title: Genome-wide transcriptome and proteome analysis on different developmental stages of Cordyceps militaris.
abstract: BACKGROUND
  Cordyceps militaris, an ascomycete caterpillar fungus, has been used as a traditional Chinese medicine for many years owing to its anticancer and immunomodulatory activities. Currently, artificial culturing of this beneficial fungus has been widely used and can meet the market, but systematic molecular studies on the developmental stages of cultured C. militaris at transcriptional and translational levels have not been determined.
  
  
  RESULTS
  We utilized high-throughput Illumina sequencing to obtain the transcriptomes of C. militaris mycelium and fruiting body. All clean reads were mapped to C. militaris genome and most of the reads showed perfect coverage. Alternative splicing and novel transcripts were predicted to enrich the database. Gene expression analysis revealed that 2,113 genes were up-regulated in mycelium and 599 in fruiting body. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to analyze the genes with expression differences. Moreover, the putative cordycepin metabolism difference between different developmental stages was studied. In addition, the proteome data of mycelium and fruiting body were obtained by one-dimensional gel electrophoresis (1-DGE) coupled with nano-electrospray ionization liquid chromatography tandem mass spectrometry (nESI-LC-MS/MS). 359 and 214 proteins were detected from mycelium and fruiting body respectively. GO, KEGG and Cluster of Orthologous Groups (COG) analysis were further conducted to better understand their difference. We analyzed the amounts of some noteworthy proteins in these two samples including lectin, superoxide dismutase, glycoside hydrolase and proteins involved in cordycepin metabolism, providing important information for further protein studies.
  
  
  CONCLUSIONS
  The results reveal the difference in gene expression between the mycelium and fruiting body of artificially cultivated C. militaris by transcriptome and proteome analysis. Our study provides an effective resource for the further developmental and medicinal research of this promising fungus.
authors.affiliation: State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei Province, People's Republic of China.
authors.forename: Yalin
authors.initials: Y
authors.lastname: Yin
authors.forename: Guojun
authors.initials: G
authors.lastname: Yu
authors.forename: Yijie
authors.initials: Y
authors.lastname: Chen
authors.forename: Shuai
authors.initials: S
authors.lastname: Jiang
authors.forename: Man
authors.initials: M
authors.lastname: Wang
authors.forename: Yanxia
authors.initials: Y
authors.lastname: Jin
authors.forename: Xianqing
authors.initials: X
authors.lastname: Lan
authors.forename: Yi
authors.initials: Y
authors.lastname: Liang
authors.forename: Hui
authors.initials: H
authors.lastname: Sun
mesh_terms: D032661:Cordyceps / Q000166:cytology / Q000235:genetics* / Q000378:metabolism*; D048690:Fruiting Bodies, Fungal; D015870:Gene Expression; D016681:Genome, Fungal; D055106:Genome-Wide Association Study / Q000379:methods; D025282:Mycelium / Q000235:genetics / Q000378:metabolism; D020543:Proteome / Q000235:genetics* / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods; D059467:Transcriptome / Q000235:genetics*
chemical_list: D020543:Proteome