 21 small nuclear RNAs (snRNAs). Likewise, the ASM genome contained 38 miRNAs, 138 tRNAs, 33 rRNAs and 19 snRNAs. According to the de novo and homology-based prediction methods, a total of 17,591 and 16,402 protein-coding genes were predicted for the AC1 and ASM genomes, respectively ( Table 1). The average length of the coding sequences in the AC1 genome was 1,618 bp, which contained five exons with an average length of 308 bp, while those of in the ASM genome exhibited an average length of 1,218 bp containing an average of four exons with an average length of 284 bp. A total of 16,569 (94%) and 10,930 (67%) genes in the AC1 and ASM genomes were homologous to known proteins in the eight databases (Supplementary Table S2).
We then identified a total of 4,168 and 2,663 SSR loci in the AC1 and ASM genomes, respectively. The density of SSR loci was similar among these two genomes, after accounting for differing genome sizes. Trinucleotide repeats (TNR) were the most common type accounted for 40% of the total loci in the two genomes (Supplementary Table S3), followed by dinucleotide repeats (DNR, 29-40%). The other types were only individually accounted for 2-4% of the total genome sizes. Tandem repeats with five repeats were the most common TNR repeat types in the two genomes, followed by tandem repeats with six repeats of DNR and TNR. Among SSR types, CG, CCG, TACC, GGTTA, ACGGCG, and CTCTTC were the most prevalent forms for corresponding repeat types in the AC1 genome, while GC, CAG, GGTA, CCTAA and CCGCAG were most prevalent in the ASM genome.

Comparative Genomic and Evolutionary Analysis for A. cornea and A. heimuer
The assembled size of AC1 genome was 73.48 Mbp larger than ASM (49.76 Mbp). A total of 4,163 single copy genes ( Figure 1C) and 5,486 homologous gene families were shared by AC1 and ASM, while 990 and 460 unique gene families were specific to each genome, respectively ( Figure 1B). Analysis of collinear genomic regions between AC1 and ASM revealed very few conserved syntenic blocks (10.60 Mbp) between the two genomes, which was accounting for 14 and 21% in AC1 and ASM, respectively (Figure 2).
To further understand the genomic evolution of A. cornea and A. heimuer, we selected 19 reported fungal genomes presenting three class, eight orders, 12 families to conduct the phylogenetic analysis. A total of 56 single-copy orthologous genes were shared among these 21 genomes, which were consequently used to construct a phylogenetic tree with the maximum likelihood (ML) method. The phylogenetic analysis indicated that four species in Auriculariales were clustered in one branch. Among them, three species in genus Auricularia were clustered as a subgroup, which A. cornea was most closely related to A. subglabra and then clustered with A. heimuer. The divergence time of Tremellomycetes and Agaricomycetes was estimated as ∼298.  (Figure 3). Further, a total of 738 gene families were significantly expanded in the A. cornea genome (p < 0.05), while only two gene families were significantly contracted. The expanded genes of A. cornea were mostly related to catalytic activity, metabolic processing, and proteins with binding functions, while the contracted genes were glucose repression regulatory protein TUP1 and WD40 repeat protein. With positive selection analysis, a total of 73 and 99 candidate genes were identified in A. cornea and A. heimuer, respectively (P < 0.01). Compared with A. heimuer, more genes in A. cornea were related to temperature adaptability, such as cellular response to oxidative stress, fungal-type cell wall organization, signal transduction, oxidation-reduction process, DNA repair/transcription protein, phosphatase activator activity, HSP70-domain-containing protein. These genes might play a crucial role in the regulation of A. cornea in adapting more higher temperature than A. heimuer.

