Chromosome-scale genome assembly of Naematelia sinensis (Jin Er mushroom) offers new insights into the distinct mating-type genomes feature and genome evolution.

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Citation abstract

Naematelia sinensis (Jin Er mushroom) is a gelatinous fungus of significant economic and medicinal value indigenous to China. As an obligate parasite that requires Stereum hirsutum for basidiomata formation, it serves as a distinctive model for investigating fungal-fungal interactions. Despite its potential as a source of bioactive polysaccharides, the scarcity of genomic data has impeded research into its secondary metabolism, cultivation, and underlying molecular mechanisms. We employed PacBio HiFi long-read sequencing and Hi-C chromatin conformation capture technology to generate the first chromosome-scale genome assemblies for four distinct mating types of N. sinensis. Genome assembly, annotation, and subsequent comparative genomic, phylogenomic, and gene family evolution analyses were conducted using standard bioinformatics pipelines. The assembled genomes span 20.73-20.82 Mb, resolved into 12 chromosomes with a contig N50 of 1.75-1.76 Mb, a GC content of 51.83-54.58%, and a BUSCO completeness of 96.8-97.1%. Annotation identified 19,390-19,612 repetitive sequences and 6,558-6,578 protein-coding genes. Comparative analysis with the related species Tremella fuciformis revealed extensive chromosomal rearrangements and inversions. The tetrapolar mating system was characterized, with mating-type loci A and B located on separate chromosomes, and elevated polymorphism was observed at the B locus. Phylogenomic analysis estimated the divergence of the Naematelia genus at approximately 154.88 million years ago and indicated a closer relationship between N. sinensis and N.aurantialba than with N. encephala. Gene family analysis highlighted frequent expansions and contractions throughout the evolutionary history of Naematelia, with an overall trend toward contraction. This study provides foundational genomic resources for N. sinensis. The high-quality genomes elucidate its genomes feature, diversity in mating systems, and evolutionary history. These resources will facilitate future research aimed at discovering bioactive compounds, developing cultivation strategies, and conducting broader studies on evolution in parasitic fungi.