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

Nur Diyana Jamaluddin, Normah Mohd. Noor, Hoe Han Goh

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)1-12
Number of pages12
JournalPhysiology and Molecular Biology of Plants
DOIs
Publication statusAccepted/In press - 20 Mar 2017

Fingerprint

Carica
Carica papaya
Bony Callus
Gene Expression Profiling
transcriptomics
callus
papayas
Genome
genome
Genes
genes
Embryonic Development
Biological Phenomena
biosynthesis
somatic embryos
somatic embryogenesis
secondary metabolites
Basic Helix-Loop-Helix Transcription Factors
Plant Development
Phosphopyruvate Hydratase

Keywords

  • 3′ mRNA sequencing
  • Embryogenic callus
  • Papaya
  • RNA-seq
  • Transcriptome

ASJC Scopus subject areas

  • Physiology
  • Molecular Biology
  • Plant Science

Cite this

Genome-wide transcriptome profiling of Carica papaya L. embryogenic callus. / Jamaluddin, Nur Diyana; Mohd. Noor, Normah; Goh, Hoe Han.

In: Physiology and Molecular Biology of Plants, 20.03.2017, p. 1-12.

Research output: Contribution to journalArticle

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