Hyperdiversity and functional potential of the coral mycobiome: characterising host-specific and environmentally driven niches across the South China Sea reefs using long-read 28S rRNA metabarcoding

Coral-associated fungi are an integral yet understudied component of the coral holobiont. To elucidate their diversity, drivers, and potential functions, we conducted a comprehensive survey of 104 coral samples representing eight genera across three environmentally distinct reef regions in the South China Sea. Utilizing long-read 28S rRNA gene sequencing and a curated multi-source reference database, we significantly enhanced the taxonomic resolution of coral-associated fungi. A total of 15,244 OTUs belonging to fungi were clustered, representing 16 phyla, 61 classes, 84 orders, 117 families, 156 genera, and 187 species. Ascomycota dominated the fungal communities, followed by Basidiomycota and Chytridiomycota. Phylogenetic analyses revealed a deeply divergent fungal lineage distinct from known phyla. Pending further molecular and morphological validation, this lineage is provisionally designated Candidate.Coralgong. For community assembly, host identity explained 11.7% of the variation in fungal community composition (R² = 0.117, p = 0.001), whereas geographic location significantly affected observed OTU richness and Pielou's evenness (p < 0.001) but not overall community composition. Mantel tests likewise revealed no significant associations between fungal community structure and the measured environmental variables. Functional predictions showed that fungal communities comprised major guilds, including animal parasites, fungal parasites, plant pathogens, endophytes, and saprotrophs. Functional community composition was primarily shaped by host identity (R² = 0.183, p = 0.001), whereas geographic effects were comparatively weak. Overall, our results demonstrate strong host-associated structuring, substantial unexplored diversity and conserved functional organization of coral fungal communities, providing a baseline coral mycobiome for future multi-omics and phylogenomic studies.