Genome and transcriptome of a pathogenic yeast, <i>Candida nivariensis</i>

Fan, Yunfan; Gale, Andrew N.; Bailey, A. B.; Barnes, Kali; Colotti, Kiersten; Mass, Michal; Morina, Luke B; Robertson, Bailey; Schwab, Remy; Tselepidakis, Niki; Timp, Winston

doi:10.1093/g3journal/jkab137

Cited by 2 publications

(1 citation statement)

References 41 publications

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“…The use of pyrosequencing has declined because of the rise of new methodologies of NGS such as Illumina [112], which are less expensive, provide longer sequences, higher sensitivity to detect low-frequency variants, have a faster turnaround time for high sample volumes, and a comprehensive genomic coverage [129].…”

Section: Next Generation Sequencing (Ngs)mentioning

confidence: 99%

Molecular Techniques and Target Selection for the Identification of Candida spp. in Oral Samples

et al. 2022

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Candida species are the causative agent of oral candidiasis, with medical devices being platforms for yeast anchoring and tissue colonization. Identifying the infectious agent involved in candidiasis avoids an empirical prescription of antifungal drugs. The application of high-throughput technologies to the diagnosis of yeast pathogens has clear advantages in sensitivity, accuracy, and speed. Yet, conventional techniques for the identification of Candida isolates are still routine in clinical and research settings. Molecular approaches are the focus of intensive research, but conversion into clinic settings requires overcoming important challenges. Several molecular approaches can accurately identify Candida spp.: Polymerase Chain Reaction, Microarray, High-Resolution Melting Analysis, Multi-Locus Sequence Typing, Restriction Fragment Length Polymorphism, Loop-mediated Isothermal Amplification, Matrix Assisted Laser Desorption Ionization-mass spectrometry, and Next Generation Sequencing. This review examines the advantages and disadvantages of the current molecular methods used for Candida spp. Identification, with a special focus on oral candidiasis. Discussion regarding their application for the diagnosis of oral infections aims to identify the most rapid, affordable, accurate, and easy-to-perform molecular techniques to be used as a point-of-care testing method. Special emphasis is given to the difficulties that health care professionals need to overcome to provide an accurate diagnosis.

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Section: Next Generation Sequencing (Ngs)mentioning

confidence: 99%

Molecular Techniques and Target Selection for the Identification of Candida spp. in Oral Samples

et al. 2022

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Chromosome level assemblies of Nakaseomyces (Candida) bracarensis uncover two distinct clades and define its adhesin repertoire

Marcet-Houben,

Księżopolska,

Gabaldón

2024

BMC Genomics

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Background The Nakaseomyces clade is formed by at least nine described species among which three can be pathogenic to humans, namely Nakaseomyces glabratus (Candida glabrata), the second most-common cause of candidiasis worldwide, and two rarer emerging pathogens: Nakaseomyces (Candida) nivarensis and Nakaseomyces (Candida) bracarensis. Early comparative genomics analyses identified parallel expansions of subtelomeric adhesin genes in N. glabratus and N. nivarensis/bracarensis, and suggested possible links with the emergence of the virulence potential in these species. However, as shown for N. glabratus, the proper assessment of subtelomeric genes is hindered by the use of incomplete assemblies and reliance on a single isolate. Results Here we sequenced seven N. bracarensis isolates and reconstructed chromosome level assemblies of two divergent strains. We show that N. bracarensis isolates belong to two diverging clades that have slightly different genomic structures. We identified the set of encoded adhesins in the two complete assemblies, and uncovered the presence of a novel adhesin motif, found mainly in N. bracarensis. Our analysis revealed a larger adhesin content in N. bracarensis than previously reported, and similar in size to that of N. glabratus. We confirm the independent adhesin expansion in these two species, which could relate to their different levels of virulence. Conclusion N. bracarensis clinical isolates belong to at least two differentiated clades. We describe a novel repeat motif found in N. bracarensis adhesins, which helps in their identification. Adhesins underwent independent expansions in N. glabratus and N. bracarensis, leading to repertoires that are qualitatively different but quantitatively similar. Given that adhesins are considered virulence factors, some of the observed differences could contribute to variations in virulence capabilities between N. glabratus and N. bracarensis.

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Genome and transcriptome of a pathogenic yeast, Candida nivariensis

Cited by 2 publications

References 41 publications

Molecular Techniques and Target Selection for the Identification of Candida spp. in Oral Samples

Molecular Techniques and Target Selection for the Identification of Candida spp. in Oral Samples

Chromosome level assemblies of Nakaseomyces (Candida) bracarensis uncover two distinct clades and define its adhesin repertoire

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