Transcriptome and Proteome Exploration to Provide a Resource for the Study of Agrocybe aegerita

Abstract

Background Agrocybe aegerita, the black poplar mushroom, has been highly valued as a functional food for its medicinal and nutritional benefits. Several bioactive extracts from A. aegerita have been found to exhibit antitumor and antioxidant activities. However, limited genetic resources for A. aegerita have hindered exploration of this species.Methodology/Principal FindingsTo facilitate the research on A. aegerita, we established a deep survey of the transcriptome and proteome of this mushroom. We applied high-throughput sequencing technology (Illumina) to sequence A. aegerita transcriptomes from mycelium and fruiting body. The raw clean reads were de novo assembled into a total of 36,134 expressed sequences tags (ESTs) with an average length of 663 bp. These ESTs were annotated and classified according to Gene Ontology (GO), Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways. Gene expression profile analysis showed that 18,474 ESTs were differentially expressed, with 10,131 up-regulated in mycelium and 8,343 up-regulated in fruiting body. Putative genes involved in polysaccharide and steroid biosynthesis were identified from A. aegerita transcriptome, and these genes were differentially expressed at the two stages of A. aegerita. Based on one-dimensional gel electrophoresis (1-DGE) coupled with electrospray ionization liquid chromatography tandem MS (LC-ESI-MS/MS), we identified a total of 309 non-redundant proteins. And many metabolic enzymes involved in glycolysis were identified in the protein database.Conclusions/SignificanceThis is the first study on transcriptome and proteome analyses of A. aegerita. The data in this study serve as a resource of A. aegerita transcripts and proteins, and offer clues to the applications of this mushroom in nutrition, pharmacy and industry.

5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea

“…Among the up-regulated pathways in S1-Pri, we are particularly interested in novel signaling pathways [62]. Two up-regulated genes in S1-Pri were assigned to the mTOR signaling pathways, and real time PCR confirmed the 5 ′ -SAGE observations for these two DEGs (CC1G_10718 & CC1G_00269).…”

De Novo Assembly of Auricularia polytricha Transcriptome Using Illumina Sequencing for Gene Discovery and SSR Marker Identification

“…The contig size distribution revealed that more than half of the ESTs (32,602; 89.4%) were between 200 and 1000 bp in length (Table 2). The GC content of A. polytricha ESTs was 61.31%, which was much higher than L. edodes (48.31%) and A. aegerita (approximately 53%) [11], [14]. GC content analysis revealed that A. polytricha transcripts have a high GC content similar to the Auricularia delicata genome (58.6%).…”

Fungal aquaporins: cellular functions and ecophysiological perspectives

“…In addition, two recent gene expression studies in two other Agaricomycotina species allowed a large-scale comparison of transcript levels in the vegetative mycelium and fruiting bodies. In Agrocybe aegerita, Wang et al (2013) found one putative MIP (AA_35507 ; Table S6 of supporting information) being upregulated in fruiting bodies, which shows high homology to aquaglyceroporins from L. bicolor (data not shown). In Coprinopsis cinerea, expression of a putative aquaglyceroporin-encoding gene (CC1G_11437T0; file 1 of supporting information) could only be detected in the primordial stage of fruiting bodies but not in the vegetative mycelium (Cheng et al 2013).…”