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Wu G, Zhao H, Li C, Rajapakse MP, Wong WC, Xu J, Saunders CW, Reeder NL, Reilman RA, Scheynius A, Sun S, Billmyre BR, Li W, Averette AF, Mieczkowski P, Heitman J, Theelen B, Schröder MS, De Sessions PF, Butler G, Maurer-Stroh S, Boekhout T, Nagarajan N, Dawson TL. Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin. PLoS Genet 2015; 11:e1005614. [PMID: 26539826 PMCID: PMC4634964 DOI: 10.1371/journal.pgen.1005614] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 09/27/2015] [Indexed: 01/27/2023] Open
Abstract
Malassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina, (Basidiomycota, fungi) that otherwise consists almost exclusively of plant pathogens. Malassezia are typically isolated from warm-blooded animals, are dominant members of the human skin mycobiome and are associated with common skin disorders. To characterize the genetic basis of the unique phenotypes of Malassezia spp., we sequenced the genomes of all 14 accepted species and used comparative genomics against a broad panel of fungal genomes to comprehensively identify distinct features that define the Malassezia gene repertoire: gene gain and loss; selection signatures; and lineage-specific gene family expansions. Our analysis revealed key gene gain events (64) with a single gene conserved across all Malassezia but absent in all other sequenced Basidiomycota. These likely horizontally transferred genes provide intriguing gain-of-function events and prime candidates to explain the emergence of Malassezia. A larger set of genes (741) were lost, with enrichment for glycosyl hydrolases and carbohydrate metabolism, concordant with adaptation to skin’s carbohydrate-deficient environment. Gene family analysis revealed extensive turnover and underlined the importance of secretory lipases, phospholipases, aspartyl proteases, and other peptidases. Combining genomic analysis with a re-evaluation of culture characteristics, we establish the likely lipid-dependence of all Malassezia. Our phylogenetic analysis sheds new light on the relationship between Malassezia and other members of Ustilaginomycotina, as well as phylogenetic lineages within the genus. Overall, our study provides a unique genomic resource for understanding Malassezia niche-specificity and potential virulence, as well as their abundance and distribution in the environment and on human skin. Malassezia are the dominant eukaryotic residents of human skin and are associated with the most common skin disorders, including dandruff, atopic dermatitis, eczema, and others. Despite significant effort, the role of Malassezia in skin disease and homeostasis remains unclear. Malassezia are also unique among fungi by requiring lipids for growth, but the breadth and genetic basis of their lipophilic lifestyle has not been comprehensively studied. Here we report the complete genomes of all 14 Malassezia species (including multiple strains of the most common species found on humans) and systematically identify features that define the genus and its sub-lineages, including horizontally transferred genes likely to represent key gain-of-function events and which may have enabled evolution of the genus from plant to animal inhabitants. Genus wide expansion of lipid hydrolases and loss of carbohydrate metabolism genes underscore the entire genus’ gradual evolution to lipid-dependency, which was confirmed even in the previously thought to be lipophilic M. pachydermatis, via genomics with experimental confirmation. Finally, these reference genomes will serve as a valuable resource for future metagenomic investigations into the role of Malassezia species in normal healthy skin and diseases.
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Affiliation(s)
- Guangxi Wu
- Computational and Systems Biology, Genome Institute of Singapore, A*STAR, Singapore
| | - He Zhao
- Procter & Gamble Singapore Innovation Center, Singapore
| | - Chenhao Li
- Computational and Systems Biology, Genome Institute of Singapore, A*STAR, Singapore
| | | | | | - Jun Xu
- Procter & Gamble Mason Business Center, Mason, Ohio, United States of America
| | - Charles W. Saunders
- Procter & Gamble Mason Business Center, Mason, Ohio, United States of America
| | - Nancy L. Reeder
- Procter & Gamble Mason Business Center, Mason, Ohio, United States of America
| | - Raymond A. Reilman
- Procter & Gamble Mason Business Center, Mason, Ohio, United States of America
| | - Annika Scheynius
- Translational Immunology Unit, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Sheng Sun
- Duke University Medical Center, Durham, North Carolina, United States of America
| | | | - Wenjun Li
- National Center for Biotechnology Information, Bethesda, Maryland, United States of America
| | - Anna Floyd Averette
- Duke University Medical Center, Durham, North Carolina, United States of America
| | - Piotr Mieczkowski
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Joseph Heitman
- Duke University Medical Center, Durham, North Carolina, United States of America
| | - Bart Theelen
- Fungal Biodiversity Centre, CBS-KNAW, Utrecht, The Netherlands
| | | | | | | | - Sebastian Maurer-Stroh
- Bioinformatics Institute, A*STAR, Singapore
- School of Biological Sciences, Nanyang Technological University (NTU), Singapore
| | - Teun Boekhout
- Fungal Biodiversity Centre, CBS-KNAW, Utrecht, The Netherlands
| | - Niranjan Nagarajan
- Computational and Systems Biology, Genome Institute of Singapore, A*STAR, Singapore
- * E-mail: (NN); (TLD)
| | - Thomas L. Dawson
- Institute of Medical Biology, A*STAR, Singapore
- * E-mail: (NN); (TLD)
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