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