Scholars@Duke
Marco Dias Coelho

Marco Dias Coelho

Assistant Research Professor in Molecular Genetics and Microbiology
Molecular Genetics and Microbiology
marco.dias.coelho@duke.edu
Box 3546, 321 CARL Building, Durham, NC 27710
Box 3546, 321 CARL Building, Durham, NC 27710

Scholarly Works - Journal articles

Fourier transform infrared spectroscopy enables rapid strain typing in M. pachydermatis.

Journal article J Clin Microbiol · July 20, 2026 Malassezia pachydermatis is a zoophilic yeast found on the skin and in the outer ear canal of many mammals. It normally maintains a commensal lifestyle, but can cause dermatitis and otitis in predisposed hosts, particularly in atopic dogs. M. pachydermatis ... Full text Link to item Cite

Aimea gen. nov. defines a novel plant-associated yeast genus in Microbotryomycetes with three novel species.

Journal article bioRxiv · April 10, 2026 Plant tissues and surfaces are among the largest microbial habitats on Earth, and commensal yeasts are common members of these communities, where they can contribute to plant-microbe interactions including the biological control of plant diseases. Here, we ... Full text Link to item Cite

Fourier transform infrared spectroscopy reveals high intraspecies diversity of Malassezia pachydermatis in dogs with atopic dermatitis.

Journal article bioRxiv · April 6, 2026 Canine atopic dermatitis (CAD) is a chronic inflammatory skin condition sometimes associated with microbial dysbiosis, including alterations in colonization by the lipophilic yeast Malassezia pachydermatis. This study investigated the population diversity ... Full text Link to item Cite

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

Journal article PLoS Genet · November 2025 The 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 ma ... Full text Open Access Link to item Cite

The complex evolution and genomic dynamics of mating-type loci in Cryptococcus and Kwoniella.

Journal article PLoS Biol · October 2025 Sexual reproduction in basidiomycete fungi is governed by MAT loci (P/R and HD), which exhibit remarkable evolutionary plasticity, characterized by expansions, rearrangements, and gene losses often associated with mating system transitions. The sister gene ... Full text Link to item Cite

Fourier transform infrared spectroscopy enables rapid species discrimination across Malassezia and strain-level typing in M. pachydermatis.

Journal article bioRxiv · September 25, 2025 Malassezia pachydermatis is a zoophilic yeast found on the skin and in the outer ear canal of many mammals. It normally maintains a commensal lifestyle but can cause dermatitis and otitis in predisposed hosts, particularly in atopic dogs. M. pachydermatis ... Full text Link to item Cite

Fungal sexual reproduction and mating-type loci.

Journal article Curr Biol · June 9, 2025 Sexual reproduction is a hallmark of eukaryotes, generating diversity and variation through recombination and allele segregation, thereby facilitating natural selection. Unlike animals and plants, fungi do not have conventional male and female sexes but in ... Full text Open Access Link to item Cite

Comparative genomics of the closely related fungal genera Cryptococcus and Kwoniella reveals karyotype dynamics and suggests evolutionary mechanisms of pathogenesis.

Journal article PLoS Biol · June 2024 In exploring the evolutionary trajectories of both pathogenesis and karyotype dynamics in fungi, we conducted a large-scale comparative genomic analysis spanning the Cryptococcus genus, encompassing both global human fungal pathogens and nonpathogenic spec ... Full text Open Access Link to item Cite

Frequent transitions in mating-type locus chromosomal organization in Malassezia and early steps in sexual reproduction.

Journal article Proc Natl Acad Sci U S A · August 8, 2023 Fungi in the basidiomycete genus Malassezia are the most prevalent eukaryotic microbes resident on the skin of human and other warm-blooded animals and have been implicated in skin diseases and systemic disorders. Analysis of Malassezia genomes revealed th ... Full text Open Access Link to item Cite

Frequent transitions in mating-type locus chromosomal organization in Malassezia and early steps in sexual reproduction.

Journal article bioRxiv · June 9, 2023 UNLABELLED: Fungi in the basidiomycete genus Malassezia are the most prevalent eukaryotic microbes resident on the skin of human and other warm-blooded animals and have been implicated in skin diseases and systemic disorders. Analysis of Malassezia genomes ... Full text Open Access Link to item Cite

Obligate sexual reproduction of a homothallic fungus closely related to the Cryptococcus pathogenic species complex.

