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.
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).
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.
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.
Asano Y, Katsumoto H, Inokuma C, Kaneko S, Ito Y, Fujiie A (1996) Cytokinin and thiamine requirements and stimulative effects of riboflavin and α-ketoglutaric acid on embryogenic callus induction from the seeds of Zoysia japonica steud. J Plant Physiol 149:413–417. doi:10.1016/S0176-1617(96)80142-8CrossRefGoogle Scholar
Ascencio-Cabral A, Gutiérrez-Pulido H, Rodríguez-Garay B, Gutiérrez-Mora A (2008) Plant regeneration of Carica papaya L. through somatic embryogenesis in response to light quality, gelling agent and phloridzin. Sci Hortic 118:155–160CrossRefGoogle Scholar
Baudino S et al (2001) Molecular characterisation of two novel maize LRR receptor-like kinases, which belong to the SERK gene family. Planta 213:1–10CrossRefPubMedGoogle Scholar
Bhattacharya J, Khuspe S (2001) In vitro and in vivo germination of papaya (Carica papaya L.) seeds. Sci Hortic 91:39–49CrossRefGoogle Scholar
Chen M, Wang P, Maeda E (1987) Somatic embryogenesis and plant regeneration in Carica papaya L. tissue culture derived from root explants. Plant Cell Rep 6:348–351CrossRefPubMedGoogle Scholar
Chen C-J, Liu Q, Zhang Y-C, Qu L-H, Chen Y-Q, Gautheret D (2011) Genome-wide discovery and analysis of microRNAs and other small RNAs from rice embryogenic callus. RNA Biol 8:538–547CrossRefPubMedGoogle Scholar
da Silva JAT, Rashid Z, Nhut DT, Sivakumar D, Gera A, Souza MT Jr, Tennant PF (2007) Papaya (Carica papaya L.) biology and biotechnology. Tree For Sci Biotechnol 1:47–73Google Scholar
de Moura Vale E et al (2014) Comparative proteomic analysis of somatic embryo maturation in Carica papaya L. Proteom Sci 12:1CrossRefGoogle Scholar
Elgadir MA, Salama M, Adam A (2014) Carica papaya as a source of natural medicine and its utilization on selected pharmacetical applications. Int J Pharm Pharm Sci 6:868–871Google Scholar
Everett N, Wach M, Ashworth D (1985) Biochemical markers of embryogenesis in tissue cultures of the maize inbred B73. Plant Sci 41:133–140CrossRefGoogle Scholar
Fabi JP, Mendes LRBC, Lajolo FM, do Nascimento JRO (2010) Transcript profiling of papaya fruit reveals differentially expressed genes associated with fruit ripening. Plant Sci 179:225–233CrossRefGoogle Scholar
Fabi JP, Broetto SG, da Silva SLGL, Zhong S, Lajolo FM, do Nascimento JRO (2014) Analysis of papaya cell wall-related genes during fruit ripening indicates a central role of polygalacturonases during pulp softening. PLoS ONE 9:e105685CrossRefPubMedPubMedCentralGoogle Scholar
Fitch MM, Manshardt RM, Gonsalves D, Slightom JL (1993) Transgenic papaya plants from Agrobacterium-mediated transformation of somatic embryos. Plant Cell Rep 12:245–249CrossRefPubMedGoogle Scholar
Fransz P, De Ruijter N, Schel J (1989) Isozymes as biochemical and cytochemical markers in embryogenic callus cultures of maize (Zea mays L.). Plant Cell Rep 8:67–70CrossRefPubMedGoogle Scholar
Galland R, Blervacq A-S, Blassiau C, Smagghe B, Decottignies J-P, Hilbert J-L (2007) Glutathione-S-transferase is detected during somatic embryogenesis in chicory. Plant Signal Behav 2:343–348CrossRefPubMedPubMedCentralGoogle Scholar
