Whole-Genome Sequencing and Comparative Genomics Analysis of the Wild Edible Mushroom (Gomphus purpuraceus) Provide Insights into Its Potential Food Application and Artificial Domestication

Abstract

Gomphus purpuraceus (Iwade) Yokoyama is a species of wild fungi that grows in southwest China, considered an edible and medicinal fungus with potential commercial prospects. However, the detailed mechanisms related to the development of mycelium and the formation of the fruiting body are unclear. To obtain a comprehensive overview of genetic features, whole-genome and comparative genomics analyses of G. purpuraceus were performed. High-quality DNA was extracted from the mycelium, which was isolated from a fresh fruiting body of G. purpuraceus. The DNA sample was subjected to sequencing using Illumina and Oxford Nanopore sequencing platforms. A genome assembly totaling 40.15 Mb in 50 contigs with an N50 length of 2.06 Mb was generated, and 8705 putative predicted genes were found. Subsequently, phylogenetic analysis revealed a close evolutionary relationship between G. purpuraceus and Gomphus bonarii. Moreover, a total of 403 carbohydrate-active enzymes (CAZymes) were identified in G. purpuraceus, which included 147 glycoside hydrolases (GHs), 85 glycosyl transferases (GTs), 8 polysaccharide lyases (PLs), 76 carbohydrate esterases (CEs), 57 auxiliary activities (AAs) and 30 carbohydrate-binding modules (CBMs). Compared with the other 13 fungi (Laccaria bicolor, Russula virescens, Boletus edulis, etc.), the number and distribution of CAZymes in G. purpuraceus were similar to other mycorrhizal fungi. Furthermore, the optimization of culture medium for G. purpuraceus showed the efficient utilization of disaccharides such as sucrose and maltose. The genome of G. purpuraceus provides new insights into its niche, food applications and potential artificial domestication.

Whole Genome Sequence of an Edible Mushroom Oudemansiella raphanipes (Changgengu)

“…For example, triterpenes from Ganoderma lucidum have been proven to have anti-cancer effects and can be used as a potential drug for cancer treatment [ 53 ]. It is worth noting that compared with other reported fungi, O. raphanipes is also predominate in the number of terpene synthesis genes [ 18 , 51 ]. NRPSs in fungi are considered to be corresponding to the virulence determinants during host-pathogen interactions, yet the exact role they play remains elusive in many cases [ 54 , 55 ].…”

“…Though it has been assigned to the genus Oudemansiella according to the combined ITS and nrLSU [ 2 ], it was also classified as a species of other genera, mostly Hymenopellis [ 1 , 11 ]. Currently, a whole-genome similarity analysis has been one of the best ways to figure out the strain taxonomy and get genetic information on the molecular mechanisms of fungal growth and breeding [ 18 , 30 , 45 ]. However, few studies have investigated the genome sequence and genetic structure of O. raphanipes .…”

“…CAZymes are important for the growth and development of wood-rotting mushrooms to thrive in environments rich in carbohydrates, especially lignocellulose and cellulose [ 18 , 56 , 57 , 58 ]. In the O. raphanipes genome, the GHs, GTs, and AAs were the main CAZymes, while PLs, CEs, and CMBs were in the minority.…”

“…As sequencing technology advances, genome sequencing has been extensively applied to investigate the genetic traits of mushrooms [ 12 , 13 , 14 ]. In particular, numerous genomes of mushrooms, including Pleurotus giganteus [ 15 ], Clitopilus passeckerianus [ 16 ], Stropharia rugosoannulata [ 17 ], Gomphus purpuraceus [ 18 ], Inonotus obliquus [ 19 ], Inonotus hispidus [ 20 ], and Laetiporus sulphureus [ 21 ], among others, have been most recently reported, which will provide valuable genetic resources and molecular markers for biological and genetic studies of edible mushrooms and also disease. Therefore, the availability of high-quality whole genomic sequencing for O. raphanipes is imperative to carry out, as it would facilitate the identification of functional candidate genes and genetic breeding of the cultivars.…”

Chromosome-Level Assembly and Comparative Genomic Analysis of Suillus bovinus Provides Insights into the Mechanism of Mycorrhizal Symbiosis

“…The MVA and MEP/DOXP pathways make up the main part of map00900 ( Figure S3 ). These results suggest that terpenoid backbone biosynthesis in S. bovinus , like in most fungi, can only proceed through the MVA pathway [ 50 , 63 , 64 ]. The core enzymes involved in the MVA pathway are listed in Table 6 .…”