Data mining study of hormone biosynthesis gene expression reveals new aspects of somatic embryogenesis regulation

  • R. T. Saptari
  • H. SusilaEmail author
Developmental Biology


Although the application of exogenous hormones and the status of endogenous hormones play a crucial factor in somatic embryogenesis (SE), our understanding of the status of endogenous hormones and the molecular framework for hormone biosynthesis during SE are still elusive. With a data mining approach, we analyzed public RNA-seq data of SE from two model plants, Arabidopsis thaliana and Oryza sativa var. Japonica, which showed that several plant hormone biosynthesis genes had distinct patterns during SE. The expressions of auxin, cytokinin, gibberellin, and ethylene biosynthesis genes were induced during SE in A. thaliana, while only jasmonic acid showed an expression increase during somatic embryogenesis in both plants. Furthermore, by analyzing public RNA sequencing and DNA affinity purification sequencing (DAP-seq), we revealed some possibilities of the role of ethylene during SE through the activity of EIN3, by increasing the expression level of major transcription factors of somatic embryo development such as AGL15, BBM, and FUS3.


Data mining Phytohormones Somatic embryogenesis Transcriptomics 



We are grateful to Z. Nasim (Korea University, South Korea) for his technical advices on bioinformatics analysis and to Dr. R. A. Putranto (Indonesian Research Institute for Biotechnology and Bioindustry, Indonesia) for the discussion during manuscript preparation.

Funding information

This paper is also made possible through the support of Indonesian Endowment Fund for Education (LPDP) to R. T. Saptari.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11627_2018_9947_MOESM1_ESM.docx (233 kb)
ESM 1 (DOCX 232 kb)


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Copyright information

© The Society for In Vitro Biology 2018

Authors and Affiliations

  1. 1.Indonesian Research Institute for Biotechnology and BioindustryBogorIndonesia
  2. 2.School of Life Science and TechnologyBandung Institute of TechnologyBandungIndonesia
  3. 3.Departement of Life SciencesKorea UniversitySeoulSouth Korea

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