Gao L, Zhang J, Hou Y, Yao Y, Ji Q (2015) RNA-seq screening of differentially-expressed genes during somatic embryogenesis in Fragaria x ananassa Duch. ‘Benihopp’. J Hortic Sci Biotechnol 90:671–681CrossRefGoogle Scholar
Gliwicka M, Nowak K, Balazadeh S, Mueller-Roeber B, Gaj MD (2013) Extensive modulation of the transcription factor transcriptome during somatic embryogenesis in Arabidopsis thaliana. PLoS ONE 8:e69261CrossRefPubMedPubMedCentralGoogle Scholar
Lai Z, Lin Y (2013) Analysis of the global transcriptome of longan (Dimocarpus longan Lour.) embryogenic callus using Illumina paired-end sequencing. BMC Genom 14:1CrossRefGoogle Scholar
Lin H-C, Morcillo F, Dussert S, Tranchant-Dubreuil C, Tregear JW, Tranbarger TJ (2009) Transcriptome analysis during somatic embryogenesis of the tropical monocot Elaeis guineensis: evidence for conserved gene functions in early development. Plant Mol Biol 70:173–192CrossRefPubMedGoogle Scholar
Litz RE, Conover RA (1981) In vitro polyembryony in Carica papaya L. ovules. Z Pflanzenphysiol 104:285–288CrossRefGoogle Scholar
Litz R, Conover R (1982) In vitro somatic embryogenesis and plant regeneration from Carica papaya L. ovular callus. Plant Sci Lett 26:153–158CrossRefGoogle Scholar
Ma Q, Zhou W, Zhang P (2014) Transition from somatic embryo to friable embryogenic callus in cassava: dynamic changes in cellular structure, physiological status, and gene expression profiles. Front Plant Sci 6:824Google Scholar
Piyatrakul P et al (2012) Some ethylene biosynthesis and AP2/ERF genes reveal a specific pattern of expression during somatic embryogenesis in Hevea brasiliensis. BMC Plant Biol 12:1CrossRefGoogle Scholar
Redig P, Shaul O, Inzé D, Van Montagu M, Van Onckelen H (1996) Levels of endogenous cytokinins, indole-3-acetic acid and abscisic acid during the cell cycle of synchronized tobacco BY-2 cells. FEBS Lett 391:175–180CrossRefPubMedGoogle Scholar
Salvo SA, Hirsch CN, Buell CR, Kaeppler SM, Kaeppler HF (2014) Whole transcriptome profiling of maize during early somatic embryogenesis reveals altered expression of stress factors and embryogenesis-related genes. PLoS ONE 9:e111407CrossRefPubMedPubMedCentralGoogle Scholar
Schmidt E, Guzzo F, Toonen M, De Vries S (1997) A leucine-rich repeat containing receptor-like kinase marks somatic plant cells competent to form embryos. Development 124:2049–2062PubMedGoogle Scholar
Sharma SK, Millam S, Hedley PE, McNicol J, Bryan GJ (2008) Molecular regulation of somatic embryogenesis in potato: an auxin led perspective. Plant Mol Biol 68:185–201CrossRefPubMedGoogle Scholar
Sun D-Q, Lu X-H, Liang G-L, Guo Q-G, Mo Y-W, Xie J-H (2011) Production of triploid plants of papaya by endosperm culture. Plant Cell Tissue Org Cult 104:23–29CrossRefGoogle Scholar
Thibaud-Nissen F, Shealy RT, Khanna A, Vodkin LO (2003) Clustering of microarray data reveals transcript patterns associated with somatic embryogenesis in soybean. Plant Physiol 132:118–136CrossRefPubMedPubMedCentralGoogle Scholar
Wickramasuriya AM, Dunwell JM (2015) Global scale transcriptome analysis of Arabidopsis embryogenesis in vitro. BMC Genom 16:1CrossRefGoogle Scholar
Xie C et al (2011) KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res. doi:10.1093/nar/gkr483Google Scholar
Xu K, Liu J, Fan M, Xin W, Hu Y, Xu C (2012) A genome-wide transcriptome profiling reveals the early molecular events during callus initiation in Arabidopsis multiple organs. Genomics 100:116–124CrossRefPubMedGoogle Scholar