title: Transcriptome sequencing and analysis of the entomopathogenic fungus Hirsutella sinensis isolated from Ophiocordyceps sinensis.
abstract: BACKGROUND
  Ophiocordyceps sinensis, a worm and fungus combined mixture which Hirsutella sinensis is parasitic on the caterpillar body, has been used as a traditional medicine or healthy food in China for thousands of years. H. sinensis is reported as the only correct anamorph of O. sinensis and its main active ingredients are similar to the natural O. sinensis.
  
  
  RESULTS
  H. sinensis L0106, asexual strain of O. sinensis, was isolated and identified in this study. Three transcriptomes of H. sinensis at different cultivation periods (growth period 3d, pre-stable period 6d and stable period 9d) were sequenced for the first time by RNA-Seq method, and 25,511 unigenes (3d), 25,214 unigenes (6d) and 16,245 unigenes (9d) were assembled and obtained, respectively. These unigenes of the three samples were further assembled into 20,822 unigenes (All), and 62.3 percent of unigenes (All) could be annotated based on protein databases. Subsequently, the genes and enzymes involved in the biosynthesis of the active ingredients according to the sequencing and annotation results were predicted. Based on the predictions, we further investigated the interaction of different pathway networks and the corresponding enzymes. Furthermore, the differentially expressed genes (DEGs) of H. sinensis grown during different developmental stages (3d-VS-6d, 3d-VS-9d and 6d-VS-9d) were globally detected and analyzed based on the data from RNA-Seq, and 764 DEGs between 3d and 6d, 1,869 DEGs between 3d and 9d, and 770 DEGs between 6d and 9d were found, respectively.
  
  
  CONCLUSIONS
  This work presented here would aid in understanding and carrying out future studies on the genetic basis of H. sinensis and contribute to the further artificial production and application of this organism. This study provided a substantial contribution and basis to further characterize the gene expression profiles of H. sinensis in the metabolic pathways of active ingredients.
authors.affiliation: Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, P R China. microliu@gmail.com.
authors.forename: Zhi-Qiang
authors.initials: ZQ
authors.lastname: Liu
authors.affiliation: Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, P R China. biotechlim@gmail.com.
authors.forename: Shan
authors.initials: S
authors.lastname: Lin
authors.affiliation: Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, P R China. peterjames245@gmail.com.
authors.forename: Peter James
authors.initials: PJ
authors.lastname: Baker
authors.affiliation: Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, P R China. wlf01025@126.com.
authors.forename: Ling-Fang
authors.initials: LF
authors.lastname: Wu
authors.affiliation: Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, P R China. sometimes1011@163.com.
authors.forename: Xiao-Rui
authors.initials: XR
authors.lastname: Wang
authors.affiliation: East China Pharmaceutical Group Limited Co., Ltd, Hangzhou, 311000, Zhejiang, P R China. wuhui@eastprotech.com.
authors.forename: Hui
authors.initials: H
authors.lastname: Wu
authors.affiliation: East China Pharmaceutical Group Limited Co., Ltd, Hangzhou, 311000, Zhejiang, P R China. xufeng@hdpharm.com.
authors.forename: Feng
authors.initials: F
authors.lastname: Xu
authors.affiliation: East China Pharmaceutical Group Limited Co., Ltd, Hangzhou, 311000, Zhejiang, P R China. why19801022@163.com.
authors.forename: Hong-Yan
authors.initials: HY
authors.lastname: Wang
authors.affiliation: Polytechnic School of Engineering, New York University, 6 MetroTech Center, Brooklyn, NY, 11201, USA. m.brathwaite@nyu.edu.
authors.forename: Mgavi Elombe
authors.initials: ME
authors.lastname: Brathwaite
authors.affiliation: Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, P R China. zhengyg@zjut.edu.cn.
authors.forename: Yu-Guo
authors.initials: YG
authors.lastname: Zheng
mesh_terms: D000818:Animals; D001483:Base Sequence; D002681:China; D059014:High-Throughput Nucleotide Sequencing; D006999:Hypocreales / Q000235:genetics* / Q000254:growth & development; D007313:Insecta / Q000235:genetics / Q000469:parasitology; D008516:Medicine, Chinese Traditional; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics*