Telomere-to-Telomere Genome Assembly of Tremella sanguinea Corroborates Its Placement in Phaeotremella and Dates Its Divergence (Tremellales)

Tremella sanguinea is a morphologically distinctive gelatinous mycoparasite of Stereum within Tremellales whose generic placement has remained unresolved for lack of high-quality genomic resources. We combined Oxford Nanopore long-read sequencing, short-read whole-genome sequencing and Hi-C chromatin conformation capture to assemble the first telomere-to-telomere (T2T) genome of this species: 21.44 Mb in nine gap-free chromosomes, with telomeric repeats recovered at all 18 chromosome ends. Phylogenomic analysis of nine Tremellales genomes, including the type species of Phaeotremella, placed T. sanguinea within Phaeotremella as sister to P. skinneri (divergence 24.50 Ma; 95% HPD 22.14–26.89) rather than within Tremella sensu stricto, corroborating at genome scale a placement previously indicated by multi-locus data, providing the first divergence-time estimates for the lineage, and reconciling its position with its dark, foliose basidiocarp morphology. Gene family evolution was contraction-biased, most strongly at the Phaeotremella crown node (92 expansions vs. 855 contractions). The carbohydrate-active enzyme repertoire of T. sanguinea (185 genes) fell within the range reported for Tremellales, whereas families that expanded on its branch were significantly enriched for transport functions, including dipeptide and allantoate transport. These results indicate that T. sanguinea acquires host-derived nutrients through uptake of small molecules rather than through an expanded hydrolytic repertoire, and provide genomic evidence for revising its generic placement within the segregate genera of Tremella sensu lato.