Identifying a melanogenesis-related candidate gene by a high-quality genome assembly and population diversity analysis in Hypsizygus marmoreus

Hypsizygus marmoreus is one of the most important edible fungi in Basidiomycete division and includes white and gray strains. However, very limited knowledge is known about the genomic structures and the genetic basis for the white/gray diversity of this mushroom. Here, we report the near-complete high-quality H. marmoreus genome at the chromosomal level. Comparative genomics analysis indicates that chromosome structures were relatively conserved, and variations in collinearity and chromosome number were mainly attributed by chromosome split/fusion events in Aragicales, whereas the fungi genome experienced many genomic chromosome fracture, fusion, and genomic replication events after the split of Aragicales from Basidiomycetes. Resequencing of 57 strains allows us to classify the population into four major groups and associate genetic variations with morphological features, indicating that white strains were not originated independently. We further generated genetic populations and identified a cytochrome P450 as the candidate causal gene for the melanogenesis in H. marmoreus based on bulked segregant analysis (BSA) and comparative transcriptome analysis. The high-quality H. marmoreus genome and diversity data compiled in this study provide new knowledge and resources for the molecular breeding of H. marmoreus as well as the evolution of Basidiomycete.

Genetic diversity analysis of Hypsizygus marmoreus with target region amplification polymorphism

Hypsizygus marmoreus is an industrialized edible mushroom. In the present paper, the genetic diversity among 20 strains collected from different places of China was evaluated by target region amplification polymorphism (TRAP) analysis; the common fragment of TRAPs was sequenced and analyzed. Six fixed primers were designed based on the analysis of H. marmoreus sequences from GenBank database. The genomic DNA extracted from H. marmoreus was amplified with 28 TRAP primer combinations, which generated 287 bands. The average of amplified bands per primer was 10.27 (mean polymorphism is 69.73%). The polymorphism information content (PIC) value for TRAPs ranged from 0.32 to 0.50 (mean PIC value per TRAP primer combination is 0.48), which indicated a medium level of polymorphism among the strains. A total of 36 sequences were obtained from TRAP amplification. Half of these sequences could encode the known or unknown proteins. According to the phylogenetic analysis based on TRAP result, the 20 strains of H. marmoreus were classified into two main groups.

Breeding of new strains of mushroom by basidiospore chemical mutagenesis

Chemical mutagenesis of basidiospores of Hypsizygus marmoreus generated new mushroom strains. The basidospores were treated with methanesulfonate methylester, an alkylating agent, to yield 400 mutant monokaryotic mycelia. Twenty fast-growing mycelia were selected and mated each other by hyphal fusion. Fifty out of the 190 matings were successful (mating rate of 26.3%), judged by the formation of clamp connections. The mutant dikaryons were cultivated to investigate their morphological and cultivation characteristics. Mutant strains No. 3 and No. 5 showed 10% and 6% increase in fruiting body production, respectively. Eight mutant strains showed delayed and reduced primordia formation, resulting in the reduced production yield with prolonged cultivation period. The number of the fruiting bodies of mutant No. 31, which displayed reduced primordial formation, was only 15, compared to the parental number of 65. Another interesting phenotype was a fruiting body with a flattened stipe and pileus. Dikaryons generated by mating with the mutant spore No. 14 produced flat fruiting bodies. Further molecular biological studies will provide details of the mechanism. This work shows that the chemical mutagenesis approach is highly utilizable in the development of mushroom strains as well as in the generation of resources for molecular genetic studies.