Haploid Genome Analysis Reveals a Tandem Cluster of Four Genes Involved in the High-Temperature Adaptation of

Coriolopsis trogii is a typical thermotolerant basidiomycete fungus, but its thermotolerance mechanisms are currently unknown. In this study, two monokaryons of C. trogii strain Ct001 were assembled: Ct001_29 had a genome assembly size of 38.85 Mb and encoded 13,113 genes, while Ct001_31 was 40.19 Mb in length and encoded 13,309 genes. Comparative intra- and interstrain genomic analysis revealed the rich genetic diversity of , which included more than 315,194 single-nucleotide polymorphisms (SNPs), 30,387 insertion/deletions (indels), and 1,460 structural variations. Gene family analysis showed that the expanded families of were functionally enriched in lignocellulose degradation activities. Furthermore, a total of 14 allelic pairs of heat shock protein 20 () genes were identified in the genome. The expression profile obtained from RNA sequencing (RNA-Seq) showed that four tandem-duplicated allelic pairs, to , had more than 5-fold higher expression at 35°C than at 25°C. In particular, and were the most highly expressed genes. Allelic expression bias was found for and ; the expression of was at least 1.34-fold higher than that of , and that of was at least 1.5-fold higher than that of . The unique structural and expression profiles of the genes revealed by these haplotype-resolved genomes provide insight into the molecular mechanisms of high-temperature adaptation in . Heat stress is one of the most frequently encountered environmental stresses for most mushroom-forming fungi. Currently available fungal genomes are mostly haploid because high heterozygosity hinders diploid genome assembly. Here, two haplotype genomes of , a thermotolerant basidiomycete, were assembled separately. A conserved tandem cluster of four genes showing allele-specific expression was found to be closely related to high-temperature adaptation in . The obtained haploid genomes and their comparison offer a more thorough understanding of the genetic background of . In addition, the responses of genes at 35°C, which may contribute to the growth and survival of at high temperatures, could inform the selection and breeding of elite strains in the future.