title: Transcriptome Sequencing of Chemically Induced Aquilaria sinensis to Identify Genes Related to Agarwood Formation.
abstract: Agarwood is a traditional Chinese medicine used as a clinical sedative, carminative, and antiemetic drug. Agarwood is formed in Aquilaria sinensis when A. sinensis trees are threatened by external physical, chemical injury or endophytic fungal irritation. However, the mechanism of agarwood formation via chemical induction remains unclear. In this study, we characterized the transcriptome of different parts of a chemically induced A. sinensis trunk sample with agarwood. The Illumina sequencing platform was used to identify the genes involved in agarwood formation.
  
  
  
  A five-year-old Aquilaria sinensis treated by formic acid was selected. The white wood part (B1 sample), the transition part between agarwood and white wood (W2 sample), the agarwood part (J3 sample), and the rotten wood part (F5 sample) were collected for transcriptome sequencing. Accordingly, 54,685,634 clean reads, which were assembled into 83,467 unigenes, were obtained with a Q20 value of 97.5%. A total of 50,565 unigenes were annotated using the Nr, Nt, SWISS-PROT, KEGG, COG, and GO databases. In particular, 171,331,352 unigenes were annotated by various pathways, including the sesquiterpenoid (ko00909) and plant-pathogen interaction (ko03040) pathways. These pathways were related to sesquiterpenoid biosynthesis and defensive responses to chemical stimulation.
  
  
  
  The transcriptome data of the different parts of the chemically induced A. sinensis trunk provide a rich source of materials for discovering and identifying the genes involved in sesquiterpenoid production and in defensive responses to chemical stimulation. This study is the first to use de novo sequencing and transcriptome assembly for different parts of chemically induced A. sinensis. Results demonstrate that the sesquiterpenoid biosynthesis pathway and WRKY transcription factor play important roles in agarwood formation via chemical induction. The comparative analysis of the transcriptome data of agarwood and A. sinensis lays the foundation for elucidating the mechanism of agarwood formation via chemical induction, and thus, enables future improvements in agarwood quality while protecting endangered wild A. sinensis.
authors.affiliation: State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Ye
authors.affiliation: State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, China.
authors.forename: Hongqing
authors.initials: H
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, China.|Guangdong Pharmaceutical University, Guangzhou, 510060, China.
authors.forename: Xin
authors.initials: X
authors.lastname: He
authors.affiliation: State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, China.|Inner Mongolia Medical University, Hohhot, 010110, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, China.
authors.forename: Weimin
authors.initials: W
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, China.
authors.forename: Haohua
authors.initials: H
authors.lastname: Li
authors.affiliation: State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, China.
authors.forename: Yunfei
authors.initials: Y
authors.lastname: Fan
authors.affiliation: State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, China.
authors.forename: Guohui
authors.initials: G
authors.lastname: Tan
authors.affiliation: State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, China.
authors.forename: Taomei
authors.initials: T
authors.lastname: Liu
authors.affiliation: Guangdong Pharmaceutical University, Guangzhou, 510060, China.
authors.forename: Xiaoxia
authors.initials: X
authors.lastname: Gao
mesh_terms: D053898:Biosynthetic Pathways; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D056726:Genetic Association Studies; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions / Q000235:genetics; D058977:Molecular Sequence Annotation; D009928:Organ Specificity; D019655:Quantitative Trait, Heritable; D012717:Sesquiterpenes / Q000378:metabolism; D013312:Stress, Physiological / Q000235:genetics; D029645:Thymelaeaceae / Q000235:genetics* / Q000502:physiology; D014157:Transcription Factors / Q000235:genetics; D059467:Transcriptome
chemical_list: D012717:Sesquiterpenes; D014157:Transcription Factors