Introduction

Ophiocordycepssinensis(syn.Cordycepssinensis)is an entomopathogenic fungus that infects larvae of Hepialidae ghost moths to form a parasitic complex called“Dong-Chong XiaCao”in Chinese(Commission，2015).“DongChongXiaCao”is a Traditional Chinese Medicine treatment that has been used for thousands of years for respiratory，renal，liver and cardiovascular diseases，hyposexuality and hyperlipidemia(Zhu et al.，1998；Yue et al.，2013).Ophiocordyceps sinensis is endemic to alpine regions on the Tibetan Plateau，with 3000 m as the lowest altitude for the distribution(Li et al.，2011).This fungus is rare in natural resources because of its strict host-specificity，limited geographical distribution and over-exploitation in recent decades(Li et al.，2011).

The mitochondrion is a cellular organelle that is required for respiratory metabolism and ATP production.In the mitochondrion，ATP synthesis is catalyzed by five mitochondrial inner membrane-bound enzyme complexes(Complexes Ⅰ-Ⅴ)(Saraste，1999；Chandel and Schumacker，2000).Complexes Ⅰ-Ⅴare NADH-ubiquinol oxidoreductase，succinate-ubiquinol oxidoreductase，ubiquinol-cytochrome C oxidoreductase，cytochrome C oxidase and ATP synthase，respectively.The mt genome encodes for 7 subunits of Complex I(NAD1～6，NAD4L)，1 subunit of ComplexⅢ(COB)，3 subunits of ComplexⅣ(COX1～3)，and 3 subunits of Complex V(ATP6，ATP8 and ATP9)(Saraste，1999).In addition to the genes encoding oxidative phosphorylation(OXPHOS)proteins，2 r RNA subunits and a set of tRNA genes are included in the fungal mt genome.Gene content is highly conserved in mitochondria of various fungi，but some characteristics，such as gene order，tRNA gene clusters，intergenic regions，mobile elements and introns，can be highly variable(Ghikas et al.，2006；Aguileta et al.，2014；Losada et al.，2014；Mardanov et al.，2014).As of December 2016，there were 179 Ascomycota mt genomes submitted to Genbank，and Sclerotinia borealis(NC_025200，203051bp)had the largest mt genome(Mardanov et al.，2014)(https：//www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi？opt=organelle&taxid=451864).Due to its small size，fast evolution，high copy number，and relatively conserved gene content，the mt genome has been successfully used in evolutionary biology and phylogeny(Vinita Joardar1 et al.，2012).

The present understanding of the mt epigenome has gone through a series of evolutions，and conflicting data about epigenomes existed in the 1970s and early 1980s due to the uneven distribution of methylation patterns and low sensitivity of detection methods(Castegna et al.，2015).A few studies have shown mt methylation while others have reported the absence of any methylation in the mitochondrion(Cummings et al.，1974；Dawid，1974；Groot and Kroon，1979；Pollack et al.，1984).The advent of next generation sequencing technologies has provided opportunities for characterizing mt genomewide cytosine methylation.In 2014，Ghosh et al.reported the first genome-wide map of human mitochondrial methylation(Ghosh et al.，2014).In 2016，Ghosh et al.revealed that it was dynamic in nature of the hydroxymethly cytosine marking in the human mitochondrial genome(Ghosh et al.，2016).However，little trace of DNA modification on mtDNA is detected in fungi.The current methodologies for epigenomics，based on bisulfite，enrichment，or sequencing and PCR，impede the processing of the epigenetic study due to the limits in the resolution，modification type，locus and cost(Mensaert et al.，2014).(https://www.daowen.com)

Single molecule，real-time(SMRT)sequencing has created significant progress in read length and sequencing of base modification sites(Flusberg et al.，2010；Feng et al.，2013).SMRT sequencing can produce read lengths of up to 40 kb and direct sequencing of base modification.The most important characteristics of SMRT sequencing are that SMRT sequencing(1)could be free from amplification biases and(2)easily sequenced the complex regions containing secondary structure in low coverage(Koren et al.，2013).DNA modifications across the genome could be directly determined by the kinetics of DNA synthesis，because SMRT sequencing monitors the processing of single DNA molecules by DNA polymerase(Eid et al.，2009；Feng et al.，2013).The biggest concern in SMRT sequencing is the relatively high error rate，which can be effectively decreased through multiple sequencing passes.Long reads and a circular consensus sequencing strategy make SMRT convenient for：de novo assembly of mitochondria，chloroplasts，and microbial genomes，especially for complex genomes；characterizing genomic structural variations；and analyzing targeted sequencing regions or modification sites(Carneiro et al.，2012；Grad et al.，2012；Chin et al.，2013；Feng et al.，2013；Koren et al.，2013).

In the current study，we sequenced themt genome of wild fungus O.sinensis using SMRT sequencing technology on a PacBio RSⅡsequencing platform.We described the gene content and genomic organization of this high-altitude fungus，and performed a comparative analysis with the sequenced Hypocreales mt genomes.The main focus in this study is on the mitogenome-wide epigenetic DNA modification pattern of O.sinensis.This is the first report on epigenetic modifications in a fungal mt genome，and it will provide the basis for further research on mt epigenetics of Hypocrealean fungi.