3.1 Characteristics of the O.sinensis mt genome
The complete mt genome of O.sinensis was a circular double-stranded DNA molecule with 157，539bp in length(Table 1，Fig.1，GenBank accession number：KY622006)，which is similar to the O.sinensis mt genome(157，510bp)reported by Li et al.(2015)and much larger than the other fungi in the same order Hypocreales(Table 1).The size variation of mt genome was caused by the length of intergenic regions，and the number，length of introns and accessory genes(Table 1)(Deng et al.，2016).Although the mtDNA size is in large variation(25，615-157，539bp)，the gene content slightly differed in Hypocreales(Table 1).There were 14 PCGs，1 rps3，27 tRNAs，and 2 rRNA subunits encoded in the mt genome.All protein and RNA coding genes were located on positive strand and orient clockwise(Fig.1，Table 2).In addition，there were 73 ORFs coding putative proteins in the O.sinensis mt genome(Table 1).
Table 1 Characteristics of mt genomes of Hypocreales fungi
Fig.1 Circular map of the O.sinensis mt genome
The scales indicate location in kb，starting with rnl.Using Circos and CLC Sequence Viewer，we integrated the gene annotation，DNA base modification，and some other information.From outermost to innermost：ring 1 with dingy yellow is CDS.Ring 2 includes protein-coding genes(lasureous)，rRNAs(blue)and tRNAs(red).ORFs are located on ring 3.Rings 4 and 5 show DNA base modifications sites in the forward and backward strand，respectively.Red lines indicate 4mC，blue lines show 6mA，while grey lines represent the other base modifications.Ring 6 with light blue as background color is the methylations for both strands in a 200bp sliding window.Red lines in the Ring 6 mean that the number of the methylation sites in the sliding window is over 10.The ribbons inside the circle connect the repeat sequences with significant(e-value＜10—7)similarity(red：identity≥90；yellow：90＞identity≥80；green：80＞identity≥70；grey：identity＜70).
In the O.sinensis mt genome，the 14 PCGs included 7 NADH dehydrogenases(nad1-nad6，nad4L)，3 cytochrome c oxidases(cox1～cox3)，3 ATP synthases(atp6，atp8，atp9)，and 1 cytochrome b gene(cob)，for encoding proteins involved in respiratory chain complexes.In addition，a rps3 gene which encodes 40S ribosomal protein S3 was found in the intron of rnl(rnl_I8).The majority of the PCGs were split by several introns into multiple short exons(Fig.1).The introns(n=54)covered ca.67.64%of the whole mt genome，with the highest number in cox1 gene(n=14).The intergenic regions have a total length of 29，350bp，accounting for 18.63% of the whole genome length(Table 1).The whole A+T content of the mt genome was 69.8%(Table 1)，consistent with the characteristic of AT-rich in the Hypocreales fungal mt genome，ranging from 69.0%to 73.5%(Table 1).
All PCGs began with a canonical start codon ATG or GTG(Table 2)and most terminated with the stop codon TAA，except cox1，cox3，and rps3.As revealed in many fungi，the ATG initiation codon of nad5 followed immediately after the termination codon of nad4L，with an overlap of a base“A”；the genes of nad2 and nad3 were uninterrupted(Kouvelis et al.，2004；Shen et al.，2015).The codon frequency analysis showed that a total of 63 codons were used for transcription，with the absence of CGC.The six most frequently used codons(TTA，ATA，TTT，AAT，TAT，and AAA)reflect the biased usage of A/T nucleotides.The fraction of codons encoding the hydrophobic amino acids(Met，Trp，Phe，Val，Leu，Ile，Pro，Ala，accounting for 42.59%)could explain the hydrophobic nature of respiratory membrane complexes(https://www.daowen.com)
Table 2 Annotation of conserved PCGs and rRNA genes of O.sinensis mt genome.
Continued table
A total of 27 tRNA genes were identified in the mt genome of O.sinensis coding for all 20 amino acids(Table 3)，alleviating the need for tRNA import into the mitochondrion from the cytoplasm(Kolesnikova et al.，2000).The presence of tRNA-W recognizing the UGA codon indicates that the O.sinensis mt genome is translated according to genetic code 4(Fox，1987).As a unique characteristic of Hypocreales mtDNAs，most of the tRNA genes in O.sinensis were organized into three clusters with minor differences，except for 5 tRNAs scattered as a single gene across the mt genome(Fig.1).The single tRNA genes were suggested to play a role in transcription or recombination events(Saccone et al.，2002).
Table 3 Transfer RNA genes in the mt genome of O.sinensis
“+”means located on the positive strand.