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Tree Genetics & Genomes

, 15:52 | Cite as

Transcriptome dynamics of cork oak (Quercus suber) somatic embryogenesis reveals active gene players in transcription regulation and phytohormone homeostasis of embryo development

  • Tiago Capote
  • Anabel Usié
  • Pedro Barbosa
  • Marcos Ramos
  • Leonor Morais-Cecílio
  • Sónia GonçalvesEmail author
Original Article
  • 29 Downloads
Part of the following topical collections:
  1. Gene Expression

Abstract

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.

Keywords

Quercus suber Somatic embryogenesis Transcriptomics Transcription factor Hormone Plant biotechnology 

Notes

Acknowledgments

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).

Funding

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).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11295_2019_1353_MOESM1_ESM.xlsx (33 kb)
Online Resource 1 Primers list and details (XLSX 32 kb)
11295_2019_1353_MOESM2_ESM.pdf (3.6 mb)
Online Resource 2 Smear plots and volcano plots (PDF 3663 kb)
11295_2019_1353_MOESM3_ESM.pdf (68 kb)
Online Resource 3 Cluster analysis of differentially expressed genes by the K-means method from the gene expression profile. Vertical axes represent relative expression values. Horizontal axes represent the 4 embryos developmental stages: ST1, ST2, ST3 and ST4. (PDF 67 kb)
11295_2019_1353_MOESM4_ESM.pdf (382 kb)
Online Resource 4 GO functional classification of differentially expressed genes on biological process at level 2, molecular function at level 3 and cellular localization at level 4 (PDF 382 kb)
11295_2019_1353_MOESM5_ESM.xlsx (1.4 mb)
Online Resource 5 GO slim annotations of all differentially expressed genes (XLSX 1413 kb)
11295_2019_1353_MOESM6_ESM.xlsx (193 kb)
Online Resource 6 Differential expression of transcription factors, transcription regulators and chromatin regulators (XLSX 192 kb)
11295_2019_1353_MOESM7_ESM.xlsx (35 kb)
Online Resource 7 Hormone related genes, blastx annotation, gene description, and expression data (XLSX 34 kb)
11295_2019_1353_MOESM8_ESM.xlsx (20 kb)
Online Resource 8 Embryogenesis related genes, blastx annotation, gene description, and expression data (XLSX 32 kb) (XLSX 19 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)Instituto Politécnico de Beja (IPBeja)BejaPortugal
  2. 2.Linking Landscape, Environment, Agriculture and Food, Instituto Superior de AgronomiaUniversity of LisbonLisbonPortugal
  3. 3.Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM)Universidade de ÉvoraÉvoraPortugal
  4. 4.Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUK

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