Studies On Genomics Of Cordyceps Tenuipes

Cordyceps tenuipes is a worldwide distributed entomogenous fungi.South Korea's Korean Food Code lists the C.tenuipes as an edible food ingredient because of its anti-inflammatory and anti-bacterial properties,the elimination of free radicals in the body,and the medicinal value of improving sleep and anti-depression.Some research results concludes from on the chemical active ingredients and pharmacological properties of C.tenuipes.However,there is a lack of information on the genomics of C.tenuipes,and very few studies found related to the genetic diversity and evolutionary relationship within the population of C.tenuipes.In this study,the whole genome of a single C.tenuipes was sequenced,its potential functional gene types were excavated,and its taxonomic status was verified through the construction of its mitochondrial evolutionary tree.Based on the whole genome re-sequencing sequence of 56 strains of C.tenuipes,the genetic structure and intraspecific differentiation of the population were studied.The main results are as follows:The genomic data of the C.tenuipes was sequenced by the second-generation sequencing platform Illumina,and a total of 4,808 Mb of valid data was obtained,384 contigs and 285 scaffolds were assembled.The N50 value was 172,867 bp,and the genome size was 30.06 Mb.The genome of the C.tenuipes contains 2,131 scattered repeats and 8,808 tandem repeats,and 7,854 protein-coding genes and 133 non-coding RNA sequences were predicted.Many protein coding sequences in KEGG and GO databases are enriched in functions related to transport and regulation,catalytic activity,metabolic and cellular processes.The proteins enriched the related coding proteins involved in neurodegenerative diseases,and the related regulatory coding proteins,especially the enzymes related to metabolism in mitochondria.In the cancer metabolism-related pathway,the enriched glutathione thiotransferase-related coding gene indicates that the genome might contain certain anti-cancer compounds.At the same time,annotations of several protein-encoding genes of superoxide dismutase have also confirmed the antioxidant function of C.tenuipes at the genetic level.As an entomogenous fungus,C.tenuipes contains many proteins related to host activity.The related attenuated proteins,pathogenic proteins and chitinases play a regulatory role in the invasion and adaptation of C.tenuipes to host environment.Total 31 secondary metabolite gene clusters were annotated in the genome of C.tenuipes,and the amount of non-ribosomal polypeptide synthetase was higher than that of Ophiocordyceps sinensis(Berk.)G.H.Sung,J.M.Sung,Hywel-Jones&Spatafora and Cordyceps militaris(L.ex Fr.)Link.According to the comparison of genomic data,C.tenuipes contains more glycoside hydrolases than that of O.sinensis,C.militaris,Isaria cicadae Miquel and Tolypoclfadium guangdongense T.H.Li,Q.Y.Lin&B.Song.In conclusion,C.tenuipes may contain more potential gene functions that need to be developed and utilized.Then the estimates of the divergence time show that C.tenuipes was differentiated at 21.4 million years ago,during the Miocene period,with conditions of climate changed dramatically.Based on the excavation of the whole genome of C.tenuipes.The mitochondrial genome of C.tenuipes was abtained with the length of 31,386 bp.A total of 14 protein-coding genes,2 ribosomal rRNA genes and 22 transporter RNA genes were annotated.The ribosomal S3 protein contained in the mitochondrial genome was conformed that it might provide a new gene marker for analyzing the taxonomic status of C.tenuipes.The mitochondrial genome phylogenetic tree of C.tenuipes was constructed by synthesizing the mitochondrial genomes of 26 species including Nectriaceae,Hypocreaceae,Ophiocordycipitaceae,Clavicipitaceae and Cordycipitaceae.The phylogenetic tree is divided into five branches according to different families.C.tenuipes is located in Cordycipitaceae(Cordyceps)and it is consistent with the taxonomic status of related nuclear gene research.Valid data(172,841 Mb)of was obtained from the re-sequencing of 56 genomes of C.tenuipes populations from Yunnan,Vietnam,and Thailand.Using LUFF00000000.1 as a reference strain,statistical variation information were obtained.Among them,the Thai strains contained a relatively large number of SNPs and InDels;the Vietnamese strains had more number of SV variants.The phylogenetic tree constructed by 56 strains of C.tenuipes based on SNP loci revealed its population structure with obvious regional aggregation characteristics.Population genetic structure analysis showed that the individual of C.tenuipes might originate from five ancestral genes,and there were some gene exchanges among the branches of each pedigree.In this study,the genomic information of the C.tenuipes was analyzed and excavated,and the composition of the protein-coding genes was clarified.It provides genomic basis for the later study of its gene metabolism and the development of related medicinal value.The phylogenetic tree of mitochondrial genome comfirmed its taxonomic status and provides data support for the development of new gene taxonomic markers.At the same time,through the study of population genomics,the genetic diversity and evolutionary regularity of the species were analyzed,which laid a foundation for studying the dynamic history of its population evolution.