Samuel O’Donnell

The paper identifies mutational signatures caused by DNA:RNA hybrids in yeast genomes, revealing a common mechanism of genetic instability through repair pathways.

The paper identifies a new Penicillium biforme lineage, cheesy, selected for food fermentation, with genetic and phenotypic differences from P. camemberti and traits advantageous for cheesemaking.

PAQman evaluates long-read eukaryotic genome assemblies using seven reference-free metrics without requiring a reference genome.

The paper identifies two distinct Starship families in Pyricularia oryzae, showing differences in sequence evolution, epigenetic modifications, and impacts on genome variation and plant-fungal interactions.

This study investigates the role of Starships, large horizontal gene transfers, in domesticated and pathogenic fungi, finding increased Starship content in strains from human-associated environments.

This study identifies Starships as active vectors of horizontal gene transfer among eukaryotic species, showing they mediate frequent and precise DNA transfer between distantly related fungi.

This study identifies horizontal gene transfers from Fusarium oxysporum to Fusarium xylarioides as a mechanism driving the repeated outbreaks of coffee wilt disease.

This study identifies structural variants in a domesticated Lachancea cidri yeast strain associated with improved fermentation traits compared to wild isolates.

The paper measures mutation rates in yeast colonies and finds that double mutations occur at higher rates than expected, suggesting transient mutator phenotypes contribute to genomic instability.

This paper presents 142 high-quality yeast genomes to improve pangenome understanding, identifying structural variants and complex genomic regions.

This study analyzes whole-genome data from 98 Geotrichum candidum strains to show domestication led to genetic and phenotypic differentiation in cheese-making strains.

The paper presents version 6 of the Chlamydomonas reinhardtii reference genome, improving assembly quality and revealing structural mutations in laboratory strains.

The paper describes the subtelomere architecture in Chlamydomonas reinhardtii using long-read sequencing and identifies repeated elements and their evolutionary dynamics.

This paper introduces a CRISPR/Cas9 method to generate precise, markerless translocations in yeast, enabling the study of chromosomal rearrangements' phenotypic effects independent of base substitutions.