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Genomic and phenotypic insights into the expanding phylogenetic landscape of the Cryptococcus genus

2025-11-01Artigo científico Acesso aberto
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dc.contributor.authorCoelho, Marco A.
dc.contributor.authorDavid-Palma, Márcia
dc.contributor.authorKachalkin, Aleksey V.
dc.contributor.authorKolařík, Miroslav
dc.contributor.authorTurchetti, Benedetta
dc.contributor.authorSampaio, José Paulo
dc.contributor.authorWingfield, Michael J.
dc.contributor.authorFisher, Matthew C.
dc.contributor.authorYurkov, Andrey M.
dc.contributor.authorHeitman, Joseph
dc.contributor.institutionUCIBIO - Applied Molecular Biosciences Unit
dc.contributor.institutionDCV - Departamento de Ciências da Vida
dc.contributor.institutionFaculdade de Ciências e Tecnologia (FCT)
dc.contributor.pblPLOS - Public Library of Science
dc.date.accessioned2026-03-06T16:16:02Z
dc.date.available2026-03-06T16:16:02Z
dc.date.issued2025-11-01
dc.descriptionPublisher Copyright: Copyright: © 2025 Coelho et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
dc.description.abstractThe fungal genus Cryptococcus includes several life-threatening human pathogens as well as diverse saprobic species whose genome architecture, ecology, and evolutionary history remain less well characterized. Understanding how some lineages evolved into major pathogens remains a central challenge and may be advanced by comparisons with their nonpathogenic counterparts. Integrative approaches have become essential for delimiting species and reconstructing evolutionary relationships, particularly in lineages with cryptic diversity or extensive chromosomal rearrangements. Here, we formally characterize six Cryptococcus species representing distinct evolutionary lineages, comprising both newly discovered and previously recognized but unnamed taxa, through a combination of phylogenomic analyses, divergence metrics, chromosomal comparisons, mating assays, and phenotypic profiling. Among pathogenic taxa, we formally name Cryptococcus hyracis sp. nov., corresponding to the previously characterized VGV lineage within the C. gattii complex. In parallel, we describe five saprobic, nonpathogenic species isolated from fruit, soil, and bark beetle galleries, spanning four phylogenetic clades. We identify a strong ecological association with bark beetles for Cryptococcus porticicola sp. nov., the only newly described nonpathogenic species with multiple sequenced strains from diverse sites. In this species, we detect strain-level chromosomal variation and evidence of sexual reproduction, along with population-level signatures of recombination. Across the genus, chromosome-level comparisons reveal extensive structural variation, including species- and strain-specific rearrangements that may restrict gene flow. We also identify multiple instances of chromosome number reduction, often accompanied by genomic signatures consistent with centromere inactivation or loss of centromeric identity. Comparative metabolic profiling with Biolog phenotype microarrays reveals clade-level differentiation and distinct substrate preferences, which may reflect metabolic divergence and habitat-specific diversification. Notably, we confirm that thermotolerance is restricted to clinically relevant taxa. These findings refine the species-level taxonomy of Cryptococcus, broaden its known genomic and ecological diversity, and strengthen the framework for investigating speciation, adaptation, and the emergence of pathogenicity within the genus.en
dc.description.versionpublishersversion
dc.description.versionpublished
dc.format.extent4901101
dc.identifier.doi10.1371/journal.pgen.1011945
dc.identifier.issn1553-7390
dc.identifier.otherPURE: 156121758
dc.identifier.otherPURE UUID: eeb5eeac-01d2-4000-918c-fbf3364e9f78
dc.identifier.otherScopus: 105022664434
dc.identifier.otherPubMed: 41212923
dc.identifier.otherWOS: 001611121400001
dc.identifier.urihttp://hdl.handle.net/10362/201068
dc.identifier.urlhttps://www.scopus.com/pages/publications/105022664434
dc.language.isoeng
dc.peerreviewedyes
dc.subjectEcology, Evolution, Behavior and Systematics
dc.subjectMolecular Biology
dc.subjectGenetics
dc.subjectGenetics(clinical)
dc.subjectCancer Research
dc.subjectSDG 3 - Good Health and Well-being
dc.titleGenomic and phenotypic insights into the expanding phylogenetic landscape of the Cryptococcus genusen
dc.typejournal article
degois.publication.firstPage
degois.publication.issue11
degois.publication.lastPage
degois.publication.titlePLoS Genetics
degois.publication.volume21
dspace.entity.typePublication
rcaap.rightsopenAccess

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