Multiple genomically independent genotypes of Ophiocordyceps sinensis may not be targets of RIP mutagenesis causing cytosine-to-thymine transitions

Abstract

It has been hypothesized that AT-biased genotypes of Ophiocordyceps sinensis are generated through repeat-induced point mutation (RIP) and coexist as ITS pseudogenes in the Hirsutella sinensis genome. This study examined the H. sinensis genome, which contains multiple GC-biased repetitive ITS copies with multiple insertion/deletion and transversion alleles; these alleles are not generated through RIP, which causes cytosine-to-thymine transitions. The repetitive ITS copies are genetically and phylogenetically distinct from the AT-biased genotypes of O. sinensis, which possess multiple transition alleles. Genotypes #2-17 are absent from the H. sinensis genome; these genotypes belong to independent O. sinensis fungi and occur in various combinations in different compartments of natural Cordyceps sinensis. Their abundances are dynamically altered in an asynchronous and disproportional manner during C. sinensis maturation. Metatranscriptomic analyses of natural C. sinensis revealed the transcriptional silencing of 5.8S genes in all C. sinensis-colonizing fungi, including H. sinensis. The transcription assay reported by Li et al. (2013) has provided incomplete, controversial evidence to support the notion that the 5.8S genes of AT-biased O. sinensis genotypes are permanently nonfunctional pseudogenes. In parallel with GC-biased genotypes, AT-biased genotypes might have been generated from a common ancestor during a long evolutionary history.