Parallel and comparative transcriptome and proteome provide insight into degeneration-related key candidates in Agaricus bisporus

BACKGROUND: Spawn degeneration is a widespread phenomenon during the production process of edible fungi, such as Agaricus bisporus. The degeneration of substrate-decomposing ability brings about the inability of decomposition and utilization of substrate, the weakened growth of mycelium, and decline of production capacity. In order to explore the underlying mechanism and key factors regulating spawn degeneration, we investigated transcriptomic and proteomic alterations using high-throughput RNA sequencing and tandem mass tag-based (TMT) quantitative proteomics technology in A. bisporus degenerated strains 2796-3, 2796-5 and normal strain As2796. RESULTS: We identified a total of 257 and 635 DEGs in degenerated strains 2796-3 and 2796-5. Furthermore, we analyzed alteration in translation level and obtained 228 and 290 DEPs. Among these differentially genes/proteins, there were 117 genes/proteins involved with substrate degradation and 16 transcription factors. Integrative analysis of proteome and transcriptome revealed that top 25 KEGG pathways with the largest sum of DEPs and DEGs were roughly the same, of which 20 pathways were common in the two degenerated strains. We found that the major of DEGs/DEPs involved in biosynthesis of amino acid, arginine and proline metabolism, tryptophan metabolism, and MAPK signaling pathway showed downregulation in degenerated strains. CONCLUSIONS: Our results suggested that transcription factors, biosynthesis of amino acid biosynthesis, arginine and proline metabolism, tryptophan metabolism, as well as MAPK signaling pathway might be associated with strain degeneration in A. bisporus. This study provided valuable databases for identifying potential candidated genes and pathways associated with degeneration. Furthermore, it would lay a foundation for molecular breeding of new A. bisporus strains with improvement of substrate utilization, anti-degenerated trait and yield.