Conclusions

SMRT sequencing was applied to characterize the O.sinensis mt genome in order to mitigate problems with assembly due to high AT and repeat content of the mt genome.The phylogenetic tree inferred from 14 PCGs supports the phylogenetic position of O.sinensis in Ophiocordycipitaceae.A total of 36 sequence sites were explored with the values of d N/dS＞1，suggesting that positive selection acts on rps3 in Hypocreales fungi.Furthermore，we have analyzed the DNA modification pattern of the mitogenome directly.This is the first report of methylation in a fungal mitochondrion，and we propose that methylations in the O.sinensis mt genome might closely relate with the environmental responses for adapting to the cold and low PO2 environments at high altitude sites where O.sinensis is endemic.

Abbreviations(https://www.daowen.com)

PCGs：protein-coding genes；SMRT：single molecule，real-time；ML：maximum likelihood；BI：Bayesian inference；NJ：neighbor-joining；d N：nonsynonymous substitution；dS：synonymous substitution；HE：homing endonuclease；modQV：modification quality values；OXPHOS：oxidative phosphorylation；SSRs：Simple sequence repeats.