A comparative transcriptomic approach to understanding the formation of cork
The transcriptome comparison of two oak species reveals possible candidates accounting for the exceptionally thick and pure cork oak phellem, such as those involved in secondary metabolism and phellogen activity.
Cork oak, Quercus suber, differs from other Mediterranean oaks such as holm oak (Quercus ilex) by the thickness and organization of the external bark. While holm oak outer bark contains sequential periderms interspersed with dead secondary phloem (rhytidome), the cork oak outer bark only contains thick layers of phellem (cork rings) that accumulate until reaching a thickness that allows industrial uses. Here we compare the cork oak outer bark transcriptome with that of holm oak. Both transcriptomes present similitudes in their complexity, but whereas cork oak external bark is enriched with upregulated genes related to suberin, which is the main polymer responsible for the protective function of periderm, the upregulated categories of holm oak are enriched in abiotic stress and chromatin assembly. Concomitantly with the upregulation of suberin-related genes, there is also induction of regulatory and meristematic genes, whose predicted activities agree with the increased number of phellem layers found in the cork oak sample. Further transcript profiling among different cork oak tissues and conditions suggests that cork and wood share many regulatory mechanisms, probably reflecting similar ontogeny. Moreover, the analysis of transcripts accumulation during the cork growth season showed that most regulatory genes are upregulated early in the season when the cork cambium becomes active. Altogether our work provides the first transcriptome comparison between cork oak and holm oak outer bark, which unveils new regulatory candidate genes of phellem development.
KeywordsCork Cork oak Phellem Rhytidome Suberin Wax
We would like to thank Professor M. Molinas (Departament de Biologia, UdG, Girona) for her useful advice and feedback during the analysis of the results and the drafting of the manuscript. The authors are grateful to Dr. R. Verdaguer, S. Fernández, S. Gómez and N. Salvatella for their help in cork harvesting. We thank Professor C. Pla (Departament de Biologia, UdG, Girona) for kindly lending the Thermocycler and Mr J. Blavia and Ms C. Carulla (Serveis Tècnics de Recerca, Universitat de Girona, Spain) for their highly skilled work with SEM. This work was supported by the Ministerio de Innovación y Ciencia [AGL2009-13745, FPI grant to P.B.], the Ministerio de Economía y Competitividad and FEDER funding [AGL2012-36725; AGL2015-67495-C2-1-R]. J.A.P.P. acknowledges the European Union’s Seventh Framework Programme for research, technological development and demonstration (EU FP7 Agreement No. 621321) and the Polish financial sources for education (2015–2019) allocated to Project No (W26/7.PR/2015).
PB, OS, JP and MF designed the experiment; PB extracted the RNA and purified the mRNA; PB, CH and CN performed bioinformatics; PB and AS performed qPCR; all authors analyzed and discussed the data. PB, MS, OS and MF wrote the manuscript.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
- Andersson-Gunnerås S, Mellerowicz EJ, Love J, Segerman B, Ohmiya Y, Coutinho PM et al (2006) Biosynthesis of cellulose-enriched tension wood in Populus: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis. Plant J 45:144–165. https://doi.org/10.1111/j.1365-313X.2005.02584.x CrossRefPubMedGoogle Scholar
- Bernal AJ, Yoo C-M, Mutwil M, Jensen JK, Hou G, Blaukopf C, Sørensen I, Blancaflor EB, Scheller HV, Willats WG (2008) Functional analysis of the cellulose synthase-like genes CSLD1, CSLD2, and CSLD4 in tip-growing Arabidopsis cells. Plant Physiol 148:1238–1253. https://doi.org/10.1104/pp.108.121939 CrossRefPubMedPubMedCentralGoogle Scholar
- Bourgis F, Kilaru A, Cao X, Ngando-Ebongue GF, Drira N, Ohlrogge JB et al (2011) Comparative transcriptome and metabolite analysis of oil palm and date palm mesocarp that differ dramatically in carbon partitioning. Proc Natl Acad Sci USA 108:12527–12532. https://doi.org/10.1073/pnas.1106502108 CrossRefPubMedPubMedCentralGoogle Scholar
- Choe S, Dilkes BP, Gregory BD, Ross AS, Yuan H, Noguchi T et al (1999) The Arabidopsis dwarf1 mutant is defective in the conversion of 24-methylenecholesterol to campesterol in brassinosteroid biosynthesis. Plant Physiol 119:897–907. https://doi.org/10.1104/pp.119.3.897 CrossRefPubMedPubMedCentralGoogle Scholar
- Compagnon V, Diehl P, Benveniste I, Meyer D, Schaller H, Schreiber L et al (2009) CYP86B1 is required for very long chain omega-hydroxyacid and alpha, omega-dicarboxylic acid synthesis in root and seed suberin polyester. Plant Physiol 150:1831–1843. https://doi.org/10.1104/pp.109.141408 CrossRefPubMedPubMedCentralGoogle Scholar
