title: De novo comparative transcriptome analysis provides new insights into sucrose induced somatic embryogenesis in camphor tree (Cinnamomum camphora L.).
abstract: BACKGROUND
  Somatic embryogenesis is a notable illustration of cell totipotency, by which somatic cells undergo dedifferentiation and then differentiate into somatic embryos. Our previous work demonstrated that pretreatment of immature zygotic embryos with 0.5 M sucrose solution for 72 h efficiently induced somatic embryo initiation in camphor tree. To better understand the molecular basis of somatic embryogenesis induced by osmotic stress, de novo transcriptome sequencing of three tissues of camphor tree (immature zygotic embryos, sucrose-pretreated immature zygotic embryos, and somatic embryos induced from sucrose-pretreated zygotic embryos) were conducted using Illumina Hiseq 2000 platform.
  
  
  RESULTS
  A total of 30.70 G high quality clean reads were obtained from cDNA libraries of the three samples. The overall de novo assembly of cDNA sequence data generated 205592 transcripts, with an average length of 998 bp. 114229 unigenes (55.56 % of all transcripts) with an average length of 680 bp were annotated with gene descriptions, gene ontology terms or metabolic pathways based on Blastx search against Nr, Nt, Swissprot, GO, COG/KOG, and KEGG databases. CEGMA software identified 237 out of 248 ultra-conserved core proteins as 'complete' in the transcriptome assembly, showing a completeness of 95.6 %. A total of 897 genes previously annotated to be potentially involved in somatic embryogenesis were identified. Comparative transcriptome analysis showed that a total of 3335 genes were differentially expressed in the three samples. The differentially expressed genes were divided into six groups based on K-means clustering. Expression level analysis of 52 somatic embryogenesis-related genes indicated a high correlation between RNA-seq and qRT-PCR data. Gene enrichment analysis showed significantly differential expression of genes responding to stress and stimulus.
  
  
  CONCLUSIONS
  The present work reported a de novo transcriptome assembly and global analysis focused on gene expression changes during initiation and formation of somatic embryos in camphor tree. Differential expression of somatic embryogenesis-related genes indicates that sucrose induced somatic embryogenesis may share or partly share the mechanisms of somatic embryogenesis induced by plant hormones. This study provides comprehensive transcript information and gene expression data for camphor tree. It could also serve as an important platform resource for further functional studies in plant embryogenesis.
authors.affiliation: Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, P. R. China. xpshi@mail.hzau.edu.cn.
authors.forename: Xueping
authors.initials: X
authors.lastname: Shi
authors.affiliation: Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, P. R. China. zhangcuijie125@126.com.
authors.forename: Cuijie
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, P. R. China. azura007@163.com.
authors.forename: Qinhong
authors.initials: Q
authors.lastname: Liu
authors.affiliation: Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, P. R. China. 13618632337@163.com.
authors.forename: Zhe
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, P. R. China. bo.zheng@mail.hzau.edu.cn.
authors.forename: Bo
authors.initials: B
authors.lastname: Zheng
authors.affiliation: Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, P. R. China. mzbao@mail.hzau.edu.cn.
authors.forename: Manzhu
authors.initials: M
authors.lastname: Bao
mesh_terms: D027423:Cinnamomum camphora / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D059014:High-Throughput Nucleotide Sequencing; D053858:Metabolic Networks and Pathways / Q000235:genetics; D058977:Molecular Sequence Annotation; D058439:Plant Somatic Embryogenesis Techniques; D012313:RNA / Q000096:biosynthesis / Q000235:genetics; D012984:Software; D013395:Sucrose / Q000378:metabolism*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D013395:Sucrose; D012313:RNA