The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces

Prahl, Rosa E. ORCID: https://orcid.org/0000-0003-1243-9881 and Khan, Shahjahan ORCID: https://orcid.org/0000-0002-0446-086X and Deo, Ravinesh C. ORCID: https://orcid.org/0000-0002-2290-6749 (2021) The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces. PLoS One, 16 (6):e0253772. pp. 1-28.

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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.


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Item Type: Article (Commonwealth Reporting Category C)
Refereed: Yes
Item Status: Live Archive
Additional Information: 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.
Faculty/School / Institute/Centre: Current - Faculty of Health, Engineering and Sciences - School of Sciences (6 Sep 2019 -)
Faculty/School / Institute/Centre: Current - Institute for Life Sciences and the Environment - Centre for Applied Climate Sciences (1 Aug 2018 -)
Date Deposited: 02 Jul 2021 01:37
Last Modified: 03 Sep 2021 04:56
Uncontrolled Keywords: Ampelomyces, Ampelomyces humuli, environmental DNA, phylogeny, ribosomal ITS2, secondary structures
Fields of Research (2008): 05 Environmental Sciences > 0599 Other Environmental Sciences > 059999 Environmental Sciences not elsewhere classified
06 Biological Sciences > 0603 Evolutionary Biology > 060307 Host-Parasite Interactions
06 Biological Sciences > 0603 Evolutionary Biology > 060309 Phylogeny and Comparative Analysis
Fields of Research (2020): 31 BIOLOGICAL SCIENCES > 3102 Bioinformatics and computational biology > 310203 Computational ecology and phylogenetics
31 BIOLOGICAL SCIENCES > 3104 Evolutionary biology > 310409 Microbial taxonomy
31 BIOLOGICAL SCIENCES > 3104 Evolutionary biology > 310403 Biological adaptation
31 BIOLOGICAL SCIENCES > 3104 Evolutionary biology > 310401 Animal systematics and taxonomy
31 BIOLOGICAL SCIENCES > 3104 Evolutionary biology > 310410 Phylogeny and comparative analysis
31 BIOLOGICAL SCIENCES > 3102 Bioinformatics and computational biology > 310206 Sequence analysis
Socio-Economic Objectives (2008): E Expanding Knowledge > 97 Expanding Knowledge > 970105 Expanding Knowledge in the Environmental Sciences
E Expanding Knowledge > 97 Expanding Knowledge > 970106 Expanding Knowledge in the Biological Sciences
D Environment > 96 Environment > 9699 Other Environment > 969999 Environment not elsewhere classified
D Environment > 96 Environment > 9604 Control of Pests, Diseases and Exotic Species > 960499 Control of Pests, Diseases and Exotic Species not elsewhere classified
Socio-Economic Objectives (2020): 28 EXPANDING KNOWLEDGE > 2801 Expanding knowledge > 280102 Expanding knowledge in the biological sciences
28 EXPANDING KNOWLEDGE > 2801 Expanding knowledge > 280111 Expanding knowledge in the environmental sciences
18 ENVIRONMENTAL MANAGEMENT > 1899 Other environmental management > 189999 Other environmental management not elsewhere classified
Identification Number or DOI: https://doi.org/10.1371/journal.pone.0253772
URI: http://eprints.usq.edu.au/id/eprint/42629

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