Cheng-Ju Yang

Forest-associated Saccharomycotina occur at low relative abundance, limiting inference about their diversity and dynamics. We sampled leaf litter weekly for 47 weeks across a subtropical forest in northern Taiwan. Enrichment, isolation and ITS sequencing recovered 687 isolates, including 613 Saccharomycotina representing 56 described species and 77 putatively novel operational taxonomic units. Rarefaction indicated unsampled culturable diversity. Among litter traps, community dissimilarity was high and dominated by taxon replacement, but neither topography nor geographic distance was associated with composition, and turnover matched randomised expectations. Richness peaked during warm, wet periods and declined in winter, and minimum temperature showed the strongest statistical association. Composition was associated with maximum temperature, minimum relative humidity, precipitation and solar radiation. Selected isolates' thermal optima covaried with collection-week temperatures, and two October Magnusiomyces magnusii isolates had higher optima than four winter isolates. Together, these findings reveal substantial culturable diversity and seasonal community restructuring consistent with temperature-related filtering.

Saccharomyces cerevisiae predominantly exists as diploid cells in nature, a life-cycle feature that limits classical genetic analyses of wild populations. Here, we establish a stable haploid strain collection derived from 33 diverse Taiwanese S. cerevisiae isolates through targeted disruption of the HO endonuclease gene. This resource spans predomesticated Asian wild lineages and enables systematic analyses of mating compatibility, reproductive isolation, and ecological trait variation. Although all pairwise hybridizations formed zygotes, many produced low spore viabilities, revealing strong postzygotic barriers. Genome analyses show that reduced hybrid fertility is primarily associated with chromosomal inversions and inter-chromosomal rearrangements rather than sequence divergence, indicating that structural variation maintains lineage separation despite geographic coexistence. Phenotypic profiling uncovered marked ecological differentiation, with the most diverged TW1 lineage favoring cooler growth conditions and a naturally occurring hybrid exhibiting heterosis with expanded thermal tolerance. While most wild strains grew poorly on maltose, two anthropogenically associated strains displayed enhanced maltose utilization linked to functional MAL ⁺ regulatory alleles and maltose-specific transporters. Together, these findings demonstrate how structural genomic variation and metabolic gene divergence drive ecological and reproductive divergence in wild S. cerevisiae and establish this haploid collection as a platform for studying yeast evolution in nature.

Marine and coastal fungi experience intense environmental variability, yet the genomic mechanisms enabling filamentous fungi to tolerate such conditions remain unclear. From 56 fungal isolates collected along the Lailai rocky shore in northern Taiwan, we selected Annulohypoxylon annulatoides for deeper investigation due to its prevalence and distinctive stress response. Phenotypic assays revealed that this strain exhibits distinct growth and recovery dynamics under salinity, temperature, and UV stress compared to conspecific strains isolated from tree bark. To investigate the genomic basis of its adaptation, we generated a high-quality 41.8 Mbp de novo genome assembly with 11,529 predicted proteins. Across Hypoxylaceae genomes, we identified variably sized and dispersed AT-rich isochores, which in A. annulatoides were enriched in repeats and displayed low gene density. Despite differences in AT content, core gene content and Pfam domain profiles remained conserved. These AT-rich isochores exhibit several sequence and structural features consistent with scaffold/matrix attachment regions (S/MARs), raising the possibility that they influence higher-order genome organisation. Comparative analyses suggest they arose through independent repeat insertions or via ancestral repeat amplifications. Together, our findings point to a role for AT-rich isochores in shaping genome architecture and potentially mediating stress-responsive regulation, supporting the broader environmental flexibility observed in Hypoxylaceae, including adaptation to dynamic coastal habitats.