What Is the Best Lens? Comparing the Resolution Power of Genome-Derived Markers and Standard Barcodes.

Angela Conti,Laura Corte,Debora Casagrande Pierantoni,Gianluigi Cardinali,Vincent Robert

doi:10.3390/microorganisms9020299

Angela Conti, Laura Corte + Show 3 more

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https://doi.org/10.3390/microorganisms9020299

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Abstract

Fungal species delimitation was traditionally carried out with multicopy ribosomal RNA (rRNA) genes, principally for their ease of amplification. Since the efficacy of these markers has been questioned, single-copy protein-encoding genes have been proposed alone or in combination for Multi-Locus Sequence Typing (MLST). In this context, the role of the many sequences obtained with Next-Generation Sequencing (NGS) techniques, in both genomics and metagenomics, further pushes toward an analysis of the efficacy of NGS-derived markers and of the metrics to evaluate the marker efficacy in discriminating fungal species. This paper aims at proposing MeTRe (Mean Taxonomic Resolution), a novel index that could be used both for measuring marker efficacy and for assessing the actual resolution (i.e., the level of separation) between species obtained with different markers or their combinations. In this paper, we described and then employed this index to compare the efficacy of two rRNAs and four single-copy markers obtained from public databases as both an amplicon-based approach and genome-derived sequences. Two different groups of species were used, one with a pathogenic species of Candida that was characterized by relatively well-separated taxa, whereas the other, comprising some relevant species of the sensu stricto group of the genus Saccharomyces, included close species and interspecific hybrids. The results showed the ability of MeTRe to evaluate marker efficacy in general and genome-derived markers specifically.

Highlights

The advent of Next-Generation Sequencing (NGS) fostered genomic studies transforming genomics from highly specialized, expensive, community-based work [1] into a routine activity with several opportunities that go well beyond the study of genomes, per se [2]
Due to the limited number of available genomes in the National Center for Biotechnology Information (NCBI), the species involved in this study were: S. bayanus, S. cerevisiae, S. kudriavzevii, S. paradoxus, S. pastorianus and S. uvarum for the Saccharomyces sensu stricto complex, while the analysis was restricted to C. albicans, C. auris, C. glabrata, C. metapsilosis, C. otrhopsilosis, C. parapsilosis and C. tropicalis for the Candida genus
We selected several species belonging to the Saccharomyces genus and to the group of the pathogenic species of the Candida genus

Summary

Introduction

The advent of Next-Generation Sequencing (NGS) fostered genomic studies transforming genomics from highly specialized, expensive, community-based work [1] into a routine activity with several opportunities that go well beyond the study of genomes, per se [2]. The long-lasting problem is an appropriate and applicable species concept [14] among the approaches that are currently used in both bacterial and fungal biology, including phylogeny, genetic segregation and phenetics [15]. Among these three approaches, phylogeny can be used for classification and for identification, it is much more computer-intensive phenetics.

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