- Enjuto M, Balcells L, Campos N, Caelles C, Arró M, Boronat A (1994) Arabidopsis thaliana contains two differentially expressed 3-hydroxy-3-methylglutaryl-CoA reductase genes, which encode microsomal forms of the enzyme. Proc Natl Acad Sci USA 91:927–931. https://doi.org/10.1073/pnas.91.3.927 CrossRefPubMedPubMedCentralGoogle Scholar
- Fahn A (1967) Plant anatomy. Pergamon Press, OxfordGoogle Scholar
- Gou JY, Yu XH, Liu CJ (2009) A hydroxycinnamoyltransferase responsible for synthesizing suberin aromatics in Arabidopsis. Proc Natl Acad Sci USA 106:18855–18860. doi: https://doi.org/10.1073/pnas.0905555106\r0905555106 CrossRefPubMedPubMedCentralGoogle Scholar
- Gray-Mitsumune M, Mellerowicz EJ, Abe H, Schrader J, Winzéll A, Sterky F, Blomqvist K, McQueen-Mason S, Teeri TT, Sundberg B (2004) Expansins abundant in secondary xylem belong to subgroup A of the alpha-expansin gene family. Plant Physiol 135:1552–1564. https://doi.org/10.1104/pp.104.039321 CrossRefPubMedPubMedCentralGoogle Scholar
- Groover AT, Mansfield SD, DiFazio SP, Dupper G, Fontana JR, Millar R et al (2006) The Populus homeobox gene ARBORKNOX1 reveals overlapping mechanisms regulating the shoot apical meristem and the vascular cambium. Plant Mol Biol 61:917–932. https://doi.org/10.1007/s11103-006-0059-y CrossRefPubMedGoogle Scholar
- Howard ET (1977) Bark structure of southern upland oaks. Wood Fiber 9:172–183Google Scholar
- Ji J, Shimizu R, Sinha N, Scanlon MJ (2010) Analyses of WOX4 transgenics provide further evidence for the evolution of the WOX gene family during the regulation of diverse stem cell functions. Plant Signal Behav 5:916–920. https://doi.org/10.1104/pp.109.149641 CrossRefPubMedPubMedCentralGoogle Scholar
- Jung JH, Park JH, Lee S, To TK, Kim JM, Seki M et al (2013) The cold signaling attenuator HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE1 activates FLOWERING LOCUS C transcription via chromatin remodeling under short-term cold stress in Arabidopsis. Plant Cell 25:4378–4390. https://doi.org/10.1105/tpc.113.118364 CrossRefPubMedPubMedCentralGoogle Scholar
- Legay S, Sivadon P, Blervacq AS, Pavy N, Baghdady A, Tremblay L et al (2010) EgMYB1, an R2R3 MYB transcription factor from eucalyptus negatively regulates secondary cell wall formation in Arabidopsis and poplar. New Phytol 188:774–786. https://doi.org/10.1111/j.1469-8137.2010.03432.x CrossRefPubMedGoogle Scholar
- Li Y, Beisson F, Koo AJK, Molina I, Pollard M, Ohlrogge JB (2007) Identification of acyltransferases required for cutin biosynthesis and production of cutin with suberin-like monomers. Proc Natl Acad Sci USA 104:18339–18344. https://doi.org/10.1073/pnas.0706984104 CrossRefPubMedPubMedCentralGoogle Scholar
- Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402. https://doi.org/10.1146/annurev.genom.9.081307.164359 CrossRefPubMedGoogle Scholar
- Molina I, Li-Beisson Y, Beisson F, Ohlrogge JB, Pollard M (2009) Identification of an Arabidopsis feruloyl-coenzyme A transferase required for suberin synthesis. Plant Physiol 151:1317–1328. https://doi.org/10.1104/pp.109.144907\rpp.109.144907 CrossRefPubMedPubMedCentralGoogle Scholar
- Serra O, Hohn C, Franke R, Prat S, Molinas M, Figueras M (2010) A feruloyl transferase involved in the biosynthesis of suberin and suberin-associated wax is required for maturation and sealing properties of potato periderm. Plant J 62:277–290. https://doi.org/10.1111/j.1365-313X.2010.04144.x CrossRefPubMedGoogle Scholar
- Soler M, Plasencia A, Larbat R, Pouzet C, Jauneau A, Rivas S et al (2017) The Eucalyptus linker histone variant EgH1.3 cooperates with the transcription factor EgMYB1 to control lignin biosynthesis during wood formation. New Phytol 213:287–299. https://doi.org/10.1111/nph.14129 CrossRefPubMedGoogle Scholar
- Troncoso-Ponce MA, Kilaru A, Cao X, Durrett TP, Fan J, Jensen JK, Thrower NA, Pauly M, Wilkerson C, Ohlrogge JB (2011) Comparative deep transcriptional profiling of four developing oilseeds. Plant J 68:1014–1027. https://doi.org/10.1111/j.1365-313X.2011.04751.x CrossRefPubMedPubMedCentralGoogle Scholar
- Verdaguer R, Soler M, Serra O, Garrote A, Fernández S, Company-Arumí D, Anticó E, Molinas M, Figueras M (2016) Silencing of the potato StNAC103 gene enhances the accumulation of suberin polyester and associated wax in tuber skin. J Exp Bot 67:5415–5427. https://doi.org/10.1093/jxb/erw305 CrossRefPubMedPubMedCentralGoogle Scholar
- Waisel Y (1995) Developmental and functional aspects of the periderm. In: Iqbal M (ed) The cambial derivatives. Gebruder Borntraeger, Stuttgart, pp 293–315Google Scholar