Transcriptome Analysis and Its Application in Identifying Genes Associated with Fruiting Body Development in Basidiomycete Hypsizygus marmoreus

Abstract

To elucidate the mechanisms of fruit body development in H. marmoreus, a total of 43609521 high-quality RNA-seq reads were obtained from four developmental stages, including the mycelial knot (H-M), mycelial pigmentation (H-V), primordium (H-P) and fruiting body (H-F) stages. These reads were assembled to obtain 40568 unigenes with an average length of 1074 bp. A total of 26800 (66.06%) unigenes were annotated and analyzed with the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and Eukaryotic Orthologous Group (KOG) databases. Differentially expressed genes (DEGs) from the four transcriptomes were analyzed. The KEGG enrichment analysis revealed that the mycelium pigmentation stage was associated with the MAPK, cAMP, and blue light signal transduction pathways. In addition, expression of the two-component system members changed with the transition from H-M to H-V, suggesting that light affected the expression of genes related to fruit body initiation in H. marmoreus. During the transition from H-V to H-P, stress signals associated with MAPK, cAMP and ROS signals might be the most important inducers. Our data suggested that nitrogen starvation might be one of the most important factors in promoting fruit body maturation, and nitrogen metabolism and mTOR signaling pathway were associated with this process. In addition, 30 genes of interest were analyzed by quantitative real-time PCR to verify their expression profiles at the four developmental stages. This study advances our understanding of the molecular mechanism of fruiting body development in H. marmoreus by identifying a wealth of new genes that may play important roles in mushroom morphogenesis.

A WD40 Protein Encoding Gene Fvcpc2 Positively Regulates Mushroom Development and Yield in Flammulina velutipes

“…Although orthologs of CPC-2 have been predicted in the genomes of several mushrooms, including model mushroom species (C. cinerea and S. commune) and cultivated mushrooms (Flammulina velutipes, Volvariella volvacea, Pleurotus ostreatus, Ganoderma lucidum, and Lentinus edodes) (Ohm et al, 2010;Stajich et al, 2010;Grigoriev et al, 2012;Bao et al, 2013;Park et al, 2014;Riley et al, 2014;Sakamoto et al, 2017), none of them has been functionally characterized. Similarly as that cpc-2 is up-regulated after crossing in N. crassa (Lehr et al, 2014), CPC-2 orthologs have an increased expression during fruiting body development in many mushroom species (Ohm et al, 2010;Yu et al, 2012;Cheng et al, 2013;Liu et al, 2015;Zhang et al, 2015;Sakamoto et al, 2017), suggesting that CPC-2 orthologs are likely involved in fruiting body development in these mushroom species. If it is true, CPC-2 ortholog encoding genes have potential to be a new group of reference genes for mushroom breeding.…”

“…The orthologs of FvCPC2 were highly conserved and widespread in different edible mushrooms. Most of the FvCPC2 ortholog encoding genes specifically expressed during fruiting body development in mushroom species (Yu et al, 2012;Zhang et al, 2015;Sakamoto et al, 2017). Thus, genes encoding FvCPC2 orthologs in other mushroom species may also have potential application in breeding.…”

Unmatched level of molecular convergence among deeply divergent complex multicellular fungi

“…To identify developmentally relevant genes, we used publicly available fruiting body transcriptomes of 5 Pezizomycotina ( 33 – 36 ) and 4 Agaricomycotina ( 37 – 39 ) species, with which it was possible to quantify gene expression across 2–13 developmental stages. Based on expression dynamics, we detected 2645–9444 developmentally regulated genes in the nine species (Fig.…”

Cyclic Dipeptides Mediating Quorum Sensing and Their Biological Effects in Hypsizygus Marmoreus

“…The relative expression of five differentially expressed genes [33] (Table 1) involved in the growth and development of H. marmoreus was analyzed by the 2 -△△ CT method under different conditions with the addition of different signal molecules. As shown in Figure 5, the addition of cyclo(Pro-Leu) (4), cyclo(Pro-Tyr) (2), and cyclo(Pro-Phe) (1) facilitated the transcription of SNAP receptor complex member 1.…”