title: Transcriptome sequencing and expression analysis of terpenoid biosynthesis genes in Litsea cubeba.
abstract: BACKGROUND
  Aromatic essential oils extracted from fresh fruits of Litsea cubeba (Lour.) Pers., have diverse medical and economic values. The dominant components in these essential oils are monoterpenes and sesquiterpenes. Understanding the molecular mechanisms of terpenoid biosynthesis is essential for improving the yield and quality of terpenes. However, the 40 available L. cubeba nucleotide sequences in the public databases are insufficient for studying the molecular mechanisms. Thus, high-throughput transcriptome sequencing of L. cubeba is necessary to generate large quantities of transcript sequences for the purpose of gene discovery, especially terpenoid biosynthesis related genes.
  
  
  RESULTS
  Using Illumina paired-end sequencing, approximately 23.5 million high-quality reads were generated. De novo assembly yielded 68,648 unigenes with an average length of 834 bp. A total of 38,439 (56%) unigenes were annotated for their functions, and 35,732 and 25,806 unigenes could be aligned to the GO and COG database, respectively. By searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG), 16,130 unigenes were assigned to 297 KEGG pathways, and 61 unigenes, which contained the mevalonate and 2-C-methyl-D-erythritol 4-phosphate pathways, could be related to terpenoid backbone biosynthesis. Of the 12,963 unigenes, 285 were annotated to the terpenoid pathways using the PlantCyc database. Additionally, 14 terpene synthase genes were identified from the transcriptome. The expression patterns of the 16 genes related to terpenoid biosynthesis were analyzed by RT-qPCR to explore their putative functions.
  
  
  CONCLUSIONS
  RNA sequencing was effective in identifying a large quantity of sequence information. To our knowledge, this study is the first exploration of the L. cubeba transcriptome, and the substantial amount of transcripts obtained will accelerate the understanding of the molecular mechanisms of essential oils biosynthesis. The results may help improve future genetic and genomics studies on the molecular mechanisms behind the chemical composition of essential oils in L. cubeba fruits.
authors.affiliation: State Key Laboratory of Forest Genetics and Tree Breeding, Chinese Academy of Forestry, Beijing, P. R. China ; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, P. R. China.
authors.forename: Xiao-Jiao
authors.initials: XJ
authors.lastname: Han
authors.forename: Yang-Dong
authors.initials: YD
authors.lastname: Wang
authors.forename: Yi-Cun
authors.initials: YC
authors.lastname: Chen
authors.forename: Li-Yuan
authors.initials: LY
authors.lastname: Lin
authors.forename: Qing-Ke
authors.initials: QK
authors.lastname: Wu
mesh_terms: D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D023281:Genomics; D032862:Litsea / Q000235:genetics* / Q000378:metabolism*; D018895:Microsatellite Repeats / Q000235:genetics; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics*; D017423:Sequence Analysis, RNA; D013729:Terpenes / Q000378:metabolism*
chemical_list: D010940:Plant Proteins; D018749:RNA, Plant; D013729:Terpenes