J. L. Steenwyk

Environmentally regulated clonal-aggregative multicellularity in a choanoflagellate

This study shows that the choanoflagellate Choanoeca flexa forms multicellular sheets through clonal or aggregative mechanisms, adapting to environmental changes in splash pools.

Characterization of Genome-wide Phylogenetic Conflict Uncovers Evolutionary Modes of Carnivorous Fungi

The paper uses phylogenomic analyses of 23 genomes to study evolutionary modes of carnivorous fungi, finding extensive phylogenetic discordance due to incomplete lineage sorting and non-vertical evolution.

The Genomes of Nematode-Trapping Fungi Provide Insights into the Origin and Diversification of Fungal Carnivorism

This study compares the genomes of nematode-trapping fungi and non-NTF to identify genomic changes linked to carnivorism and adaptation to post-Permian-Triassic extinction environments.

Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast Hanseniaspora uvarum

This study investigates the evolutionary changes in core histone gene regulation in Hanseniaspora uvarum, revealing lineage-specific regulatory solutions and a novel regulatory mode linked to gene loss and adaptive cell cycle dynamics.

Genome-wide patterns of non-coding sequence variation in the major fungal pathogen Aspergillus fumigatus

This study identifies greater sequence variation in non-coding regions of A. fumigatus genes compared to protein-coding regions, suggesting a role in phenotypic differences between strains.

A genome-scale Opisthokonta tree of life: toward phylogenomic resolution of ancient divergences

The paper reconstructs a taxon-rich Opisthokonta tree of life using genome-scale data, suggesting a Mesoproterozoic origin and unresolved deep divergences within Holozoa.

Diverse signatures of convergent evolution in cacti-associated yeasts

This study identifies convergent evolution in cacti-associated yeasts using genomic and phenotypic data, finding thermotolerance and horizontal gene transfer as key adaptive traits.

A phylogenetic approach to explore the Aspergillus fumigatus conidial surface-associated proteome and its role in pathogenesis

The paper identifies conidial surface proteins in Aspergillus fumigatus and shows their role in immune evasion during infection.

Evolutionary origin, population diversity, and diagnostics for a cryptic hybrid pathogen

This study identifies and characterizes the cryptic fungal pathogen Aspergillus latus, revealing its hybrid origin and developing genomic and phenotypic markers for accurate diagnosis.

Genomic and ecological factors shaping specialism and generalism across an entire subphylum

The paper analyzes genomic, metabolic, and ecological data from nearly all Saccharomycotina yeast species to show that intrinsic genetic factors, not trade-offs or extrinsic factors, drive variation in niche breadth.

The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi

This study examines the evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi across 35 genomes, finding conserved resistance genes and fragmented BGCs in most species.

Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus

The paper uses genome-scale phylogenomics to analyze 711 Aspergillus genomes, revealing taxonomic issues and strain misidentifications.

Lack of universal mutational biases in a fungal phylum

The paper analyzes mutational biases across 537 fungal strains from Ascomycota, finding variation in A|T and G|C substitution patterns and showing that genome composition is influenced by both mutational bias and selection.

OrthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

OrthoSNAP identifies single-copy orthologs from gene family trees, increasing the number of markers for molecular evolution studies by splitting and pruning gene families.

Extensive sequence divergence of non-coding regions between Aspergillus fumigatus, a major fungal pathogen of humans, and its relatives

The paper identifies extensive non-coding sequence divergence in A. fumigatus compared to related species, highlighting its potential role in virulence.

Regulation of gliotoxin biosynthesis and protection in Aspergillus species

This study identifies conserved transcription factors and genes involved in gliotoxin protection in Aspergillus species through RNA-sequencing and deletion screening.

An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function

The paper constructs an orthologous gene coevolution network from 332 budding yeast species to explore eukaryotic cellular and genomic structure and function, revealing insights into gene connectivity and environmental fitness.

Aspergillus fumigatus acetate utilisation impacts virulence traits and pathogenicity

This paper investigates how acetate utilization by Aspergillus fumigatus affects virulence traits and pathogenicity, showing its role in secondary metabolite secretion, cell wall composition, and in vivo virulence.

Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum

The paper examines gene loss in the DNA mismatch repair pathway across fungal species, finding extensive MMR gene loss in powdery mildew lineages associated with increased mutation rates.

An evolutionary genomic approach reveals both conserved and species-specific genetic elements related to human disease in closely related Aspergillus fungi

This study uses comparative genomics to identify conserved and species-specific genetic elements related to pathogenicity in Aspergillus fungi, revealing evolutionary patterns linked to human disease.

Genomic and phenotypic analysis of COVID-19-associated pulmonary aspergillosis isolates of Aspergillus fumigatus

The paper analyzes the genomes and phenotypes of four Aspergillus fumigatus isolates from COVID-19 patients, finding minor genomic differences and variable virulence traits.

PhyKIT: a UNIX shell toolkit for processing and analyzing phylogenomic data

PhyKIT provides a UNIX shell toolkit for processing and analyzing phylogenomic data, offering functions to evaluate sequence alignments, trees, and evolutionary relationships.

A genome-scale phylogeny of Fungi; insights into early evolution, radiations, and the relationship between taxonomy and phylogeny

The paper constructs a genome-scale fungal phylogeny using 1,644 species and multiple data matrices, finding robust relationships and identifying taxonomic discrepancies.

Aspergillus fumigatus G-protein coupled receptors GprM and GprJ are important for the regulation of the cell wall integrity pathway, secondary metabolite production, and virulence

This paper investigates the role of GprM and GprJ GPCRs in A. fumigatus, showing they regulate cell wall integrity, secondary metabolite production, and virulence.

Signatures of optimal codon usage predict metabolic ecology in budding yeasts

This study shows that optimal codon usage in metabolic pathways correlates with ecological niches in budding yeasts, suggesting codon optimization can reveal metabolic ecology.

Feature Frequency Profile-based phylogenies are inaccurate

This paper evaluates the accuracy of FFP-based phylogenies and finds they perform poorly compared to standard methods like concatenation and coalescence.

ClipKIT: a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

ClipKIT trims multiple sequence alignments to retain phylogenetically-informative sites, improving phylogenomic inference accuracy and efficiency.

Recurrent loss of abaA, a master regulator of asexual development in filamentous fungi, correlates with changes in genomic and morphological traits

The paper investigates the loss of abaA, a master regulator of asexual development in fungi, and shows its correlation with morphological changes in asexual fruiting bodies across multiple fungal lineages.

Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota

This study constructs a genome-scale phylogeny of Ascomycota fungi, revealing contrasting modes of genome evolution across subphyla.

Biosynthetic gene clusters, secondary metabolite profiles, and cards of virulence in the closest nonpathogenic relatives of Aspergillus fumigatus

The paper compares secondary metabolite profiles and biosynthetic gene clusters between the pathogenic Aspergillus fumigatus and its nonpathogenic relatives A. fischeri and A. oerlinghausenensis, identifying conserved and diverged virulence-associated traits.