The complete mitochondrial genome of the Chan‐hua fungus Isaria cicadae: a tale of intron evolution in Cordycipitaceae

Abstract

Summary Isaria cicadae is an entomogenous fungus of great medicinal value. Its nuclear genome has been reported, while its mitogenome remains unknown. Herein, we first described its mitogenome and then inferred intron evolution from both intraspecific and interspecific perspectives. The fungus represented the largest mitogenome (56.6 kb in strain CCAD02) known in Cordycipitaceae due to the presence of 25 introns interrupting nine genes. Comparison of three I. cicadae strains revealed intron presence/absence dynamics at six intron loci plus a few indels and single nucleotide polymorphisms. Phylogenetic analyses confirmed the placement of I. cicadae in Cordycipitaceae. Comparison of 10 Cordycipitaceae species revealed a high degree of synteny and conserved genetic content. They, however, varied in intron numbers (1–25 per species) with overall 34 intron loci identified, which resulted in more than twofold variations in mitogenome sizes (24.5–56.6 kb). An rnl intron encoding ribosomal protein S3 was present in all species, suggesting its early invasion in Cordycipitaceae, while further divergence occurred for this intron. The other introns identified in this study were present in some, but not all of the species and have undergone multiple gains and losses in Cordycipitaceae. This study greatly enhanced our understanding of intron evolution in Cordycipitaceae.

The complete mitochondrial genome of medicinal fungus Taiwanofungus camphoratus reveals gene rearrangements and intron dynamics of Polyporales

“…The dynamic changes of these introns contributed to variations of mitochondrial genome size and organization. Introns were considered to be a mobile genetic element 65 , while homologous introns had the same insertion site in the coding region of PCGs 43 . The same Pcls had high sequence similarities, while different Pcls showed low similarities in nucleotide sequences.…”

Large inverted repeats identified by intra-specific comparison of mitochondrial genomes provide insights into the evolution of Agrocybe aegerita

“…According to RNA secondary structures, the introns are classified into two major groups [9] . Group I introns, predominant in fungal mitochondrial genomes [10] , are further clustered into several sub-groups [9] . ORFs in group I introns are usually homing endonuclease genes (HEGs) functioning for transfer and site-specific integration of their host introns.…”

“…These features make it suitable for distinguishing closely related species or even intra-specific isolates, as well as deduction of recent evolutionary events. Intra-specific mtDNA comparison has been used in fungal species such as Cordyceps militaris [24] , Schizosaccharomyces pombe [25] , Isaria cicadae [10] , and Colletotrichum lindemuthianum [26] . These studies provided new insights into population evolution, identification of highly polymorphic regions, and isolate-specific markers [24] .…”

Complete mitogenome of the entomopathogenic fungus Akanthomyces lecanii

“…For the two neighboring gene pairs, nad2/nad3 and nad4L/nad5, corresponding genes overlap by one nucleotide, which is characteristic of Cordycipitaceae (Fan et al 2019). Not an intergenic free-standing ORF is identified.…”