers need to be used for successful amplification of molecular markers. The internal transcribed spacer region is the preferred DNA barcode for fungi. However, inter- and intra-specific distances in ITS sequences highly vary among some fungal groups; consequently, it is not a solely reliable tool for species delineation. Ampelomyces, mycoparasites of the fungal phytopathogen order Erysiphales, can have ITS genetic differences up to 15%; this may lead to misidentification with other closely related unknown fungi. Indeed, Ampelomyces were initially misidentified as other pycnidial mycoparasites, but subsequent research showed that they differ in pycnidia morphology and culture characteristics. We investigated whether the ITS2 nucleotide content and secondary structure was different between Ampelomyces ITS2 sequences and those unrelated to this genus. To this end, we retrieved all ITS sequences referred to as Ampelomyces from the GenBank database. This analysis revealed that fungal ITS environmental DNA sequences are still being deposited in the database under the name Ampelomyces, but they do not belong to this genus. We also detected variations in the conserved hybridization model of the ITS2 proximal 5.8S and 28S stem from two Ampelomyces strains. Moreover, we suggested for the first time that pseudogenes form in the ITS region of this mycoparasite. A phylogenetic analysis based on ITS2 sequences-structures grouped the environmental sequences of putative Ampelomyces into a different clade from the Ampelomyces-containing clades. Indeed, when conducting ITS2 analysis, resolution of genetic distances between Ampelomyces and those putative Ampelomyces improved. Each clade represented a distinct consensus ITS2 S2, which suggested that different pre-ribosomal RNA (pre-rRNA) processes occur across different lineages. This study recommends the use of ITS2 S2s as an important tool to analyse environmental sequencing and unveiling the underlying evolutionary processes. |
Keywords | Ampelomyces, Ampelomyces humuli, environmental DNA, phylogeny, ribosomal ITS2, secondary structures |
ANZSRC Field of Research 2020 | 310203. Computational ecology and phylogenetics |
310409. Microbial taxonomy | |
310403. Biological adaptation | |
310401. Animal systematics and taxonomy | |
310410. Phylogeny and comparative analysis | |
310206. Sequence analysis | |
Public Notes | Copyright: © 2021 Prahl et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
Byline Affiliations | School of Sciences |
Institution of Origin | University of Southern Queensland |
https://research.usq.edu.au/item/q674v/the-role-of-internal-transcribed-spacer-2-secondary-structures-in-classifying-mycoparasitic-ampelomyces
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