Transcriptional variation and RNA polymorphism among different Lentinula edodes (Berk.) Pegler strains.

Background: Lentinula edodes is a commercially important mushroom known for its nutritional and therapeutic values. However, the molecular mechanisms underlying the distinct nutritional and physiological attributes of various L. edodes strains are not well understood. This study focused on three Lentinula strains (DMRO-356, DMRO-623, and DMRO-388s) with different nutritional and productivity profiles. Illumina sequencing was used to perform a whole-transcriptome analysis, conducting 100-base pair paired-end sequencing of total messenger RNA (mRNA) in duplicate, resulting in 28-48 million sequencing reads per strain. After rigorous data filtering, over 99% of high-quality reads were retained, and more than 95% were aligned to the Lentinula genome.

Results: Differential gene expression analyses identified 2210 differentially expressed genes between DMRO-356 and DMRO-623, 862 between DMRO-356 and DMRO-388s, and 2212 between DMRO-623 and DMRO-388s. Significant genetic variations were found among the strains, including 7753 single nucleotide polymorphisms (SNPs) in DMRO-356 versus DMRO-623 and 4080 SNPs in DMRO-356 versus DMRO-388s. Additionally, 349 insertions/deletions (InDels) were found in DMRO-356/DMRO-623 and 218 in DMRO-356/DMRO-388 s. Non-synonymous SNPs, which alter amino acid compositions, were analyzed, showing a preference for polar over charged amino acids.

Conclusion: These differentially expressed genes were associated with various nutritional and developmental processes, highlighting the importance of genetic variations in shaping amino acid composition and potentially affecting protein function. This study is the first comprehensive exploration of transcriptional differences among Lentinula strains available for its cultivation, providing valuable insights to enhance mushroom quality and productivity. © 2024 Society of Chemical Industry.