Lab papers from March to October 2025

A roundup of papers from the middle and later part of 2025 with lab members and collaborators.

Fungal pathogens and antifungal resistance

• Giant transposons promote strain heterogeneity in a major fungal pathogen (mBio). Emile Gluck-Thaler, Robert Cramer, Aaron Vogan, and colleagues, including Jason Stajich, analyzed 519 Aspergillus fumigatus strains and found 20 distinct giant transposons that generate genomic heterogeneity, mobilizing genes with roles in biofilm-related virulence and biosynthetic gene clusters.
• Coordinated regulation of Mdr1- and Cdr1-mediated protection from antifungals by the Mrr1 transcription factor in emerging Candida species (mBio). With Deborah Hogan’s lab at Dartmouth and Carolina Piña Páez, this work used CUT&RUN to define the Mrr1 regulon in Candida lusitaniae, showing that Mrr1 coordinates two multi-drug transporters and identifying a conserved binding motif.
• Morphological and genetic characterization of novel Sarocladium spinificis strains in association with Coccidioides posadasii (bioRxiv preprint). A collaboration with Bridget Barker’s lab on a Sarocladium strain that suppresses Coccidioides growth.
• Comparative Genomics Reveals Intra and Inter Species Variation in the Pathogenic Fungus Batrachochytrium dendrobatidis (Genome Biology and Evolution). From Mark Yacoub’s PhD work on the amphibian pathogen.

Chytrid cell biology

• Dynamic remodeling of centrioles and the microtubule cytoskeleton in the lifecycle of chytrid fungi (Molecular Biology of the Cell). With Tim Stearns’s and Lillian Fritz-Laylin’s groups, this study uses RNA-sequencing and expansion microscopy to show how centrioles and the microtubule cytoskeleton are remodeled as chytrids grow from zoospore to multinucleate coenocyte.

Extreme environments, soils, and microbiomes

• Increased aridity is associated with diversity and composition changes in the biocrust mycobiome (bioRxiv preprint). Kian Kelly, Xin-zhan Liu, and colleagues examine how aridity shapes fungal communities in biological soil crusts.
• Draft genome sequence of an uncultured archaeon from Antarctic endolithic communities (Microbiology Resource Announcements). Claudia Coleine and colleagues.
• Soil drivers of fungal, bacterial and plant diversity in contaminated Southern Californian sites: Implications for dryland bioremediation (Science of the Total Environment). A survey of seven contaminated Southern California sites with Tania Kurbessoian, which identifies native plants that accumulate copper and soil factors that shape microbial communities, as candidates for dryland bioremediation.
• Celebrating the fifth edition of the International Symposium on Fungal Stress (ISFUS) (Fungal Biology).

Genomes, tools, and data

• Kingdom-wide CRISPR guide design with ALLEGRO (Nucleic Acids Research). A UC Riverside collaboration with Ian Wheeldon’s and Stefano Lonardi’s labs and Xin-zhan Liu. ALLEGRO uses integer linear programming to design compact sgRNA libraries targeting over 2,000 fungal species, with edits confirmed in four yeasts.
• A roadmap for equitable reuse of public microbiome data (Nature Microbiology). Proposes a Data Reuse Information (DRI) tag tied to an ORCID so data creators can ask to be contacted before reuse.
• A haplotype-resolved chromatin landscape connects cis-regulatory variants to trait variation in Citrus (BMC Genomics). With Danelle Seymour’s and Susan Wessler’s labs, including Talieh Ostovar and Jinfeng Chen. A locally phased mandarin genome links haplotype-specific chromatin states to allele-specific gene expression and fruit traits.
• Draft genome of Conoideocrella luteorostrata ARSEF 14590 and Genome annotation of Aspergillus melleus strain CBS 546.65 (Microbiology Resource Announcements). Two genome announcements.
• Activation of the Trichodimerol Pathway through Deletion of mcrA in Marine Penicillium rubens YAP001 (ACS Chemical Biology). With Clay Wang’s lab at USC, activating a secondary metabolite pathway to produce sorbicillinoids and trichodimerol.