Jason Stajich

Eukaryotic MAGs recovered from deep metagenomic sequencing of the seagrass, Zostera marina, include a novel chytrid in the order Lobulomycetales

This study uses deep metagenomic sequencing to recover MAGs from Zostera marina, identifying a novel chytrid in the Lobulomycetales order and other eukaryotic lineages with genomic novelty.

Assessing the Evolutionary Trajectory of Arbuscular Mycorrhizal Conserved Genes in Seagrasses and Aquatic Close Relatives

The paper examines the evolutionary patterns of AMF-related genes in aquatic and terrestrial plants, finding gene losses or divergence in aquatic lineages but retention in some seagrass species.

Genome variation of Sporothrix schenckii and Sporothrix brasiliensis

The paper analyzes genome variation in Sporothrix species to understand their evolutionary strategies and drug resistance mechanisms.

orthoSynAssign: refine orthogroups using synteny information

orthoSynAssign refines orthogroups using synteny information, improving precision and scalability for phylogenomic analyses.

Unraveling the diversity and functional potential of cyanosphere microbiomes assembled from terrestrial cyanobacteria

This study uses metagenomics to analyze cyanosphere microbiomes associated with terrestrial cyanobacteria, revealing host-specific and environmentally influenced microbial communities and functional differences.

A long non-coding RNA regulates in vitro and in vivo triazole antifungal susceptibility in Aspergillus fumigatus

The paper identifies a long non-coding RNA, afu-182, that regulates azole antifungal susceptibility in Aspergillus fumigatus both in vitro and in vivo.

An epigenetic mechanism of azole tolerance facilitates acquired antifungal resistance in Aspergillus fumigatus

This study identifies IngB as an epigenetic regulator of azole tolerance in Aspergillus fumigatus, showing that its loss enables rapid acquired resistance under azole stress.

Novel Glomeromycotina-Moss Associations Identified in California Dryland Biocrusts

The paper identifies novel Glomeromycotina-moss associations in California dryland biocrusts using metabarcoding and microscopy, revealing distinct fungal communities and potential climate change impacts.

Effects of environmental setting and diet on the gut microbial ecology of eastern hellbenders (Cryptobranchus alleganiensis alleganiensis)

This study examines how zoo management and diet affect the gut microbiome of eastern hellbenders, finding that wild diets and release into natural habitats can restore microbial communities closer to wild-type patterns.

Phyling: phylogenetic inference from annotated genomes

Phyling is a tool for phylogenetic inference from protein sequences, offering faster performance than OrthoFinder with comparable accuracy.

Orchard management alters citrus root and rhizosphere microbiomes with functional consequences for plant performance

This study shows that orchard management practices alter citrus root and rhizosphere microbiomes, which in turn affect plant performance through microbial community changes.

Coordinated regulation of Mdr1- and Cdr1-mediated protection from antifungals by the Mrr1 transcription factor in emerging Candida spp.

This study identifies Mrr1 as a transcription factor coordinating MDR1 and CDR1 expression in Candida lusitaniae, contributing to antifungal resistance through efflux pumps and stress response genes.

Inferring fungal cis-regulatory networks from genome sequences via unsupervised and interpretable representation learning.

The paper infers fungal cis-regulatory networks from genome sequences using unsupervised and interpretable representation learning, identifying conserved motif signals that predict gene expression and regulation.

Genomic plasticity of the mating-type loci underlies reproductive strategy transitions in Rhodotorula yeasts

This study examines genomic changes in mating-type loci across Rhodotorula yeast species, revealing structural divergence and inheritance patterns associated with shifts in reproductive strategies.

Dynamic remodeling of centrioles and the microtubule cytoskeleton in the lifecycle of chytrid fungi

The paper studies centriole and microtubule cytoskeleton remodeling in chytrid fungi during their lifecycle using bioinformatics, RNA sequencing, and expansion microscopy.

Kingdom-Wide CRISPR Guide Design with ALLEGRO

ALLEGRO designs universal CRISPR sgRNA libraries targeting multiple fungal species, validated experimentally across three fungi and extended to others.

Giant transposons promote strain heterogeneity in a major fungal pathogen

This study identifies giant transposons called Starships in Aspergillus fumigatus that generate genomic and phenotypic heterogeneity across strains.

A Novel Sarocladium spinificis Strain Suppresses Coccidioides posadasii Growth: Morphological and Genetic Perspectives

This study characterizes two clinical Sarocladium spinificis strains that inhibit Coccidioides posadasii growth, revealing their genomic features and potential antifungal properties.

Increased aridity is associated with diversity and composition changes in the biocrust mycobiome

The paper examines how increased aridity affects the fungal community composition in biocrusts, finding greater homogeneity and shifts toward extremotolerant taxa in drier environments.

Genomic streamlining of seagrass-associated Colletotrichum sp. may be related to its adaptation to a marine monocot host

This study presents the genome of a seagrass-associated Colletotrichum sp. and finds it has a streamlined genome with fewer genes and gene families compared to related species, possibly linked to its marine ecological niche.

A genomic resource for exploring bacterial-viral dynamics in seagrass ecosystems

The paper generates genomic resources for bacterial and viral communities in seagrass ecosystems, revealing potential roles for viruses in carbon cycling.

Description of new micro-colonial fungi species Neophaeococcomyces mojavensis, Coniosporium tulheliwenetii, and Taxawa tesnikishii cultured from biological soil crusts

The paper describes three new micro-colonial fungi species isolated from desert biological soil crusts using culture-dependent methods and genomic analysis.

Haplotype phased genome of 'Fairchild' mandarin highlights influence of local chromatin state on gene expression

The paper uses a phased genome of the Fairchild mandarin to analyze how haplotype-specific chromatin states influence allele-specific gene expression.

Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi

This paper presents a largely-complete genome of Entomophthora muscae, revealing insights into its large genome size, transposon activity, and unique biological features.

Genomes and transcriptomes help unravel the complex life cycle of the blastoclad fungus, Coelomomyces lativittatus, an obligate parasite of mosquitoes and microcrustaceans

The paper generates draft genomes and transcriptomes for Coelomomyces lativittatus, analyzing gene expression across life stages to understand its biology and life cycle.

A chromosomal-level reference genome of the widely utilized Coccidioides posadasii laboratory strain "Silveira"

The paper presents a chromosomal-level genome assembly of the Coccidioides posadasii Silveira strain using SMRT sequencing, improving genome annotation and enabling future genomic studies.

Combined Pan-, Population-, and Phylo-Genomic Analysis of Aspergillus fumigatus Reveals Population Structure and Lineage-Specific Diversity

This study combines pan-, population-, and phylo-genomic analyses of Aspergillus fumigatus to reveal population structure, lineage-specific diversity, and ecological drivers of virulence.

Improved draft reference genome for the Glassy-winged Sharpshooter (Homalodisca vitripennis), a vector for Pierce's disease

The paper improves the reference genome of the glassy-winged sharpshooter, providing a higher-quality assembly and annotation, along with endosymbiont genomes for future research.

A NEW CASE OF DIPLOIDY WITHIN A HAPLOID GENUS OF ENTOMOPATHOGENIC FUNGI

The paper reports the first documented case of diploidy in the haploid genus Metarhizium, specifically in the isolate M. acridum ARSEF 324, using SMRT sequencing and genomic analysis.

Structural characterization and evolutionary analyses of the Coccidioides immitis and Coccidioides posadasii mitochondrial genomes

The paper assembles and annotates mitochondrial genomes of Coccidioides immitis and C. posadasii, and assesses population variation across 77 genomes, identifying common genes and introns.