Genomic insights and SSR marker development for trait improvement in Pleurotus giganteus for tropical cultivation

Pleurotus giganteus is a medium-high temperature mushroom crop with strong potential for commercial cultivation in tropical regions. Understanding its genomic and genetic diversity is key to developing improved germplasm. In this study, we performed de novo genome sequencing of strain PG79, which exhibits fast growth and desirable morphology but is sensitive to heat and disease, and compared it with PG46, a heat-tolerant, disease-resistant strain with slower growth and long stipes. Both genomes were similar in size (PG79: 40.46 Mb; PG46: 40.11 Mb) but differed in non-coding gene content, with PG79 containing more rRNA and snRNA genes. PG79 harbored more genes related to substrate utilization, growth and development, and secondary metabolism, such as GH5, terpene, T1PKS, and NRPS-like genes. The genomes shared high synteny (84%) with limited structural variation. Molecular clock analysis estimated divergence at ~ 8.6 million years ago, with PG79 showing gene family expansions related to signal transduction, biosynthesis, and recombination. Population genomic analysis of 32 strains revealed clear differentiation among wild, cultivated, and hybrid groups, though cultivated strains exhibited reduced genetic diversity. From the PG46 genome, 16, 5, and 7 novel SSR markers were developed for monokaryon identification, mating type differentiation, and hybrid verification, respectively. PG46 and PG79, with complementary traits and distinct genetic backgrounds, were used as breeding parents. Among hybrids, PGH6 showed excellent agronomic performance, including heat tolerance, compact morphology, short growth cycle, and high nutritional value. Our study successfully obtained an improved Pleurotus giganteus strain by combining genomic analysis with marker-assisted breeding. This study provided valuable genomic resources and a marker-assisted breeding framework to accelerate the improvement of P. giganteus for tropical mushroom cultivation.