Exploring the polymorphism and origins of accessory chromosomes in Tremella fuciformis: insights into genome divergence and structural variation

Accessory chromosomes, while not essential for normal growth and development, have been extensively studied in Ascomycota fungi, but their presence in basidiomycetes is less documented. In this study, whole-genome sequencing was conducted on 16 strains of Tremella fuciformis from diverse sources, resulting in 27 complete haplotype genome sequences for comparative analysis. These genomes showed significant size variation, exceeding one-third, mainly due to accessory chromosomes and repetitive sequences in core chromosomes. They contain 8 to 10 core chromosomes, and their polymorphism is mainly caused by the fusion or separation of chromosomes. Each genome contained between 2 to 10 accessory chromosomes, totaling 107, with their distribution reflecting phylogenetic relationships and mating specificity with Annulohypoxylon stygium. Accessory chromosomes were small, rich in transposons or repetitive sequences, and had lower gene densities, yet their homology similarity was notably higher than that of core chromosomes. They exhibited rapid and diverse structural variations (SVs), resulting in a lower proportion of shared genes within each branch compared to core chromosomes. Both accessory and core chromosomes showed a high frequency of chromosomal copy number variation during the growth and transformation of the two morphological cell types. Most genes on the accessory chromosomes were not homologous to those on the core chromosomes, and the proteins they encode lacked matching sequences in the NCBI nr database. This research is the first to reveal the diversity of accessory chromosomes in Basidiomycota, providing new insights into their origin, as they are believed to have originated from unexplored species before the speciation of T. fuciformis.