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.
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Abbreviations
- ADH:
-
Alcohol dehydrogenase
- BAP:
-
Benzylaminopurine
- bHLH:
-
Basic/HELIX–LOOP–HELIX
- CPM:
-
Count per million
- GO:
-
Gene ontology
- GST:
-
Glutathione S-transferase
- KEGG:
-
Kyoto encyclopaedia of genes and genomes
- LEA:
-
Late embryogenesis abundant
- NAA:
-
α-Naphthaleneacetic acid
- PAL:
-
Phenylalanine ammonia lyase
- SERK:
-
Somatic embryogenesis receptor-like kinase
References
Andriotis VM, Kruger NJ, Pike MJ, Smith AM (2010) Plastidial glycolysis in developing Arabidopsis embryos. New Phytol 185:649–662. doi:10.1111/j.1469-8137.2009.03113.x
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)80142-8
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 118:155–160
Baudino S et al (2001) Molecular characterisation of two novel maize LRR receptor-like kinases, which belong to the SERK gene family. Planta 213:1–10
Bhattacharya J, Khuspe S (2001) In vitro and in vivo germination of papaya (Carica papaya L.) seeds. Sci Hortic 91:39–49
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi:10.1093/bioinformatics/btu170
Chen M, Chen C (1992) Plant regeneration from Carica protoplasts. Plant Cell Rep 11:404–407
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 6:348–351
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 8:538–547
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 1:47–73
de Moura Vale E et al (2014) Comparative proteomic analysis of somatic embryo maturation in Carica papaya L. Proteom Sci 12:1
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 6:868–871
Everett N, Wach M, Ashworth D (1985) Biochemical markers of embryogenesis in tissue cultures of the maize inbred B73. Plant Sci 41:133–140
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 179:225–233
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:e105685
Fehér A, Pasternak TP, Dudits D (2003) Transition of somatic plant cells to an embryogenic state. Plant Cell Tissue Org Cult 74:201–228. doi:10.1023/a:1024033216561
Fitch MM, Manshardt RM, Gonsalves D, Slightom JL (1993) Transgenic papaya plants from Agrobacterium-mediated transformation of somatic embryos. Plant Cell Rep 12:245–249
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 8:67–70
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 2:343–348
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 90:671–681
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:e69261
Lai Z, Lin Y (2013) Analysis of the global transcriptome of longan (Dimocarpus longan Lour.) embryogenic callus using Illumina paired-end sequencing. BMC Genom 14:1
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. doi:10.1038/nmeth.1923
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 70:173–192
Litz RE, Conover RA (1981) In vitro polyembryony in Carica papaya L. ovules. Z Pflanzenphysiol 104:285–288
Litz R, Conover R (1982) In vitro somatic embryogenesis and plant regeneration from Carica papaya L. ovular callus. Plant Sci Lett 26:153–158
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 6:824
Maere S, Heymans K, Kuiper M (2005) BiNGO: A cytoscape plugin to assess overrepresentation of geneontology categories in biological networks. Bioinformatics 21:3448–3449. doi:10.1093/bioinformatics/bti551
Marsoni M, Bracale M, Espen L, Prinsi B, Negri AS, Vannini C (2008) Proteomic analysis of somatic embryogenesis in Vitis vinifera. Plant Cell Rep 27:347–356. doi:10.1007/s00299-007-0438-0
Ming R et al (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452:991–996
Moll P, Ante M, Seitz A, Reda T (2014) QuantSeq 3′ mRNA sequencing for RNA quantification. Nat Methods. doi:10.1038/nmeth.f.376
Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:W182–W185. doi:10.1093/nar/gkm321
Murashige T, Skoog F (1962) A Revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol Plant 15:473–497. doi:10.1111/j.1399-3054.1962.tb08052.x
Pandey SP, Somssich IE (2009) The role of WRKY transcription factors in plant immunity. Plant Physiol 150:1648–1655
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 12:1
Porter BW, Aizawa KS, Zhu YJ, Christopher DA (2008) Differentially expressed and new non-protein-coding genes from a Carica papaya root transcriptome survey. Plant Sci 174:38–50. doi:10.1016/j.plantsci.2007.09.013
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 391:175–180
Roberts A, Pachter L (2013) Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Meth 10:71–73. doi:10.1038/nmeth.2251
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:e111407
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 124:2049–2062
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 68:185–201
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 104:23–29
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 132:118–136
Urasaki N et al (2012) Digital transcriptome analysis of putative sex-determination genes in (Carica papaya). PLoS ONE 7:e40904. doi:10.1371/journal.pone.0040904
Wickramasuriya AM, Dunwell JM (2015) Global scale transcriptome analysis of Arabidopsis embryogenesis in vitro. BMC Genom 16:1
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/gkr483
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 100:116–124
Ye J et al (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. doi:10.1093/nar/gkl031
Yu T-A, Yeh S-D, Cheng Y-H, Yang J-S (2000) Efficient rooting for establishment of papaya plantlets by micropropagation. Plant Cell Tissue Org Cult 61:29–35
Acknowledgements
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.
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The authors declare no competing financial interests. There is no restriction on publication of the data or information described in this manuscript.
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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.
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The collection of sequences generated in this study is available under NCBI BioProject accession PRJNA323966 and Sequence Read Archive (SRA) database (Accession Numbers SRR4087172 and SRR4087196).
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Jamaluddin, N.D., Mohd Noor, N. & Goh, HH. Genome-wide transcriptome profiling of Carica papaya L. embryogenic callus. Physiol Mol Biol Plants 23, 357–368 (2017). https://doi.org/10.1007/s12298-017-0429-8
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DOI: https://doi.org/10.1007/s12298-017-0429-8