The Chromosome-scale Reference Genome Of Phlebopus Portentosus Provides Insight Into The Evolution Of Mating System And Nutrition Mode

The Phlebopus portentosus is an edible mushroom classified in the Boletinellaceae(Boletales).P.portentosus is found in the tropical and subtropical regions.They are highly-prized for their edible and medicinal value compared with ordinary mushrooms.The lack of high-quality reference for P.portentosus has hindered the progress in breeding program.In the present study,we report the first high-quality reference genome of P.portentosus by combing Pac Bio sequencing,Illmunia sequencing and Hic sequencing platforms,which will greatly promote the genetic improvement of this species.We obtained a high-quality reference genome of P.portentosus with a total length of33,570,361 bp,which were anchored into the eleven chromosomes.The length of each chromosome varied from 1.82 Mb to 4.68 Mb.The contig N50 of the genome assembly was1.20 Mb.A number of methods,including Illumina reads mapping,transcripts mapping and Benchmarking Universal Single-Copy Orthologs,were used to asses the quality of genome assembly.Our results showed that the genome assembly are of high-quality and continuous,which ensure the downstream data analyses.The repeat sequence annotation showed that approximately 22.28% of the P.portentosus genome consisted of transposable elements(TEs).A total of 8,725 simple sequence repeat were identified in the P.portentosus genome with an overall length of126,519 bp.A total of 8,901 gene models were predicted with an average length of 1,845 bp.A total of 103 t RNA genes,95 r RNA genes,106 sno RNA genes,34 sn RNA genes and 1mi RNA genes were identified in the P.portentosus genome,respectively.The nutrition type is of great interest for the research community but is still unclear in P.portentosus.A total of 46 fungal genomes with known nutritional types were downloaded from JGI database.We analyzed the number and subfamilies distribution of the active enzyme genes related to cellulose degradation,hemicellulose degradation and pectin degradation.By clustering P.portentosus with other fungal genomes,we found that P.portentosus was clustered with most symbiotic fungi.The finding indicates that P.portentosus may be symbiotic rather than saprophytic.Secondary metabolites are important natural compounds produced by fungal species.In this study,we identified a total of five polyketides synthase genes(PKS),two nonribosomal peptide synthase genes(NRPS),seven NRPS-like genes and one PKS-NRPS hybrid genes.Comprehensive comparative analyses revealed that secondary metabolites backbone genes rapidly expanded in multicellular fungi,which may be influenced by their ecological niches.Comparative genomics analyses was performed between P.portentosus and the 16 other representative fungal species from Ascomycota and Basidiomycota.A total of 976single-copy gene families were identified and then used for the construction of phylogenetic tree.Results showed that P.portentosus and Boletus edulis diverged from their common ancestor ～126 million years ago(MYA).Boletales is phylogenetically sister to Agaricales and diverged ～260 MYA.Comparative genomics analysis also showed that a lot of gene families related to peroxidase have been expanded in P.portentosus genome.Mating-type gene is essencial for the reproductive development.We identified two mating-type A genes,two pheromone precursor genes and five pheromone receptor genes.The pheromone-receptor pathway was constructed by combing with the KAAS annotation.In conclusion,the obtained high-quality chromosome-level genome of P.portentosus will further our understanding of this edible and medicinal fungus.The genome sequence of P.portentosus will provide new insights into the evolution of nutrition mode and co-evolution with animals,which will largely accelerate the breeding program and yield increase.