Implications for Biomass Decomposition by CAZyme Families
To evaluate the composition of CAZymes used in biomass degradation by AC1 and ASM, we identified the predicted protein sequences of the two genomes to the CAZyme database. AC1 possessed 460 CAZyme genes higher than ASM (316), which both contained GH, AA, PL, GT, CE, and CBM families (Supplementary Table S4 and Supplementary Figure S1). Among these, GHs and AAs were most abundant in the AC1 and ASM genomes and are primarily involved in the degradation of cellulose, hemicellulose, lignin, chitin, pectin, and starch in agroindustrial wastes. A total of 240 and 83 genes encoded GHs and AAs in the AC1 genome, respectively, while 169 and 42 were present in that of ASM, respectively. Twenty-seven expanded GH gene subgroups were identified in the AC1 genome compared to that for ASM, which included cellulose-degrading GHs (GH5, GH6, GH7, and GH12), hemicellulose-degrading GHs (GH10 and GH43), pectin-degrading GHs (GH28 and 105), chitindegrading GHs (GH18) and starch-degrading GHs (GH31 and GH133). All AA subgroups were belonged to expanded gene families in AC1 compared to ASM. In particular, more than twice the number of AA genes encoding AA3, AA6, and AA9 were present in the AC1 genome compared to that of ASM. The numbers and types of gene encoding GTs, PLs, and CEs were similar in both AC1 and ASM genomes. Most of the CBMs observed in the two genomes were present in the N-terminal or C-terminal regions of the GH, AA, and CE family proteins. For example, genes encoding CEs and AAs contained an additional CBM1 region including CE5, CE1, CE15, AA9, and AA8 (AA12). In addition, genes encoding GHs exhibited more diversity of additional CBMs including CBM1 in GH7 and GH6, CBM5 in GH18, and CBM35 in GH43. Moreover, many CAZyme genes identified as belonging to the same subgroup were clustered in the AC1 genome. For example, two, five, and five genes encoding CE5, AA3, and GH16 genes were clustered on contigs 16, 19, and 18 of the AC1 genome, respectively.

Genes Involved in Secondary Metabolite Biosynthesis
Terpenoids are one of the primary types of secondary metabolite (SM), which are pharmacologically active in A. cornea. To identify genes involved in terpenoid biosynthesis, we blasted  the protein coding genes against the antiSMASH database. A total of 21 and four terpene gene clusters were identified in the AC1 and ASM genomes, respectively. Of these, one gene encoding lanosterol synthase associated with the biosynthesis of the triterpenoid ganoderic acid was shared between the AC1 and ASM genomes. Further, KEGG annotation of all predictedproteins in the AC1 genome was yielded 26 genes encoding 18 enzymes involved in terpenoid backbone biosynthesis (ko00900) through the mevalonate pathway. Three genes encoding farnesyltransferase, squalene monooxygenase, and a squalene-hopene/tetraprenyl-β-curcumene cyclase involved in triterpenoid biosynthesis were also identified in the AC1 genome. In addition, we identified three genes encoding a trichodiene synthase participated in sesquiterpenoid biosynthesis.
We also identified Cytochrome P450 (CYP) genes associated with terpenoid biosynthesis and other fungal SMs in the AC1 genome. A total of 187 putative CYP sequences comprising 62 families were identified in the AC1 genome by querying the Fungal Cytochrome P450 Database. Among these, five genes in the CYP5144 family were predicted to be involved in triterpenoid biosynthesis. Furthermore, a number of genes were identified from CYP families that may have potential roles in fungal secondary metabolism including CYP51 (sterol 14α-demethylase) and CYP53 (benzoate 4-hydroxylase). Overall, the CYP505 family was the most abundant within the AC1 genome, comprising 17 genes that are associated with the degradation of plant cuticles in plant-associated fungi.

Genomic Variation Among A. cornea and A. heimuer Populations
To investigate genomic variation among and within A. cornea and A. heimuer populations, we performed whole genome resequencing of 24 Wood Ear strains including 12 A. cornea and 12 A. heimuer strains. A total of 59.19 Gbp high-quality clean data were generated on the Illumina HiSeq platform, with average depth for each strain of 23×. We firstly performed the estimation of genomic variation among A. cornea and A. heimuer populations. Using the AC1 genome as a reference, after quality filtering, the overage rates of all 12 A. cornea strains were ranged from 79-99%, while that for the 12 A. heimuer strains were only 23-27% (Supplementary Figure S2A and Supplementary  Table S5). Using the ASM genome as a reference, the coverage rates of all 12 A. heimuer strains were 87-94%, while that for the 12 A. cornea strains were only 19-21% (