Journal article Elife · June 17, 2022 eLife digest. Fungi are enigmatic organisms that flourish in soil, on decaying plants, or during infection of animals or plants. Growing in myriad forms, from single-celled yeast to multicellular molds and mushrooms, fungi have also evolved ... Full text Open Access Link to item Cite

Dynamic genome plasticity during unisexual reproduction in the human fungal pathogen Cryptococcus deneoformans.

Journal article PLoS Genet · November 2021 Genome copy number variation occurs during each mitotic and meiotic cycle and it is crucial for organisms to maintain their natural ploidy. Defects in ploidy transitions can lead to chromosome instability, which is a hallmark of cancer. Ploidy in the haplo ... Full text Link to item Cite

Multiple Pathways to Homothallism in Closely Related Yeast Lineages in the Basidiomycota.

Journal article mBio · February 16, 2021 Sexual reproduction in fungi relies on proteins with well-known functions encoded by the mating type (MAT) loci. In the Basidiomycota, MAT loci are often bipartite, with the P/R locus encoding pheromone precursors and pheromone receptors and the HD locus e ... Full text Open Access Link to item Cite

Factors enforcing the species boundary between the human pathogens Cryptococcus neoformans and Cryptococcus deneoformans.

Journal article PLoS Genet · January 2021 Hybridization has resulted in the origin and variation in extant species, and hybrids continue to arise despite pre- and post-zygotic barriers that limit their formation and evolutionary success. One important system that maintains species boundaries in pr ... Full text Link to item Cite

The Untapped Australasian Diversity of Astaxanthin-Producing Yeasts with Biotechnological Potential-Phaffia australis sp. nov. and Phaffia tasmanica sp. nov.

Journal article Microorganisms · October 24, 2020 Phaffia is an orange-colored basidiomycetous yeast genus of the order Cystofilobasidiales that contains a single species, P. rhodozyma. This species is the only fungus known to produce the economically relevant carotenoid astaxanthin. Although Phaffia was ... Full text Open Access Link to item Cite

HGT in the human and skin commensal Malassezia: A bacterially derived flavohemoglobin is required for NO resistance and host interaction.

Journal article Proc Natl Acad Sci U S A · July 7, 2020 The skin of humans and animals is colonized by commensal and pathogenic fungi and bacteria that share this ecological niche and have established microbial interactions. Malassezia are the most abundant fungal skin inhabitant of warm-blooded animals and hav ... Full text Open Access Link to item Cite

Centromere scission drives chromosome shuffling and reproductive isolation.

Journal article Proc Natl Acad Sci U S A · April 7, 2020 A fundamental characteristic of eukaryotic organisms is the generation of genetic variation via sexual reproduction. Conversely, significant large-scale genome structure variations could hamper sexual reproduction, causing reproductive isolation and promot ... Full text Link to item Cite

Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages.

Journal article PLoS Genet · March 2020 Centromeres are chromosomal regions that serve as platforms for kinetochore assembly and spindle attachments, ensuring accurate chromosome segregation during cell division. Despite functional conservation, centromere DNA sequences are diverse and often rep ... Full text Link to item Cite

Loss of centromere function drives karyotype evolution in closely related Malassezia species.

Journal article eLife · January 2020 Genomic rearrangements associated with speciation often result in variation in chromosome number among closely related species. Malassezia species show variable karyotypes ranging between six and nine chromosomes. Here, we experimentally identified ... Full text Cite

The Evolution of Sexual Reproduction and the Mating-Type Locus: Links to Pathogenesis of Cryptococcus Human Pathogenic Fungi.

Journal article Annual review of genetics · December 2019 Cryptococcus species utilize a variety of sexual reproduction mechanisms, which generate genetic diversity, purge deleterious mutations, and contribute to their ability to occupy myriad environmental niches and exhibit a range of pathogenic potentia ... Full text Open Access Cite

Genetic and genomic evolution of sexual reproduction: echoes from LECA to the fungal kingdom.

Journal article Curr Opin Genet Dev · October 2019 Sexual reproduction is vastly diverse and yet highly conserved across the eukaryotic domain. This ubiquity suggests that the last eukaryotic common ancestor (LECA) was sexual. It is hypothesized that several critical processes in sexual reproduction, inclu ... Full text Open Access Link to item Cite

Convergent evolution of linked mating-type loci in basidiomycete fungi.

