Complete genome sequences and comparative secretomic analysis for the industrially cultivated edible mushroom Lyophyllum decastes reveals insights on evolution and lignocellulose degradation potential

Abstract

Lyophyllum decastes, also known as Luronggu in China, is a culinary edible and medicinal mushroom that was widely cultivated in China in recent years. In the present study, the complete high-quality genome of two mating compatible L. decastes strain was sequenced. The L. decastes LRG-d1-1 genome consists of 47.7 Mb in 15 contigs with a contig N90 of 2.08 Mb and 14,499 predicted gene models. Phylogenetic analysis revealed that L. decastes exhibits a close evolutionary relationship to the Termitomyces and Hypsizygus genus and was diverged from H. marmoreus ~ 45.53 Mya ago. Mating A loci of L. decastes compose of five and four HD genes in two monokaryotic strains, respectively. Mating B loci compose of five STE genes in both two monokaryotic strains. To accelerate the cross-breeding process, we designed four pairs of specific primers and successfully detected both mating types in L. decastes. As a wood-rotting mushroom, a total of 541 genes accounting for 577 CAZymes were identified in the genome of L. decastes. Proteomic analysis revealed that 1,071 proteins including 182 CAZymes and 258 secreted enzymes were identified from four groups (PDB, PDB + bran, PDB + cotton hull, and PDB + sawdust). Two laccases and a quinone reductase were strongly overproduced in lignin-rich cultures, and the laccases were among the top-3 secreted proteins, suggesting an important role in the synergistic decomposition of lignin. These results revealed the robustness of the lignocellulose degradation capacity of L. decastes. This is the first study to provide insights into the evolution and lignocellulose degradation of L. decastes.

Comparative transcriptome analysis on candidate genes associated with fruiting body growth and development in Lyophyllum decastes

“…3 . Significantly, BLAST comparison was performed between the 15,451 unigenes in this study and 14,499 genes in the study by Xu et al (2023) , which revealed that 74.25% unigenes can be found in the 14,499 genes with an identity of 85%.…”

“…The contigs were initially assembled, and a further assembly process was subsequently conducted, resulting in the formation of 15,451 unigenes. According to a recent research, 14,499 gene models have been predicted from the genome of L. decastes ( Xu et al, 2023 ). Compared with these previously predicted genes, the average GC content of the unigenes in this research (51.78%) is simililar to that of L. decastes LGR-d1-1 (50.25%) and LRG-d1-5 (50.38%).…”

Complete mitochondrial genomes of edible mushrooms: features, evolution, and phylogeny

“…Third‐generation sequencing technologies have emerged, allowing for more accurate and comprehensive genome sequencing of medicinal and edible mushrooms. These technologies have facilitated research on various aspects of these fungi, including their life cycles, mating types, nutritional patterns, and biosynthesis of bioactive metabolites (Sun et al 2023a, Xu et al 2023a). The genomes of over 30 edible fungi, such as Agaricus bisporus (button mushroom), Antrodia cinnamomea (Niu‐Chang‐Chih), Agaricus bitorquis (Pavement mushroom), Cordyceps militaris (Scarlet Caterpillarclub), Flammulina velutipes (Velvet shank), Grifolia frondosa (Hen of the woods), Ganoderma sinense (Lingzhi), Hericium erinaceus (lion's mane mushroom), Pleurotus ostreatus (oyster mushroom), Pleurotus eryngii (King Trumpet Mushroom), and others have been successfully deciphered, which further aid in their medicinal utilization and industrial development.…”

The development and nutritional quality of Lyophyllum decastes affected by monochromatic or mixed light provided by light-emitting diode

“…Lyophyllum decastes ( L. decastes ), also known as fried chicken mushroom, belongs to the order Agaricales, family Tricholomataceae, and genus Lyophyllum. It is named for its resemblance to the medicinal plant pilose antler ( 1 ). L. decastes is a large fungus widely distributed in temperate regions of the northern hemisphere, which can be used for both food and medicine.…”