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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; Mellor, Joseph C; Meyer, Wieland; Robert, Vincent Albert Romain Ghislain; Vu, D.; Cardinali, Gianluigi.

In: IMA Fungus, 09.06.2018, p. 91-105.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Harvard

Colabella, C, Corte, L, Roscini, L, Bassetti, M, Mellor, JC, Meyer, W, Robert, VARG, Vu, D & Cardinali, G 2018, 'NGS barcode sequencing in taxonomy and diagnostics, an application in "Candida" pathogenic yeasts with a metagenomic perspective' IMA Fungus, pp. 91-105. DOI: 10.5598/imafungus.2018.09.01.07

APA

Colabella, C., Corte, L., Roscini, L., Bassetti, M., Mellor, J. C., Meyer, W., ... Cardinali, G. (2018). NGS barcode sequencing in taxonomy and diagnostics, an application in "Candida" pathogenic yeasts with a metagenomic perspective. IMA Fungus, 91-105. DOI: 10.5598/imafungus.2018.09.01.07

Vancouver

Colabella C, Corte L, Roscini L, Bassetti M, Mellor JC, Meyer W et al. NGS barcode sequencing in taxonomy and diagnostics, an application in "Candida" pathogenic yeasts with a metagenomic perspective. IMA Fungus. 2018 Jun 9;91-105. Available from, DOI: 10.5598/imafungus.2018.09.01.07

Author

Colabella, Claudia ; Corte, Laura ; Roscini, Luca ; Bassetti, Matteo ; Mellor, Joseph C ; Meyer, Wieland ; Robert, Vincent Albert Romain Ghislain ; Vu, D. ; Cardinali, Gianluigi. / NGS barcode sequencing in taxonomy and diagnostics, an application in "Candida" pathogenic yeasts with a metagenomic perspective. In: IMA Fungus. 2018 ; pp. 91-105

BibTeX

@article{14edd49d0cf8452b89674d915a7d10f5,
title = "NGS barcode sequencing in taxonomy and diagnostics, an application in {"}Candida{"} pathogenic yeasts with a metagenomic perspective",
abstract = "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.",
author = "Claudia Colabella and Laura Corte and Luca Roscini and Matteo Bassetti and Mellor, {Joseph C} and Wieland Meyer and Robert, {Vincent Albert Romain Ghislain} and D. Vu and Gianluigi Cardinali",
year = "2018",
month = "6",
day = "9",
doi = "10.5598/imafungus.2018.09.01.07",
language = "English",
pages = "91--105",
journal = "IMA Fungus",
issn = "2210-6340",
publisher = "International Mycological Association",

}

RIS

TY - JOUR

T1 - NGS barcode sequencing in taxonomy and diagnostics, an application in "Candida" pathogenic yeasts with a metagenomic perspective

AU - Colabella,Claudia

AU - Corte,Laura

AU - Roscini,Luca

AU - Bassetti,Matteo

AU - Mellor,Joseph C

AU - Meyer,Wieland

AU - Robert,Vincent Albert Romain Ghislain

AU - Vu,D.

AU - Cardinali,Gianluigi

PY - 2018/6/9

Y1 - 2018/6/9

N2 - 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.

AB - 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.

U2 - 10.5598/imafungus.2018.09.01.07

DO - 10.5598/imafungus.2018.09.01.07

M3 - Article

SP - 91

EP - 105

JO - IMA Fungus

T2 - IMA Fungus

JF - IMA Fungus

SN - 2210-6340

ER -

ID: 9426192