De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia

Abstract

The genes associated with fruiting body formation of Sparasis latifolia are valuable for improving mushroom breeding. To investigate this process, 4.8 × 108 RNA-Seq reads were acquired from three stages: hyphal knot (SM), primordium (SP), and primordium differentiation (SPD). The de novo assembly generated a total of 48,549 unigenes, of which 71.53% (34,728) unigenes could be annotated by at least one of the KEGG (Kyoto Encyclopedia of Genes and Genomes), GO (Gene Ontology), and KOG (Eukaryotic Orthologous Group) databases. KEGG and KOG analyses respectively mapped 32,765 unigenes to 202 pathways and 19,408 unigenes to 25 categories. KEGG pathway enrichment analysis of DEGs (differentially expressed genes) indicated primordium initiation was significantly related to 66 pathways, such as “Ribosome”, “metabolism of xenobiotics by cytochrome P450”, and “glutathione metabolism” (among others). The MAPK and mTOR signal transduction pathways underwent significant adjustments during the SM to SP transition. Further, our research revealed the PI3K-Akt signaling pathway related to cell proliferation could play crucial functions during the development of SP and SPD. These findings provide crucial candidate genes and pathways related to primordium differentiation and development in S. latifolia, and advances our knowledge about mushroom morphogenesis.

Transcriptome Analysis Revealed the Mechanism of Inhibition of Saprophytic Growth of Sparassis latifolia by Excessive Oxalic Acid

“…Our transcriptome analysis and gene expression profiles in comparison among groups revealed that the expression levels of multiple genes in these signal pathways were significantly down-regulated by excessive oxalic acid, thereby impairing the expression of these pathways and inhibiting the saprophytic growth of S. latifolia mycelia. Moreover, our previous study also revealed that the MAPK, PI3K–Akt, and mTOR signaling pathways play important roles in primordium formation and fruiting body development [ 52 ]. Therefore, many down-regulated genes in these signal pathways will seriously restrict the mycelial growth and the fruiting body development of the S. latifolia , leading to the prolongation of the cultivation cycle.…”

The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research

“…Tools for de novo transcriptome assembly such as the Trinity software can make transcriptomic analysis without reference genomes more feasible [ 113 ]. Trinity has been successfully utilized for de novo assemblies of transcriptomes and metatranscriptomes containing signatures from multiple kingdoms [ 114 – 116 ]. Other tools and methods for separating host and symbiont reads in holobiont systems have been designed that minimize the chimeras that can typically arise from de novo transcriptome analyses [ 117 ].…”