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

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 ba...

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Autores principales:	Rosa E Prahl, Shahjahan Khan, Ravinesh C Deo
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e4ad4a01cbfc4d74a0dd86e9160794f0
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spelling	oai:doaj.org-article:e4ad4a01cbfc4d74a0dd86e9160794f02021-12-02T20:15:44ZThe role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces.1932-620310.1371/journal.pone.0253772https://doaj.org/article/e4ad4a01cbfc4d74a0dd86e9160794f02021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0253772https://doaj.org/toc/1932-6203Many 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.Rosa E PrahlShahjahan KhanRavinesh C DeoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 6, p e0253772 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Rosa E Prahl Shahjahan Khan Ravinesh C Deo The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces.
description	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.
format	article
author	Rosa E Prahl Shahjahan Khan Ravinesh C Deo
author_facet	Rosa E Prahl Shahjahan Khan Ravinesh C Deo
author_sort	Rosa E Prahl
title	The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces.
title_short	The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces.
title_full	The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces.
title_fullStr	The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces.
title_full_unstemmed	The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces.
title_sort	role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic ampelomyces.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/e4ad4a01cbfc4d74a0dd86e9160794f0
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The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces.

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