Transcriptome dynamics of cork oak (Quercus suber) somatic embryogenesis reveals active gene players in transcription regulation and phytohormone homeostasis of embryo development
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Cork oak (Quercus suber L.) is one of the most important Mediterranean forest tree species. The last decades have been marked by a decline in this species. Implementation of breeding programs is fundamental to revert this trend. Somatic embryogenesis is the system of choice for clonal propagation, constituting a valuable tool for embryo production and improved genotype testing. In this study, the cork oak transcriptome during somatic embryogenesis was characterized in four stages of development to identify relevant genes in the process and to understand the molecular and biochemical events occurring in each specific stage. A total 66,693 candidate coding regions were predicted from the generated de novo transcriptome assembly. Differential gene expression analysis identified 11,507 genes distributed in 30 clusters with distinct gene expression patterns and enriched in various biological process GO terms. Results show 1159 differentially expressed genes coding for transcription regulators, namely transcription factors (76%) with important roles in embryogenesis, like orthologous of AINTEGUMENTA-like, PLETHORA, CYTOKININ RESPONSE FACTOR, GATA transcription factors, and AUXIN RESPONSE FACTORs genes. Results also show 250 differentially expressed phytohormone-related genes involved in important aspects of embryogenesis as tissue specification, differentiation, and embryogenesis competence. Finally, we identified a group of genes with functions in cellular protection and abiotic stress tolerance coding for LATE EMBRYOGENESIS ABUNDANT proteins. Cork oak embryogenesis transcriptome characterization represents a tool for future biotechnological applications. Our results provide a molecular insight into embryo development, establishing a basis for further research towards improvement of somatic embryogenesis in cork oak.
KeywordsQuercus suber Somatic embryogenesis Transcriptomics Transcription factor Hormone Plant biotechnology
The authors acknowledge Fundação para a Ciência e a Tecnologia (FCT) for awarding a PhD grant to Tiago Capote (SFRH/BD/69785/2010) and for funding António Marcos Ramos, Anabel Usié, and Pedro Barbosa through the Project Investigador FCT IF/01015/2013/CP1209/CT0001 - Genomics and bioinformatics applied to Portuguese plant and animal genetic resources, the project PTDC/AGR-FOR/3356/2014, and the research unit LEAF Unit UID/AGR/04129/2013. We also thank the Program Alentejo 2020 funded through the European Fund for Regional Development under the scope of LENTIDEV – A molecular approach to cork porosity (REF: ALT20-03-0145-FEDER-000020).
Fundação para a Ciência e a Tecnologia (FCT) funded the PhD grant for Tiago Capote (SFRH/BD/69785/2010). António Marcos Ramos, Anabel Usié, and Pedro Barbosa were funded by the Project Investigador FCT IF/01015/2013/CP1209/CT0001 - Genomics and bioinformatics applied to Portuguese plant and animal genetic resources. This work was funded by Program Alentejo 2020, through the European Fund for Regional Development under the scope of LENTIDEV – A molecular approach to cork porosity (REF: ALT20-03-0145-FEDER-000020).
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Conflict of interest
The authors declare that they have no conflict of interest.
- Abid G, Jacquemin J, Sassi K, Muhovski Y (2010) Gene expression and genetic analysis during higher plants embryogenesis. Biotechnol Agron Soc Environ 14:667–680Google Scholar
- Allen CD, Macalady AK, Chenchouni H, Bachelet D, McDowell N, Vennetier M, Kitzberger T, Rigling A, Breshears DD, Hogg EH(T), Gonzalez P, Fensham R, Zhang Z, Castro J, Demidova N, Lim JH, Allard G, Running SW, Semerci A, Cobb N (2010) A global overview of drought and heat-induced tree mortality reveals emerging climate change risks for forests. For Ecol Manag 259:660–684. https://doi.org/10.1016/j.foreco.2009.09.001 CrossRefGoogle Scholar
- Benjamins R, Scheres B (2008) Auxin: the looping star in plant development. Annu Rev Plant Biol 59:443–465. https://doi.org/10.1146/annurev.arplant.58.032806.103805 CrossRefPubMedGoogle Scholar
- Gaedeke N, Klein M, Kolukisaoglu U, Forestier C, Müller A, Ansorge M, Becker D, Mamnun Y, Kuchler K, Schulz B, Mueller-Roeber B, Martinoia E (2001) The Arabidopsis thaliana ABC transporter AtMRP5 controls root development and stomata movement. EMBO J 20:1875–1887. https://doi.org/10.1093/emboj/20.8.1875 CrossRefPubMedPubMedCentralGoogle Scholar
- Gao M, Gropp G, Wei S (2012) Combinatorial networks regulating seed development and seed filling. In: Ken-Ichi Sato (ed) Embryogenesis. InTech, pp 189–228Google Scholar
- Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652. https://doi.org/10.1038/nbt.1883 CrossRefPubMedPubMedCentralGoogle Scholar
- Hecht V, Vielle-Calzada JP, Hartog MV, Schmidt EDL, Boutilier K, Grossniklaus U, de Vries SC (2001) The Arabidopsis SOMATIC EMBRYOGENESIS RECEPTOR KINASE 1 gene is expressed in developing ovules and embryos and enhances embryogenic competence in culture. Plant Physiol 127:803–816. https://doi.org/10.1104/pp.010324 CrossRefPubMedPubMedCentralGoogle Scholar
- Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics 30:1236–1240. https://doi.org/10.1093/bioinformatics/btu031 CrossRefPubMedPubMedCentralGoogle Scholar
- Joshi N, Fass J (2011) Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files (version 1.33) [software]. Available at https://github.com/najoshi/sickle
- Kim S, Choi H, Ryu H-J, Park JH, Kim MD, Kim SY (2004) ARIA, an Arabidopsis arm repeat protein interacting with a transcriptional regulator of abscisic acid-responsive gene expression, is a novel abscisic acid signaling component. Plant Physiol 136:3639–3648. https://doi.org/10.1104/pp.104.049189 CrossRefPubMedPubMedCentralGoogle Scholar
- Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079. https://doi.org/10.1093/bioinformatics/btp352 CrossRefPubMedPubMedCentralGoogle Scholar
- Lu Y, Li C, Wang H, Chen H, Berg H, Xia Y (2011) AtPPR2, an Arabidopsis pentatricopeptide repeat protein, binds to plastid 23S rRNA and plays an important role in the first mitotic division during gametogenesis and in cell proliferation during embryogenesis. Plant J 67:13–25. https://doi.org/10.1111/j.1365-313X.2011.04569.x CrossRefPubMedPubMedCentralGoogle Scholar
- Milhinhos A, Prestele J, Bollhöner B, Matos A, Vera-Sirera F, Rambla JL, Ljung K, Carbonell J, Blázquez MA, Tuominen H, Miguel CM (2013) Thermospermine levels are controlled by an auxin-dependent feedback loop mechanism in Populus xylem. Plant J 75:685–698. https://doi.org/10.1111/tpj.12231 CrossRefPubMedGoogle Scholar
- Mockaitis K, Estelle M (2008) Auxin receptors and plant development: a new signaling paradigm. Annu Rev Cell Dev Biol 24:55–80. https://doi.org/10.1146/annurev.cellbio.23.090506.123214 CrossRefPubMedGoogle Scholar
- Murashige T, Skoog F (1962) A revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol Plant 15:473–497. https://doi.org/10.1111/j.1399-3054.1962.tb08052.x CrossRefGoogle Scholar
- Prasad K, Grigg SP, Barkoulas M, Yadav RK, Sanchez-Perez GF, Pinon V, Blilou I, Hofhuis H, Dhonukshe P, Galinha C, Mähönen AP, Muller WH, Raman S, Verkleij AJ, Snel B, Reddy GV, Tsiantis M, Scheres B (2011) Arabidopsis PLETHORA transcription factors control phyllotaxis. Curr Biol 21:1123–1128. https://doi.org/10.1016/j.cub.2011.05.009 CrossRefPubMedGoogle Scholar
- Rashotte AM, Mason MG, Hutchison CE, Ferreira FJ, Schaller GE, Kieber JJ (2006) A subset of Arabidopsis AP2 transcription factors mediates cytokinin responses in concert with a two-component pathway. Proc Natl Acad Sci U S A 103:11081–11085. https://doi.org/10.1073/pnas.0602038103 CrossRefPubMedPubMedCentralGoogle Scholar
- Rodríguez-Sanz H, Manzanera JA, Solís MT, Gómez-Garay A, Pintos B, Risueño MC, Testillano PS (2014) Early markers are present in both embryogenesis pathways from microspores and immature zygotic embryos in cork oak, Quercus suber L. BMC Plant Biol 14:1–18. https://doi.org/10.1186/s12870-014-0224-4 CrossRefGoogle Scholar
- Shen W-H, Parmentier Y, Hellmann H, Lechner E, Dong A, Masson J, Granier F, Lepiniec L̈, Estelle M, Genschik P (2002) Null mutation of AtCUL1 causes arrest in early embryogenesis in Arabidopsis. Mol Biol Cell 13:1916–1928. https://doi.org/10.1091/mbc.E02-02-0077 CrossRefPubMedPubMedCentralGoogle Scholar
- Spitzer C, Reyes FC, Buono R, Sliwinski MK, Haas TJ, Otegui MS (2009) The ESCRT-related CHMP1A and B proteins mediate multivesicular body sorting of auxin carriers in Arabidopsis and are required for plant development. Plant Cell 21:749–766. https://doi.org/10.1105/tpc.108.064865 CrossRefPubMedPubMedCentralGoogle Scholar
- Tanaka H, Watanabe M, Watanabe D, Tanaka T, Machida C, Machida Y (2002) ACR4, a putative receptor kinase gene of Arabidopsis thaliana, that is expressed in the outer cell layers of embryos and plants, is involved in proper embryogenesis. Plant Cell Physiol 43:419–428. https://doi.org/10.1093/pcp/pcf052 CrossRefPubMedGoogle Scholar
- Wu XM, Kou SJ, Liu YL, Fang YN, Xu Q, Guo WW (2015) Genomewide analysis of small RNAs in nonembryogenic and embryogenic tissues of citrus: microRNA- and siRNA-mediated transcript cleavage involved in somatic embryogenesis. Plant Biotechnol J 13:383–394. https://doi.org/10.1111/pbi.12317 CrossRefPubMedGoogle Scholar