Biology subjects

Ju, Y.-M.

Publications and source records attributed to Ju, Y.-M..

3 recordsLinked to original sources

bioRxiv2025

Dynamic evolution of AT-rich isochores shapes the genome of an intertidal fungus Annulohypoxylon annulatoides

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.

genomics↗

bioRxiv2021

Secondary metabolism drives ecological breadth in the Xylariaceae

Global, large-scale surveys of phylogenetically diverse plant and lichen hosts have revealed an extremely high richness of endophytes in the Xylariales, one of the largest clades of filamentous fungi and a significant source of novel secondary metabolites (SMs). Endophytes may produce host protective antimicrobial or insecticidal SMs, as well as compounds that facilitate symbiotic establishment through suppression or degradation of host immune response, but the ecological roles of most SMs are unknown. Here we characterized metabolic gene clusters in 96 genomes of endophytes and closely related saprotrophs and pathogens in two clades of Xylariales (Xylariaceae s.l. and Hypoxylaceae). Hundreds of genes appear horizontally transferred to xylarialean fungi from distantly related fungi and bacteria, including numerous genes in secondary metabolite gene clusters (SMGCs). Although all xylarialean genomes contain hyperabundant SMGCs, we show that increased gene duplications, horizontal gene transfers (HGTs), and SMGC content in Xylariaceae s.l. taxa are linked to greater phylogenetic host breadth, larger biogeographic distributions, and increased capacity for lignocellulose decomposition compared to Hypoxylaceae taxa. Overall, our results suggest that xylarialean endophytes capable of dual ecological modes (symbiotic and saprotrophic) experience greater selection to diversify SMGCs to both increase competitiveness within microbial communities and facilitate diverse symbiotic interactions.

genomics↗

bioRxiv2017

Rolling a mycobiome down a hill: endophytes in the Taiwanese Cloud Forest

Fungal endophytes of plants are ubiquitous and important to host plant health. Despite their ecological importance, landscape-level patterns of microbial communities in plant hosts are not well-characterized. Fungal wood-inhabiting and foliar endophyte communities from multiple tree hosts were sampled at multiple spatial scales across a 25 ha subtropical research plot in northern Taiwan, using culture-free, community DNA amplicon sequencing methods. Fungal endophyte communities were distinct between leaves and wood, but the mycobiomes were highly variable across and within tree species. Of the variance that could be explained, host tree species was the most important driver of mycobiome community-composition. Within a single tree species, \"core\" mycobiomes were characterized using cooccurrence analysis. These core groups of endophytes in leaves and wood show divergent spatial patterns. For wood endophytes, a more consistent, \"minimal\" core mycobiome coexisted with the host across the extent of the study. For leaf endophytes, the core fungi resembled a more dynamic, \"gradient\" model of the core microbiome, changing across the topography and distance of the study.

microbiology↗