This study aimed to elucidate the molecular mechanisms underlying phenotypic divergence between two Lentinula edodes strains, Le_L and Le_S, which exhibit distinct fruiting body morphologies. While phenotypic variation among mushroom strains has been widely observed, the relative contributions of transcriptional regulation and structural genomic variation to these differences remain poorly understood. Comparative transcriptome analysis identified 8541 differentially expressed genes (DEGs), revealing clear functional divergence between the two strains. Genes upregulated in Le_S were predominantly enriched in ribosomal components and translation-related processes, indicating enhanced protein synthesis activity. In contrast, Le_L-upregulated genes were associated with transporters, transcription factors, and diverse metabolic pathways, suggesting broader regulatory and physiological functions. Protein–protein interaction network analysis further highlighted distinct regulatory architectures, with ribosomal proteins forming highly interconnected hub gene modules in Le_S, whereas Le_L hub genes were functionally diverse and included multiple members of the Major Facilitator Superfamily (MFS). Ortholog analysis across 33 L. edodes strains demonstrated that most hub genes were conserved, indicating their roles as core genetic components. Despite widespread genome-wide variation, including 7931 SNPs and 1149 INDELs, sequence variation within hub genes was limited, and allele-specific expression analysis revealed no significant allelic imbalance. In contrast, presence–absence variation (PAV) analysis identified structural differences affecting MFS transporter genes, which were absent in Le_S but present and upregulated in Le_L. Collectively, these findings suggest that structural genomic variation, particularly involving transporter genes, may play a more prominent role than sequence-level variation in driving phenotypic divergence. This study provides new insights into the genetic basis of strain-specific traits in L. edodes and highlights the importance of integrating multi-level genomic analyses.

Nutrient use efficiency (NUE) is widely recognized as an important indicator to evaluate the availability (uptake, utilization and recovery) of mineral nutrients. Sorghum-sudangrass hybrid tends to increase in cultivation scale due to vigorous growth and higher yield. Therefore, the aim of this study was to provide the optimal NPK fertilization rates for sorghum-sudangrass hybrid based on nutrient use efficiency and yield. The fertilization rates of N, P 2 O 5 or K 2 O were divided into four levels; 0%, 50%, 100% and 200%. Biomass yield of sorghum-sudangrass hybrid at harvesting stage showed an increasing trend with fertilization levels but was not significantly within treatment groups. Uptake of N or K was significantly increase by fertilization levels of N or K 2 O, whereas P uptake was similar in all P 2 O 5 fertilization levels. NUE was significant in N treatments, whereas P-and K-use efficiency did not differ significantly among different fertilization rates. Consequently, this study suggests that the recommended rates of N (175 kg ha-1), P 2 O 5 (150 kg ha-1), and K 2 O (150 kg ha-1) were optimal for ensuring biomass production and nutrient use efficiency in the sorghum-sudangrass hybrid.