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| Status |
Public on Jun 16, 2021 |
| Title |
A time-course transcriptomic analysis during the cork growing season highlights the regulatory and developmental processes from phellogen to phellem formation |
| Organism |
Quercus suber |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The phellogen or cork cambium is a bifacial stem cell population from which derivatives are formed by periclinal divisions and specified on opposing sides as phelloderm (inwardly) and phellem or cork (outwardly). Altogether the three layers constitute the periderm which covers and protects the radially-grown organs (stems, roots and tubers) and wounded tissues from dehydration and pathogen attack. The phellem is the final responsible of the protective function of periderm and despite its vital importance, just the suberin biosynthetic process has been studied molecularly while other processes are poorly understood. To shed some light on the phellem cell development from its formation to its final maturation, we used the innercork living material of cork planks extracted from cork oak (Quercus suber) in which we analysed the transcriptome at three time-points: at the beginning (April), maximum (June) and final (July) cork seasonal growth. Since cork presents seasonal growth and the process from phellogen derivative proliferation and specification to phellem cells is continuous, the time-course cork samples were used to approach the phellem cell formation and development. The June enrichment of phellem cells undergoing suberization was confirmed transcriptionally, observing highest expression of suberin-related genes in this month, thus validating our strategy. To highlight the major molecular processes embracing from phellogen to mature phellem cell, the differentially expressed genes between time-points were clustered based on their expression pattern. April transcriptome upregulates the processes involved in the meristem proliferation and maintenance and the triggering of cell differentiation, in agreement with the enrichment of phellogenic cells from which phellem cells are specified. The processes upregulated in Juny and July cork samples, were secondary metabolic processes compatible with the biosynthesis of secondary metabolites deposited within phellem cell wall such as suberin, lignin, extractives including fatty aciyl-derived compounds and triterpenes and also soluble aromatic compounds. The processes with a maximum in July showed upregulation of polyssacharides- and lignin-related processes compatible with a reinforcement of the cork cell wall, presumably related with the latecork formation with smaller and thickened-cells at the end of the growing season. For the above mentioned processes, we discuss the putative function of the most relevant genes in the context of phellem ontogeny. This work provides the most important molecular mechanisms during phellem cell development and provide relevant data for the understanding of the seasonal growth of cork, a material of important circular economic value.
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| Overall design |
Sample: Innercork material (phellem + phellogenic tissue) of freshly-harvested virgin cork planks from cork oak (Quercus suber) trees growing naturally in Romanyà de la Selva (Girona, Spain). Replicates: Each replicate was harvested from a different tree. 4 samples were from cork planks harvested in April, 3 samples harvested in June and 4 samples harvested in July.
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| Contributor(s) |
Fernández-Piñán S, Boher P, Soler M, Molinas M, Figueras M, Serra O |
| Citation(s) |
34103550 |
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| Submission date |
Aug 02, 2020 |
| Last update date |
Jun 16, 2021 |
| Contact name |
Olga Serra |
| E-mail(s) |
olga.serra@udg.edu
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| Organization name |
Universitat de Girona
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| Department |
Biologia
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| Lab |
Laboratori del Suro
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| Street address |
C/ Maria Aurèlia Capmany, 40
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| City |
Girona |
| State/province |
Girona |
| ZIP/Postal code |
17003 |
| Country |
Spain |
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| Platforms (1) |
| GPL28954 |
Illumina HiSeq 2500 (Quercus suber) |
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| Samples (11)
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| GSM4705968 |
Innercork April replicate 1 [ap1_11162_CGATGT] |
| GSM4705969 |
Innercork April replicate 2 [ap2_11163_TGACCA] |
| GSM4705970 |
Innercork April replicate 3 [ap3_11164_CAGATC] |
| GSM4705971 |
Innercork April replicate 4 [ap4_11165_CCGTCC] |
| GSM4705972 |
Innercork June replicate 1 [ju1_11166_GTTTCG] |
| GSM4705973 |
Innercork June replicate 2 [ju3_11167_ATCACG] |
| GSM4705974 |
Innercork June replicate 3 [ju4_11168_GCCAAT] |
| GSM4705975 |
Innercork July replicate 1 [jl1_11169_ACTTGA] |
| GSM4705976 |
Innercork July replicate 2 [jl2_11170_TAGCTT] |
| GSM4705977 |
Innercork July replicate 3 [jl3_11171_GGCTAC] |
| GSM4705978 |
Innercork July replicate 4 [jl4_11172_CTTGTA] |
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| Relations |
| BioProject |
PRJNA650215 |
| SRA |
SRP275507 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE155544_rlog_data.txt.gz |
3.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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