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NGS barcode sequencing in taxonomy and diagnostics, an application in “Candida” pathogenic yeasts with a metagenomic perspective
Species identification of yeasts and other Fungi is currently carried out with Sanger sequences of selected molecular markers, mainly from the ribosomal DNA operon, characterized by hundreds of tandem repeats of the 18S, ITS1, 5.8S, ITS2 and LSU loci. The ITS region has been recently proposed as a p...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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International Mycological Association
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048569/ https://www.ncbi.nlm.nih.gov/pubmed/30018874 http://dx.doi.org/10.5598/imafungus.2018.09.01.07 |
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author | Colabella, Claudia Corte, Laura Roscini, Luca Bassetti, Matteo Tascini, Carlo Mellor, Joseph C. Meyer, Wieland Robert, Vincent Vu, Duong Cardinali, Gianluigi |
author_facet | Colabella, Claudia Corte, Laura Roscini, Luca Bassetti, Matteo Tascini, Carlo Mellor, Joseph C. Meyer, Wieland Robert, Vincent Vu, Duong Cardinali, Gianluigi |
author_sort | Colabella, Claudia |
collection | PubMed |
description | Species identification of yeasts and other Fungi is currently carried out with Sanger sequences of selected molecular markers, mainly from the ribosomal DNA operon, characterized by hundreds of tandem repeats of the 18S, ITS1, 5.8S, ITS2 and LSU loci. The ITS region has been recently proposed as a primary barcode marker making this region the most used one in taxonomy, phylogeny and diagnostics. The introduction of NGS is providing tools of high efficacy and relatively low cost to amplify two or more markers simultaneously with great sequencing depth. However, the presence of intra-genomic variability between the repeats requires specific analytical procedures and pipelines. In this study, 286 strains belonging to 11 pathogenic yeasts species were analysed with NGS of the region spanning from ITS1 to the D1/D2 domain of the LSU encoding ribosomal DNA. Results showed that relatively high heterogeneity can hamper the use of these sequences for the identification of single strains and even more of complex microbial mixtures. These observations point out that the metagenomics studies could be affected by species inflection at levels higher than currently expected. |
format | Online Article Text |
id | pubmed-6048569 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | International Mycological Association |
record_format | MEDLINE/PubMed |
spelling | pubmed-60485692018-07-17 NGS barcode sequencing in taxonomy and diagnostics, an application in “Candida” pathogenic yeasts with a metagenomic perspective Colabella, Claudia Corte, Laura Roscini, Luca Bassetti, Matteo Tascini, Carlo Mellor, Joseph C. Meyer, Wieland Robert, Vincent Vu, Duong Cardinali, Gianluigi IMA Fungus Article Species identification of yeasts and other Fungi is currently carried out with Sanger sequences of selected molecular markers, mainly from the ribosomal DNA operon, characterized by hundreds of tandem repeats of the 18S, ITS1, 5.8S, ITS2 and LSU loci. The ITS region has been recently proposed as a primary barcode marker making this region the most used one in taxonomy, phylogeny and diagnostics. The introduction of NGS is providing tools of high efficacy and relatively low cost to amplify two or more markers simultaneously with great sequencing depth. However, the presence of intra-genomic variability between the repeats requires specific analytical procedures and pipelines. In this study, 286 strains belonging to 11 pathogenic yeasts species were analysed with NGS of the region spanning from ITS1 to the D1/D2 domain of the LSU encoding ribosomal DNA. Results showed that relatively high heterogeneity can hamper the use of these sequences for the identification of single strains and even more of complex microbial mixtures. These observations point out that the metagenomics studies could be affected by species inflection at levels higher than currently expected. International Mycological Association 2018-05-22 2018-06 /pmc/articles/PMC6048569/ /pubmed/30018874 http://dx.doi.org/10.5598/imafungus.2018.09.01.07 Text en © 2018 International Mycological Association http://creativecommons.org/licenses/by-nc-nd/3.0/legalcode You are free to share - to copy, distribute and transmit the work, under the following conditions: Attribution: You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). Non-commercial: You may not use this work for commercial purposes. No derivative works: You may not alter, transform, or build upon this work. For any reuse or distribution, you must make clear to others the license terms of this work, which can be found at http://creativecommons.org/licenses/by-nc-nd/3.0/legalcode. Any of the above conditions can be waived if you get permission from the copyright holder. Nothing in this license impairs or restricts the author’s moral rights. |
spellingShingle | Article Colabella, Claudia Corte, Laura Roscini, Luca Bassetti, Matteo Tascini, Carlo Mellor, Joseph C. Meyer, Wieland Robert, Vincent Vu, Duong Cardinali, Gianluigi NGS barcode sequencing in taxonomy and diagnostics, an application in “Candida” pathogenic yeasts with a metagenomic perspective |
title | NGS barcode sequencing in taxonomy and diagnostics, an application in “Candida” pathogenic yeasts with a metagenomic perspective |
title_full | NGS barcode sequencing in taxonomy and diagnostics, an application in “Candida” pathogenic yeasts with a metagenomic perspective |
title_fullStr | NGS barcode sequencing in taxonomy and diagnostics, an application in “Candida” pathogenic yeasts with a metagenomic perspective |
title_full_unstemmed | NGS barcode sequencing in taxonomy and diagnostics, an application in “Candida” pathogenic yeasts with a metagenomic perspective |
title_short | NGS barcode sequencing in taxonomy and diagnostics, an application in “Candida” pathogenic yeasts with a metagenomic perspective |
title_sort | ngs barcode sequencing in taxonomy and diagnostics, an application in “candida” pathogenic yeasts with a metagenomic perspective |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048569/ https://www.ncbi.nlm.nih.gov/pubmed/30018874 http://dx.doi.org/10.5598/imafungus.2018.09.01.07 |
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