SMRT Sequencing Revealed Mitogenome Characteristics and Mitogenome-Wide DNA Modification Pattern in Ophiocordyceps sinensis

Abstract

Single molecule, real-time (SMRT) sequencing was used to characterize mitochondrial (mt) genome of Ophiocordyceps sinensis and to analyze the mt genome-wide pattern of epigenetic DNA modification. The complete mt genome of O. sinensis, with a size of 157,539 bp, is the fourth largest Ascomycota mt genome sequenced to date. It contained 14 conserved protein-coding genes (PCGs), 1 intronic protein rps3, 27 tRNAs and 2 rRNA subunits, which are common characteristics of the known mt genomes in Hypocreales. A phylogenetic tree inferred from 14 PCGs in Pezizomycotina fungi supports O. sinensis as most closely related to Hirsutella rhossiliensis in Ophiocordycipitaceae. A total of 36 sequence sites in rps3 were under positive selection, with dN/dS >1 in the 20 compared fungi. Among them, 16 sites were statistically significant. In addition, the mt genome-wide base modification pattern of O. sinensis was determined in this study, especially DNA methylation. The methylations were located in coding and uncoding regions of mt PCGs in O. sinensis, and might be closely related to the expression of PCGs or the binding affinity of transcription factor A to mtDNA. Consequently, these methylations may affect the enzymatic activity of oxidative phosphorylation and then the mt respiratory rate; or they may influence mt biogenesis. Therefore, methylations in the mitogenome of O. sinensis might be a genetic feature to adapt to the cold and low PO2 environment at high altitude, where O. sinensis is endemic. This is the first report on epigenetic modifications in a fungal mt genome.

Mitochondrial genome, comparative analysis and evolutionary insights into the entomopathogenic fungus Hirsutella thompsonii

“…In this study, we newly presented the mitogenome of the mite‐pathogenic fungus H. thompsonii , which was 60–66 kb in size (Table ). The mitogenome size of the fungus is similar to species of the same genus, including Hirsutella minnesotensis (52.2 kb) (Zhang et al ., ), Hirsutella rhossiliensis (62.9 kb) (Yan et al ., ) and Hirsutella vermicola (53.8 kb) (Zhang et al ., ), although great mitogenome size variations of Ophiocordycipitaceae species have been documented, from 24.9 kb in Tolypocladium inflatum (Zhang et al ., ) to 157.5 kb in Ophiocordyceps sinensis (Li et al ., ; Kang et al ., ). Size variations of these mitogenomes were mainly attributed to variable numbers of introns (from 1 to 54) and variable lengths of intergenic regions (from 4.1 to 21.9 kb) (Zhang et al ., ; ).…”

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

“…In addition, although I. cicadae has the largest mitogenome in Cordycipitaceae, fungal mitogenomes that are even larger in size and richer in introns than the I. cicadae mitogenome are reported. For example, the Chinese caterpillar fungus Ophiocordyceps sinensis has a mitogenome of 157.5 kb due to the presence of 54 introns (Kang et al, 2017). The blue-stain fungus Endoconidiophora resinifera has a mitogenome of 220.2 kb, containing as many as 81 introns (Zubaer et al, 2018).…”

Comparison of the Mitochondrial Genome Sequences of Six Annulohypoxylon stygium Isolates Suggests Short Fragment Insertions as a Potential Factor Leading to Larger Genomic Size

“…The six mtDNAs were 131,996–147,325 bp in length. To our knowledge, only eight completely sequenced and well annotated fungal mtDNAs are larger than 150 kb (Losada et al, 2014 ; Mardanov et al, 2014 ; Salavirta et al, 2014 ; Kanzi et al, 2016 ; Nowrousian, 2016 ; Kang et al, 2017 ). One of the common features for those large mtDNAs was that all of them contain an abundance of introns, many of which carry homing endonuclease genes (group I type) or reverse transcriptase genes (group II type).…”

“…and Candida orthopsilosis , are around 20 kb in size with few or no introns and few or no non-conserved genes. Several large mitochondrial genomes in fungi (more than 150 kb) have been released in the organelle genome database in NCBI recently, including those of Rhizoctonia solani AG-1 and AG3 (Losada et al, 2014 ), Sclerotinia borealis F-4128 (Mardanov et al, 2014 ), Pyronema omphalodes CBS 100304 (Nowrousian, 2016 ), Chrysoporthe austroafricana (Kanzi et al, 2016 ), Ustilago bromivora UB2112, Phellinus noxius FFPRI411160, Ophiocordyceps sinensis (Kang et al, 2017 ), and Phlebia radiata 79 (Salavirta et al, 2014 ). One common features among large fungal mtDNAs is that they contain many introns.…”