Yu-Ching Liu

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.

Background: The variation in fungal community composition within a single habitat space has been extensively studied in forest ecosystems. However, the spatial and temporal distribution of fungi across contiguous habitats, particularly at a local scale and in tropical regions, remains underexplored. In this study, we examined the fungal community composition across multiple habitats proximal to each other over two seasons in seven Fagaceae species in Taiwanese broadleaf forests. We tested how local spatial scale and habitat influence community assembly. Results: Using a metabarcoding approach, we sequenced ITS3/ITS4 amplicons from 864 samples collected from four distinct habitats—leaves, twigs, litter, and soil. We identified 11,600 fungal amplicon sequence variants (ASVs), with community composition differing significantly between habitats proximal to each other. Phyllosphere (leaves and twigs) fungi exhibited higher diversity compared to soil. Habitat type and long-term precipitation emerged as the most influential factors driving fungal diversity and composition, with a clear distance-decay relationship observed in leaf and twig but not in soil. Random forest analysis accurately classified habitats based on ASVs’ relative abundances, with strong predictors were mostly endemic ASVs prevalent in soil. Misclassified samples were due to secondary contact of fungi between adjacent habitats. Co-occurrence network analysis revealed more complex and deterministic networks in leaf and twig habitats, while soil was driven by stochastic processes and contained most endemic ASVs. A Cladosporium sp. emerged as a keystone species, maintaining network stability across forests. Conclusion: This study reveals how local spatial variation and habitat shape distinct fungal communities in tropical forests, with deterministic processes dominating in some habitats and stochasticity playing a key role in others. We show local fungal taxa were strong habitat predictors and drivers of community cohesion. These findings highlight the importance of studying coexisting habitats to gain a deeper understanding of fungal biogeography and ecosystem function.

Leaves of the carnivorous sundew plants (Drosera spp.) secrete mucilage that hosts microorganisms, but whether this microbiota contributes to prey digestion is unclear. We identified the acidophilic fungus Acrodontium crateriforme as the dominant species in the mucilage microbial communities, thriving in multiple sundew species across the global range. The fungus grows and sporulates on sundew glands as its preferred acidic environment, and its presence in traps increased the prey digestion process. A. crateriforme has a reduced genome similar to other symbiotic fungi. During A. crateriforme–Drosera spatulata coexistence and digestion of prey insects, transcriptomes revealed significant gene co-option in both partners. Holobiont expression patterns during prey digestion further revealed synergistic effects in several gene families including fungal aspartic and sedolisin peptidases, facilitating prey digestion in leaves, as well as nutrient assimilation and jasmonate signalling pathway expression. This study establishes that botanical carnivory is defined by adaptations involving microbial partners and interspecies interactions.

Carnivorous plant leaves, such as those of the spoon-leaved sundew Drosera spatulata , secrete mucilage which hosts microorganisms potentially aiding in prey digestion. We characterised the mucilage microbial communities and identified the acidophilic fungus Acrodontium crateriforme as the ecologically dominant species. The fungus grows and sporulates on sundew glands as its preferred acidic environment. We show that the A. crateriforme has a reduced genome similar to that of other symbiotic fungi. Based on the transcriptomes when encountering prey insects, we revealed a high degree of genes co-option in each species during fungus-plant coexistence and digestion. Expression patterns of the holobiont during digestion further revealed synergistic effects in several gene families including fungal aspartic and sedolisin peptidases, facilitating the digestion of sundew’s prey, as well as transporters and dose-dependent responses in plant genes involved in jasmonate signalling pathway. This study establishes that botanical carnivory is defined by multidimensional adaptations correlated with interspecies interactions.

Obtaining sufficient genetic material from a limited biological source is currently the primary operational bottleneck in studies investigating biodiversity and genome evolution. In this study, we employed multiple displacement amplification (MDA) and Smartseq2 to amplify nanograms of genomic DNA and mRNA, respectively, from individual Caenorhabditis elegans. Although reduced genome coverage was observed in repetitive regions, we produced assemblies covering 98% of the reference genome using long-read sequences generated with Oxford Nanopore Technologies (ONT). Annotation with the sequenced transcriptome coupled with the available assembly revealed that gene predictions were more accurate, complete and contained far fewer false positives than de novo transcriptome assembly approaches. We sampled and sequenced the genomes and transcriptomes of 13 nematodes from early-branching species in Chromadoria, Dorylaimia and Enoplia. The basal Chromadoria and Enoplia species had larger genome sizes, ranging from 136.6 to 738.8 Mb, compared with those in the other clades. Nine mitogenomes were fully assembled, and displayed a complete lack of synteny to other species. Phylogenomic analyses based on the new annotations revealed strong support for Enoplia as sister to the rest of Nematoda. Our result demonstrates the robustness of MDA in combination with ONT, paving the way for the study of genome diversity in the phylum Nematoda and beyond.

