Auricularia heimuer is one of the most popular edible fungi in China. In this study, the whole genome of A. heimuer was sequenced on the Illumina HiSeq X system and compared with other mushrooms genomes. As a wood-rotting fungus, a total of 509 carbohydrate-active enzymes (CAZymes) were annotated in order to explore its potential capabilities on wood degradation. The glycoside hydrolases (GH) family genes in the A. heimuer genome were more abundant than the genes in the other 11 mushrooms genomes. The A. heimuer genome contained 102 genes encoding class III, IV, and V ethanol dehydrogenases. Evolutionary analysis based on 562 orthologous single-copy genes from 15 mushrooms showed that Auricularia formed an early independent branch of Agaricomycetes. The mating-type locus of A. heimuer was located on linkage group 8 by genetic linkage analysis. By combining the genome sequence analysis with the genetic linkage map, the mating-type locus of A. heimuer was located on scaffold45 and consisted of two subunits, α and β. Each subunit consisted of a pair of homeodomain mating-type protein genes HD1 and HD2. The mapping revealed conserved synteny at the whole mating-type loci and mirror symmetry relations near the β subunit between A. heimuer and Exidia glandulosa. This study proposed the potential for the bioethanol production by consolidated bioprocessing of A. heimuer. It will promote understanding of the lignocellulose degradation system and facilitate more efficient conversion of the agricultural wastes used for mushroom cultivation. It also will advance the research on the fruiting body development and evolution of A. heimuer.

The cultivation of Auricularia heimuer, a species of edible mushroom, heavily relies on the availability of wood resources serving as substrate for the growth of the species. To ensure the sustainable development of the A. heimuer industry and optimize the utilization of corncob as a substrate, this study sought to investigate the potential use of corncob as a substrate for the cultivation of A. heimuer. The purpose of this study was to explore the utilization of corncob lignocellulose by A. heimuer at the mycelium, primordium, and fruiting stages, by specifically examining the expression profiles of both carbohydrate-active enzymes (CAZymes) and the transcriptome of differentially expressed genes (DEGs) relevant to corncob biomass degradation. The results revealed 10,979, 10,630, and 11,061 DEGs at the mycelium, primordium, and fruiting stages, respectively, while 639 DGEs were identified as carbohydrate-active enzymes. Of particular interest were 46 differentially expressed CAZymes genes that were associated directly with lignocellulose degradation. Furthermore, the study found that A. heimuer exhibited adaptive changes that enabled it to effectively utilize the cellulose present in the corncob. These changes were observed primarily at the primordium and fruiting stages. Key genes involved in lignocellulose degradation were also identified, including g6952, g8349, g12487, and g2976 at the mycelium stage, g5775, g2857, g3018, and g11016 at the primordium stage, and g10290, g2857, g12385, g7656, and g8953 at the fruiting stage. This study found that lytic polysaccharide monooxygenase (LPMO) played a crucial role in the degradation of corncob cellulose, further highlighting the complexity of the molecular mechanisms involved in the degradation of lignocellulose biomass by A. heimuer. The study sheds light on the molecular mechanisms underlying the ability of A. heimuer to degrade corncob biomass, with implications for the efficient utilization of lignocellulose resources. The findings from this study may facilitate the development of innovative biotechnologies for the transformation of corncob biomass into useful products.

Auricularia heimuer is a wood-rotting edible mushroom, and with the continuous development of the industry, the research on its grass-rotting cultivation is becoming more and more important. In this study, A. heimuer was cultivated using herbaceous substrate (reed) completely replacing the traditional woody substrate (oak), and the correlation between the relative expression of cellulase gene, cellulase activity, cellulose degradation and yield of different strains of A. heimuer were studied by combining qRT-PCR technology at different growth stages. The results showed that the cellulose degradation were positively correlated with the yield of reed and sawdust substrate at two growth stages, and were positively correlated with three cellulase activities. The relative expression of four cellulase genes were positively correlated with enzyme activity. There were inter-strain differences in the expression of the enzyme genes, which were basically consistent with the trend of the enzyme activity of the strains; g5372 and g7270 were more actively expressed in the mycelium period, while g9664 and g10234 were more actively expressed in the fruiting period. The results of SEM showed that the mycelium of A15 and A125 were different in their ability to degrade and utilize lignocellulose in reed substrate. The parental hybridization test further verified that qRT-PCR could be used as a rapid method to evaluate the cellulose degradation ability of A. heimuer strains. Seven strains (A12, A15, A184, A224, Z6, Z12, and Z18) with high cellulose degradation ability were screened. This study provides a reference for further understanding the role of A. heimuer cellulase genes in the degradation and metabolism of cellulose and for breeding new varieties more suitable for herbaceous substrate cultivation.

