Mitochondrial genome and transcription of Shiraia-like species reveal evolutionary aspects in protein-coding genes

Shiraia-related species are well-known bambusicolous fungi in Dothideomycetes class, with high value in traditional medicine for producing hypocrellin, as an anticipated photosensitiser. The complete mitogenomes of hypocrellin-producing Pseudoshiraiaconidialis strains were analysed in the present study, with functional gene variations through comparative genomics and transcriptomics. Five strains (ZZZ816, CNUCC1353PR, JAP103846, CNUCC C72, CNUCC C151) were sequenced, which indicated similar genome characteristics. Two of them possess an extra atp6 gene, and the associated variable fragment "HSP1-HSP2-atp6_2" correlates closely with hypocrellin production capacity. Therefore, these five strains were divided into three groups: ZZZ816 and CNUCC1353PR possessing high production efficiency, CNUCC C72 and JAP103846 with low yield and CNUCC C151 as a transition type. The gene expression changes were screened under various conditions. ZZZ816-related species showed significant changes in mitochondrial genes, especially HSP1, HSP2 and atp6_2, linked closely to hypocrellin synthesis and stress response; rps3 expression also consistently correlated with hypocrellin production. JAP103846 group showed a stable expression pattern divergently, except for rps3 suppression by blue light. These findings would provide new insights into secondary metabolite regulation and ROS resistance. Above all, this study conducted the comprehensive analysis of Shiraia-like fungi mitogenomes and functional gene expression, which can update the understanding of fungal evolution and potential for improved hypocrellin production.