Evidence for putative mitochondrial long non-coding RNAs and HEG-derived transcripts in Monilinia laxa from long-read transcriptomics

Abstract The mitochondrial transcriptome of fungi remains poorly characterized beyond protein-coding genes. Using long-read PacBio RNA sequencing, we report the first evidence for putative mitochondria-encoded long non-coding RNAs (lncRNAs) in a fungal organism, discovered in two isolates of the phytopathogenic ascomycete Monilinia laxa . A total of 15 and 12 putative lncRNAs were identified in isolates Ni-B3-A2 and MM-B4-A4, respectively, including sense-strand transcripts and natural antisense transcripts (NATs) positioned upstream of or overlapping core mitochondrial genes. Additionally, putative free-standing transcripts from intergenic homing endonuclease genes (HEGs) are reported for the first time in a fungal species. These findings provide evidence for previously undescribed transcriptional diversity in fungal mitochondria, establishing a framework for future functional investigation of mitochondrial non-coding transcriptomes across the fungal kingdom.