title: Computational identification and systematic classification of novel GRAS genes in Isatis indigotica.
abstract: Isatis indigotica Fort., belonging to Cruciferae, is one of the most commonly used plants in traditional Chinese medicine. The accumulation of the effective components of I. indigotica is related with its growth conditions. The GRAS genes are members of a multigene family of transcriptional regulators that play a crucial role in plant growth. Although the activities of many GRAS genes have long been recognized, only in recent years were some of them identified and functionally characterized in detail. In the present study, 41 GRAS genes were identified from I. indigotica through bioinformatics methods for the first time. They were classified into ten groups according to the classification of Arabidopsis and rice. The characterization, gene structure, conserved motifs, disordered N-terminal domains, and phylogenetic reconstruction of these GRASs were analyzed. Forty-three orthologous gene pairs were shared by I. indigotica and Arabidopsis, and interaction networks of these orthologous genes were constructed. Furthermore, gene expression patterns were investigated by analysis in methyl jasmonate (MeJA)-treated I. indigotica hairy roots based on RNA-seq data. In conclusion, this comprehensive analysis would provide rich resources for further studies of GRAS protein functions in this plant.
authors.affiliation: Department of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, China; Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Department of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, China. Electronic address: qli@smmu.edu.cn.
authors.forename: Qing
authors.initials: Q
authors.lastname: Li
authors.affiliation: Department of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.
authors.forename: Jun-Feng
authors.initials: JF
authors.lastname: Chen
authors.affiliation: Department of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, China. Electronic address: chenwanshengsmmu@aliyun.com.
authors.forename: Wan-Sheng
authors.initials: WS
authors.lastname: Chen
mesh_terms: D019295:Computational Biology; D020869:Gene Expression Profiling; D017343:Genes, Plant; D031219:Isatis / Q000235:genetics*; D008516:Medicine, Chinese Traditional; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D014157:Transcription Factors
keywords: Conserved motifs; GRAS transcriptional regulators; Gene expression; Isatis indigotica; Phylogenetic analysis