Journal article PLoS Genet · September 2019 Sexual development is a key evolutionary innovation of eukaryotes. In many species, mating involves interaction between compatible mating partners that can undergo cell and nuclear fusion and subsequent steps of development including meiosis. Mating compat ... Full text Link to item Cite

Mating-System Evolution: All Roads Lead to Selfing.

Journal article Curr Biol · August 5, 2019 Fungi reproduce via both heterothallic outcrossing and homothallic selfing modes, and transitions between the two are common throughout the tree of life. A new study reports that the transition from heterothallism to homothallism is common and has repeated ... Full text Link to item Cite

Genetic and Genomic Analyses Reveal Boundaries between Species Closely Related to Cryptococcus Pathogens.

Journal article mBio · June 11, 2019 Speciation is a central mechanism of biological diversification. While speciation is well studied in plants and animals, in comparison, relatively little is known about speciation in fungi. One fungal model is the Cryptococcus genus, which is best known fo ... Full text Link to item Cite

Convergent recombination cessation between mating-type genes and centromeres in selfing anther-smut fungi.

Journal article Genome Res · June 2019 The degree of selfing has major impacts on adaptability and is often controlled by molecular mechanisms determining mating compatibility. Changes in compatibility systems are therefore important evolutionary events, but their underlying genomic mechanisms ... Full text Link to item Cite

Cryptococcus deuterogattii VGIIa Infection Associated with Travel to the Pacific Northwest Outbreak Region in an Anti-Granulocyte-Macrophage Colony-Stimulating Factor Autoantibody-Positive Patient in the United States.

Journal article mBio · February 12, 2019 The region encompassing the Pacific Northwest (PNW), Vancouver Island, Oregon, and Washington has been the location of an ongoing Cryptococcus gattii outbreak since the 1990s, and there is evidence that the outbreak is expanding along the West Coast into C ... Full text Link to item Cite

Multiple convergent supergene evolution events in mating-type chromosomes.

Journal article Nat Commun · May 21, 2018 Convergent adaptation provides unique insights into the predictability of evolution and ultimately into processes of biological diversification. Supergenes (beneficial gene linkage) are striking examples of adaptation, but little is known about their preva ... Full text Link to item Cite

Evolutionary strata on young mating-type chromosomes despite the lack of sexual antagonism.

Journal article Proc Natl Acad Sci U S A · July 3, 2017 Sex chromosomes can display successive steps of recombination suppression known as "evolutionary strata," which are thought to result from the successive linkage of sexually antagonistic genes to sex-determining genes. However, there is little evidence to ... Full text Link to item Cite

Fungal Sex: The Basidiomycota.

Journal article Microbiol Spectr · June 2017 Fungi of the Basidiomycota, representing major pathogen lineages and mushroom-forming species, exhibit diverse means to achieve sexual reproduction, with particularly varied mechanisms to determine compatibilities of haploid mating partners. For species th ... Full text Link to item Cite

Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma.

Journal article BMC Genomics · November 9, 2016 BACKGROUND: The class Tremellomycete (Agaricomycotina) encompasses more than 380 fungi. Although there are a few edible Tremella spp., the only species with current biotechnological use is the astaxanthin-producing yeast Phaffia rhodozyma (Cystofilobasidia ... Full text Open Access Link to item Cite

Stepwise Functional Evolution in a Fungal Sugar Transporter Family.

Journal article Mol Biol Evol · February 2016 Sugar transport is of the utmost importance for most cells and is central to a wide range of applied fields. However, despite the straightforward in silico assignment of many novel transporters, including sugar porters, to existing families, their exact bi ... Full text Link to item Cite

Jaminaea phylloscopi sp. nov. (Microstromatales), a basidiomycetous yeast isolated from migratory birds in the Mediterranean basin.

Journal article Int J Syst Evol Microbiol · February 2016 During a survey of yeasts vectored by migratory birds in the Mediterranean basin, isolations from the cloacae of members of the order Passeriformes collected in Ustica (Italy) were performed. Based on phylogenetic analysis of the D1/D2 domain of the 26S rR ... Full text Link to item Cite

Evolution of Mating Systems in Basidiomycetes and the Genetic Architecture Underlying Mating-Type Determination in the Yeast Leucosporidium scottii.

Journal article Genetics · September 2015 In most fungi, sexual reproduction is bipolar; that is, two alternate sets of genes at a single mating-type (MAT) locus determine two mating types. However, in the Basidiomycota, a unique (tetrapolar) reproductive system emerged in which sexual identity is ... Full text Link to item Cite

Sex in the cold: taxonomic reorganization of psychrotolerant yeasts in the order Leucosporidiales.

