Physiology and Molecular Biology of Plants

, Volume 23, Issue 2, pp 357–368 | Cite as

Genome-wide transcriptome profiling of Carica papaya L. embryogenic callus

  • Nur Diyana Jamaluddin
  • Normah Mohd Noor
  • Hoe-Han Goh
Research Article


Genome-wide transcriptome profiling is a powerful tool to study global gene expression patterns in plant development. We report the first transcriptome profile analysis of papaya embryogenic callus to improve our understanding on genes associated with somatic embryogenesis. By using 3′ mRNA-sequencing, we generated 6,190,687 processed reads and 47.0% were aligned to papaya genome reference, in which 21,170 (75.4%) of 27,082 annotated genes were found to be expressed but only 41% was expressed at functionally high levels. The top 10% of genes with high transcript abundance were significantly enriched in biological processes related to cell proliferation, stress response, and metabolism. Genes functioning in somatic embryogenesis such as SERK and LEA, hormone-related genes, stress-related genes, and genes involved in secondary metabolite biosynthesis pathways were highly expressed. Transcription factors such as NAC, WRKY, MYB, WUSCHEL, Agamous-like MADS-box protein and bHLH important in somatic embryos of other plants species were found to be expressed in papaya embryogenic callus. Abundant expression of enolase and ADH is consistent with proteome study of papaya somatic embryo. Our study highlights that some genes related to secondary metabolite biosynthesis, especially phenylpropanoid biosynthesis, were highly expressed in papaya embryogenic callus, which might have implication for cell factory applications. The discovery of all genes expressed in papaya embryogenic callus provides an important information into early biological processes during the induction of embryogenesis and useful for future research in other plant species.


3′ mRNA sequencing Embryogenic callus Papaya RNA-seq Transcriptome 



Alcohol dehydrogenase






Count per million


Gene ontology


Glutathione S-transferase


Kyoto encyclopaedia of genes and genomes


Late embryogenesis abundant


α-Naphthaleneacetic acid


Phenylalanine ammonia lyase


Somatic embryogenesis receptor-like kinase



We thank Kok-Keong Loke for helping with the RNA-seq analysis by generating the modified papaya genome reference for read alignment. This research was supported by the Malaysian Ministry of Science, Technology and Innovation (MOSTI) Sciencefund Grant 02-01-02-SF0907 and Universiti Kebangsaan Malaysia Research University Grant (GGPM-2011-053).

Authors Contributions

NDJ and HHG conceived and designed the experiments. NDJ performed the experiments. NDJ and HHG analysed the data. NDJ, NMN and HHG wrote the paper.

Compliance with ethical standards

Conflict of interest

The authors declare no competing financial interests. There is no restriction on publication of the data or information described in this manuscript.

Ethical approval

This study was conducted according to compliance with ethical standards. This study does not involve the use of any human, animal and endangered or protected plant species as materials.

Supplementary material

12298_2017_429_MOESM1_ESM.pdf (12.8 mb)
Supplementary material 1 (PDF 13152 kb)
12298_2017_429_MOESM2_ESM.pdf (610 kb)
Supplementary material 2 (PDF 609 kb)


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Copyright information

© Prof. H.S. Srivastava Foundation for Science and Society 2017

Authors and Affiliations

  1. 1.Institute of Systems BiologyUniversiti Kebangsaan Malaysia, UKMBangiMalaysia

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