title: Transcriptome profiling and digital gene expression by deep sequencing in early somatic embryogenesis of endangered medicinal Eleutherococcus senticosus Maxim.
abstract: Somatic embryogenesis (SE) has been studied as a model system to understand molecular events in physiology, biochemistry, and cytology during plant embryo development. In particular, it is exceedingly difficult to access the morphological and early regulatory events in zygotic embryos. To understand the molecular mechanisms regulating early SE in Eleutherococcus senticosus Maxim., we used high-throughput RNA-Seq technology to investigate its transcriptome. We obtained 58,327,688 reads, which were assembled into 75,803 unique unigenes. To better understand their functions, the unigenes were annotated using the Clusters of Orthologous Groups, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes databases. Digital gene expression libraries revealed differences in gene expression profiles at different developmental stages (embryogenic callus, yellow embryogenic callus, global embryo). We obtained a sequencing depth of >5.6 million tags per sample and identified many differentially expressed genes at various stages of SE. The initiation of SE affected gene expression in many KEGG pathways, but predominantly that in metabolic pathways, biosynthesis of secondary metabolites, and plant hormone signal transduction. This information on the changes in the multiple pathways related to SE induction in E. senticosus Maxim. embryogenic tissue will contribute to a more comprehensive understanding of the mechanisms involved in early SE. Additionally, the differentially expressed genes may act as molecular markers and could play very important roles in the early stage of SE. The results are a comprehensive molecular biology resource for investigating SE of E. senticosus Maxim.
authors.affiliation: College of Life Sciences, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Tao
authors.affiliation: College of Life Sciences, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: College of Life Sciences, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wu
authors.affiliation: College of Life Sciences, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
authors.forename: Qiuyu
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China.
authors.forename: Hongmei
authors.initials: H
authors.lastname: Yuan
authors.affiliation: Crop Breeding Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China.
authors.forename: Lijuan
authors.initials: L
authors.lastname: Zhao
authors.affiliation: Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China.
authors.forename: Wendong
authors.initials: W
authors.lastname: Guo
authors.affiliation: College of Life Sciences, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China. Electronic address: yxiangling@yahoo.com.
authors.forename: Xiangling
authors.initials: X
authors.lastname: You
mesh_terms: D028001:Eleutherococcus / Q000196:embryology* / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D053858:Metabolic Networks and Pathways; D058977:Molecular Sequence Annotation; D010940:Plant Proteins / Q000235:genetics*; D058439:Plant Somatic Embryogenesis Techniques; D010946:Plants, Medicinal / Q000196:embryology / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D010940:Plant Proteins
keywords: Digital gene expression; Eleutherococcus senticosus Maxim.; Gene Ontology; Somatic embryogenesis; Transcriptome