Auricularia heimuer is a widely cultivated jelly mushroom. The fruiting bodies are categorized into cluster and chrysanthemum types. With changing consumer demands and the need to reduce bio-waste, the demand for clustered fruiting bodies is increasing. Therefore, gene mining for fruiting body types is a matter of urgency. We determined that the A. heimuer locus for fruiting body type was located at one end of the genetic linkage map. The locus was localized between the markers D23860 and D389 by increasing the density of the genetic linkage map. BlastN alignment showed that the marker SCL-18 was also located between D23860 and D389, and a total of 25 coding genes were annotated within this interval. Through parental transcriptome analysis and qRT-PCR verification, the locus g7219 was identified as the gene controlling the fruiting body type. A single-nucleotide substitution in the TATA box of g7219 was detected between the parents. By PCR amplification of the promoter region of g7219, the TATA-box sequences of the cluster- and chrysanthemum-type strains were found to be CATAAAA and TATAAAA, respectively. This study provides a foundation for the breeding of fruiting body types and strain improvement of A. heimuer.

Substrate type exerts a critical influence on the growth, development, and nutritional quality of Auricularia heimuer. In this study, agricultural waste-derived corncob was used as the treatment group (T1), with sawdust serving as the control (CK), to systematically investigate the variation in free amino acid (FAA) content and transcriptomic expression profiles in fruiting bodies of A. heimuer under the two substrate conditions. Principal component analysis (PCA) revealed a clear separation between CK and T1 samples in terms of FAA composition, indicating that substrate type significantly affects FAA profiles. The corncob substrate notably increased the total FAA content in A. heimuer (2624.57 mg/kg), representing an 11.4% elevation compared to the sawdust group (2355.86 mg/kg), and markedly enhanced the proportion of flavor-associated amino acids (49.2% vs. 42.6%). In particular, the umami amino acid content was 74% higher than in the CK group. Transcriptome analysis identified 20 differentially expressed genes associated with FAA biosynthesis and degradation, including key enzymes involved in umami amino acid metabolism, such as aspartate decarboxylase (ADC), glutamate decarboxylase (GAD), and glutamate N-acetyltransferase (GNA), which were downregulated in T1. This suggests that glutamate and aspartate may have accumulated due to suppressed catabolism. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis further indicated that the differentially expressed genes were significantly enriched in pathways related to branched-chain amino acid metabolism, carbon metabolism, and secondary metabolism. Collectively, these findings demonstrate that corncob substrate significantly alters the accumulation and metabolic profile of FAAs in A. heimuer by modulating the expression of key metabolic enzymes, providing a theoretical foundation for the efficient cultivation of A. heimuer using agricultural waste and for enhancing its flavor quality.

Mitochondria play a pivotal role in fungal growth, development, and metabolic regulation, yet their significance has often been overlooked in traditional breeding programs. Auricularia heimuer, the second most widely cultivated edible fungus in China, has attracted increasing attention due to its nutritional and health-promoting properties, underscoring the urgent need for the development of functional cultivars and the elucidation of mitochondrial regulatory mechanisms. In this study, we constructed isonuclear alloplasmic strains with identical nuclear genotypes but distinct mitochondrial backgrounds. Comparative analyses of mycelial growth, fruiting body morphology, and nutritional composition were conducted, alongside transcriptomic profiling. The results showed no significant morphological differences on sawdust-based medium; however, on PDA medium, the strains exhibited notable differences in growth rate, melanin content, β-glucan levels, iron ion concentration, and amino acid content. Transcriptomic analysis identified 3385 differentially expressed genes (DEGs), which were enriched in pathways related to lysine biosynthesis, purine metabolism, DNA replication, and repair. Key DEGs involved in lysine biosynthesis were found to encode aminoadipate reductase (AAR) and saccharine dehydrogenase (SDH), with AAR localized in the cytoplasm and potentially regulating lysine synthesis through its enzymatic activity. This study highlights the critical influence of mitochondrial genes on the metabolic composition and transcriptional landscape of A. heimuer, providing a theoretical foundation for genetic improvement and the development of functional fungal cultivars.