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

IMA Fungus
Claudia ColabellaGianluigi Cardinali

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.

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Citations

Jan 27, 2019·Microorganisms·Debora Casagrande PierantoniGianluigi Cardinali
Dec 3, 2020·Integrative Zoology·Ahmad MahmoudiEhsan Mostafavi
Feb 3, 2021·Microorganisms·Angela ContiLaura Corte
Feb 20, 2021·World Journal of Microbiology & Biotechnology·Prassan ChoudharyAnil Kumar Saxena

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Methods Mentioned

BETA
electrophoresis

Software Mentioned

FASTQ
Geneious assembler
BBMap
Bowtie2
Geneious
Geneious R9
Megablast
BLAST
Excel®

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