Journal article FEMS Yeast Res · June 2015 Species of Leucosporidiales are a group of psychrotolerant yeasts with biotechnological potential. In the present work, we studied the phenotypic, genetic and sexual characteristics of three species of this genus (Leucosporidium scottii, Leucosporidiella c ... Full text Link to item Cite

Draft Genome Sequence of Sporidiobolus salmonicolor CBS 6832, a Red-Pigmented Basidiomycetous Yeast.

Journal article Genome Announc · May 21, 2015 We report the genome sequencing and annotation of the basidiomycetous red-pigmented yeast Sporidiobolus salmonicolor strain CBS 6832. The current assembly contains 395 scaffolds, for a total size of about 20.5 Mb and a G+C content of ~61.3%. The genome ann ... Full text Link to item Cite

Extensive intra-kingdom horizontal gene transfer converging on a fungal fructose transporter gene.

Journal article PLoS Genet · June 2013 Comparative genomics revealed in the last decade a scenario of rampant horizontal gene transfer (HGT) among prokaryotes, but for fungi a clearly dominant pattern of vertical inheritance still stands, punctuated however by an increasing number of exceptions ... Full text Link to item Cite

Living and thriving on the skin: Malassezia genomes tell the story.

Journal article mBio · March 19, 2013 Our understanding of the interactions between normal skin microbiota and the human host has been greatly extended by recent investigations. In their recent study in mBio, A. Gioti et al. (mBio 4[1]:e00572-12, 2013) sequenced the genome of the atopic eczema ... Full text Link to item Cite

Linkage to the mating-type locus across the genus Microbotryum: insights into nonrecombining chromosomes.

Journal article Evolution · November 2012 Parallels have been drawn between the evolution of nonrecombining regions in fungal mating-type chromosomes and animal and plant sex chromosomes, particularly regarding the stages of recombination cessation forming evolutionary strata of allelic divergence ... Full text Link to item Cite

Functionality of the Paracoccidioides mating α-pheromone-receptor system.

Journal article PLoS One · 2012 Recent evidence suggests that Paracoccidioides species have the potential to undergo sexual reproduction, although no sexual cycle has been identified either in nature or under laboratory conditions. In the present work we detected low expression levels of ... Full text Link to item Cite

Phaeoacremonium species associated with Eutypa dieback and esca of grapevines in Algeria

Journal article Phytopathologia Mediterranea · December 1, 2011 Algerian grapevines showing symptoms of Eutypa dieback and esca were examined for the presence of Phaeoacremonium species. Species were identified on the basis of morphological and cultural characteristics as well as DNA sequence data (β-tubulin and actin) ... Cite

Evidence for maintenance of sex determinants but not of sexual stages in red yeasts, a group of early diverged basidiomycetes.

Journal article BMC Evol Biol · August 31, 2011 BACKGROUND: The red yeasts are an early diverged group of basidiomycetes comprising sexual and asexual species. Sexuality is based on two compatible mating types and sexual identity is determined by MAT loci that encode homeodomain transcription factors, p ... Full text Link to item Cite

The dynamics of the yeast community of the Tagus river estuary: testing the hypothesis of the multiple origins of estuarine yeasts.

Journal article Antonie Van Leeuwenhoek · October 2010 Yeasts are common inhabitants of different types of aquatic habitats, including marine and estuarine waters and rivers. Although numerous studies have surveyed yeast occurrence in these habitats, the identification of autochthonous populations has been pro ... Full text Link to item Cite

A deviation from the bipolar-tetrapolar mating paradigm in an early diverged basidiomycete.

Journal article PLoS Genet · August 5, 2010 In fungi, sexual identity is determined by specialized genomic regions called MAT loci which are the equivalent to sex chromosomes in some animals and plants. Usually, only two sexes or mating types exist, which are determined by two alternate sets of gene ... Full text Link to item Cite

Identification of mating type genes in the bipolar basidiomycetous yeast Rhodosporidium toruloides: first insight into the MAT locus structure of the Sporidiobolales.

Journal article Eukaryot Cell · June 2008 Rhodosporidium toruloides is a heterothallic, bipolar, red yeast that belongs to the Sporidiobolales, an order within a major lineage of basidiomycetes, the Pucciniomycotina. In contrast to other basidiomycetes, considerably less is known about the nature ... Full text Link to item Cite