Obtaining sufficient genetic material from a limited biological source is currently the primary operational bottleneck in studies investigating biodiversity and genome evolution. In this study, we employed multiple displacement amplification (MDA) and Smartseq2 to amplify nanograms of genomic DNA and mRNA, respectively from individual Caenorhabditis elegans . Although reduced genome coverage was observed in repetitive regions, we produced assemblies covering 98% of the reference genome using long-read sequences generated with Oxford Nanopore Technologies (ONT). Annotation with the sequenced transcriptome coupled with the available assembly revealed that gene predictions were more accurate, complete and contained far fewer false positives than de novo transcriptome assembly approaches. We sampled and sequenced the genomes and transcriptomes of 13 nematodes from Dorylaimia, Enoplia, and early-branching species in Chromadoria. These free-living species had larger genome sizes, ranging from 147-792 Mb, compared to those of the parasitic lifestyle. Nine mitogenomes were fully assembled and displaying a complete lack of synteny to other species. Phylogenomic analyses based on the new annotations revealed strong support for Enoplia as sister to the rest of Nematoda. Our result demonstrates the robustness of MDA in combination with ONT, paving the way for the study of genome diversity in the phylum Nematoda and beyond.

Aphelenchoides besseyi is a plant‐parasitic nematode (PPN) in the family Aphelenchoididae capable of infecting more than 200 plant species. A. besseyi is also a species complex with strains exhibiting varying pathogenicity to plants. We present the genome and annotations of six Aphelenchoides species, four of which belonged to the A. besseyi species complex. Most Aphelenchoides genomes have a size of 44.7–47.4 Mb and are among the smallest in clade IV, with the exception of A. fujianensis, which has a size of 143.8 Mb and is one of the largest. Phylogenomic analysis successfully delimited the species complex into A. oryzae and A. pseudobesseyi and revealed a reduction of transposon elements in the last common ancestor of Aphelenchoides. Synteny analyses between reference genomes indicated that three chromosomes in A. besseyi were derived from fission and fusion events. A systematic identification of horizontal gene transfer (HGT) genes across 27 representative nematodes allowed us to identify two major episodes of acquisition corresponding to the last common ancestor of clade IV or major PPNs, respectively. These genes were mostly lost and differentially retained between clades or strains. Most HGT events were acquired from bacteria, followed by fungi, and also from plants; plant HGT was especially prevalent in Bursaphelenchus mucronatus. Our results comprehensively improve the understanding of HGT in nematodes.

Aphelenchoides besseyi is a plant-parasitic nematode (PPN) in the Aphelenchoididae family capable of infecting more than 200 plant species. A. besseyi is also a species complex with strains exhibiting varying pathogenicity to plants. We present the genome and annotations of six Aphelenchoides species, four of which belonged to the A. besseyi species complex. Most Aphelenchoides genomes have a size of 44.7-47.4 Mb and are amongst the smallest in clade IV, with the exception of A. fujianensis , which has a size of 143.8 Mb and is the largest. Phylogenomic analysis successfully delimited the species complex into A. oryzae and A. pseudobesseyi and revealed a reduction of transposon elements in the last common ancestor of Aphelenchoides . Synteny analyses between reference genomes indicated that three chromosomes in A. besseyi were derived from fission and fusion events. A systematic identification of horizontal gene transfer (HGT) genes across 27 representative nematodes allowed us to identify two major episodes of acquisition corresponding to the last common ancestor of clade IV or major PPNs, respectively. These genes were mostly lost and differentially retained between clades or strains. Most HGT events were acquired from bacteria, followed by fungi, and also from plants; plant HGT was especially prevalent in Bursaphelenchus mucronatus . Our results comprehensively improve the understanding of horizontal gene transfer in nematodes.