Genome, transcriptome, and metabolome analyses provide new insights into the resource development in an edible fungus Dictyophora indusiata

Abstract

Dictyophora indusiata (Vent. Ex Pers.) Fisch. (DI) is an edible and medicinal fungus widely used in East Asian countries. However, during DI cultivation, the formation of fruiting bodies cannot be regulated, which leads to yield and quality losses. The present study performed a combined genome, transcriptome, and metabolome analysis of DI. Using Nanopore and Illumina sequencing approaches, we created the DI reference genome, which was 67.32 Mb long with 323 contigs. We identified 19,909 coding genes on this genome, of which 46 gene clusters were related to terpenoid synthesis. Subsequent transcriptome sequencing using five DI tissues (cap, indusia, mycelia, stipe, and volva) showed high expression levels of genes in the cap, indicating the tissue’s importance in regulating the fruiting body formation. Meanwhile, the metabolome analysis identified 728 metabolites from the five tissues. Mycelium was rich in choline, while volva was rich in dendronobilin; stipe had monosaccharides as the primary component, and the cap was the main source of indole acetic acid (IAA) synthesis. We confirmed the importance of tryptophan metabolism for DI fruiting body differentiation based on KEGG pathway analysis. Finally, the combined multiomics analysis identified three new genes related to IAA synthesis of the tryptophan metabolic pathway in the cap, which may regulate DI fruiting body synthesis and improve DI quality. Thus, the study’s findings expand our understanding of resource development and the molecular mechanisms underlying DI development and differentiation. However, the current genome is still a rough draft that needs to be strengthened.

Soil chemistry, metabarcoding, and metabolome analyses reveal that a sugarcane—Dictyophora indusiata intercropping system can enhance soil health by reducing soil nitrogen loss

“…Dictyophora indusiata (DI), which is in the family Phallaceae, is an economically valuable, edible mushroom that is used in Chinese cuisine ( Duan et al, 2023 ). DI is also widely used as a Chinese medicine material ( Wang et al, 2021 ).…”

Dictyophora indusiata and Bacillus aryabhattai improve sugarcane yield by endogenously associating with the root and regulating flavonoid metabolism

“…In this study’s intercropping system, D. indusiata significantly improved the metabolism of sugarcane roots through root symbiosis. Studies have found that the D. indusiata fruiting bodies synthesize IAA ( Duan et al., 2023b ), and D. indusiata improves soil metabolism, accumulating carbohydrate metabolites ( Duan et al., 2023a ). These earlier reports suggested that D. indusiata promotes plant growth metabolism.…”

“…Therefore, we conducted an experiment intercropping sugarcane and D. indusiata from March to October 2022. The studies have reported that the intercropping system, D. indusiata and sugarcane, enhances soil chemical properties and activates soil metabolism ( Duan et al., 2023a ); Additionally, the same genomic and metabolomic study revealed that the fruiting body of D. indusiata could synthesize IAA (indole-3-acetic acid) ( Duan et al., 2023b ), which probably leads to improved soil fertility and sugarcane yield. These preliminary studies suggest that intercropping D. indusiata with sugarcane benefits both species.…”

Integrative Analysis of Transcriptome and Metabolome Sheds Light on Flavonoid Biosynthesis in the Fruiting Body of Stropharia rugosoannulata

“…This preference stems from several challenges associated with the heterothallic sexual reproduction stage and outcrossing during cultivation, including chromosome doubling and the complex reproductive system of mushrooms [38][39][40][41]. Selecting dikaryotic mycelium or fruiting bodies with reproductive abilities for genome sequencing has been observed to lead to high sequence heterozygosity, an inflated genome size, and unsatisfactory assembly effects [42][43][44]. This phenomenon is exemplified in mushroom species like Leucocalocybe mongolica [41], Sanghuangporus baumii [45], and Pleurotus tuoliensis [46], which have yielded high-quality genomes when sequenced and assembled with monokaryotic strains.…”

“…This phenomenon is exemplified in mushroom species like Leucocalocybe mongolica [41], Sanghuangporus baumii [45], and Pleurotus tuoliensis [46], which have yielded high-quality genomes when sequenced and assembled with monokaryotic strains. Conversely, genome sequencing from dikaryotic mycelium or fruiting bodies of mushrooms like Dictyophora indusiate [42], Russula griseocarnosa [43], and Agrocybe cylindracea [44] has shown high sequence heterozygosity (N50 < 1 Mb), largerthan-actual genome sizes, and unsatisfactory assembly effects.…”