title: 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.
  
  
  RESULTS
  To 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
  This 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.
authors: State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.
authors: Man
authors: M
authors: Wang
authors: Bianli
authors: B
authors: Gu
authors: Jie
authors: J
authors: Huang
authors: Shuai
authors: S
authors: Jiang
authors: Yijie
authors: Y
authors: Chen
authors: Yalin
authors: Y
authors: Yin
authors: Yongfu
authors: Y
authors: Pan
authors: Guojun
authors: G
authors: Yu
authors: Yamu
authors: Y
authors: Li
authors: Barry Hon Cheung
authors: BH
authors: Wong
authors: Yi
authors: Y
authors: Liang
authors: Hui
authors: H
authors: Sun
mesh_terms: D055362:Agrocybe / Q000235:genetics* / Q000378:metabolism*; D004591:Electrophoresis, Polyacrylamide Gel; D004734:Energy Metabolism / Q000235:genetics; D020224:Expressed Sequence Tags; D048690:Fruiting Bodies, Fungal / Q000235:genetics / Q000378:metabolism; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods; D053263:Gene Regulatory Networks / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D025282:Mycelium / Q000235:genetics / Q000378:metabolism; D011134:Polysaccharides / Q000096:biosynthesis; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods; D020133:Reverse Transcriptase Polymerase Chain Reaction; D021241:Spectrometry, Mass, Electrospray Ionization; D013256:Steroids / Q000096:biosynthesis; D053719:Tandem Mass Spectrometry; D059467:Transcriptome / Q000235:genetics*; D018875:Vocabulary, Controlled
chemical_list: D005656:Fungal Proteins; D011134:Polysaccharides; D020543:Proteome; D013256:Steroids