Dataset Information

Characterization of the cork formation and production transcriptome in Quercus cerris?×?suber hybrids.

ABSTRACT: Cork oak is the main cork-producing species worldwide, and plays a significant economic, ecological and social role in the Mediterranean countries, in particular in Portugal and Spain. The ability to produce cork is limited to a few species, hence it must involve specific regulation mechanisms that are unique to these species. However, to date, these mechanisms remain largely understudied, especially with approaches involving the use of high-throughput sequencing technology. In this study, the transcriptome of cork-producing and non-cork-producing Quercus cerris?×?suber hybrids was analyzed in order to elucidate the differences between the two groups of trees displaying contrasting phenotypes for cork production. The results revealed the presence of a significant number of genes exclusively associated with cork production, in the trees that developed cork. Moreover, several gene ontology subcategories, such as cell wall biogenesis, lipid metabolic processes, metal ion binding and apoplast/cell wall, were only detected in the trees with cork production. These results indicate the existence, at the transcriptome level, of mechanisms that seem to be unique and necessary for cork production, which is an advancement in our knowledge regarding the genetic regulation behind cork formation and production.

SUBMITTER: Meireles B

PROVIDER: S-EPMC6041232 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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Publications

Characterization of the cork formation and production transcriptome in <i>Quercus cerris</i> × <i>suber</i> hybrids.

Meireles Brígida B Usié Ana A Barbosa Pedro P Fortes Ana Margarida AM Folgado André A Chaves Inês I Carrasquinho Isabel I Costa Rita Lourenço RL Gonçalves Sónia S Teixeira Rita Teresa RT Ramos António Marcos AM Nóbrega Filomena F

Physiology and molecular biology of plants : an international journal of functional plant biology 20180411 4

Cork oak is the main cork-producing species worldwide, and plays a significant economic, ecological and social role in the Mediterranean countries, in particular in Portugal and Spain. The ability to produce cork is limited to a few species, hence it must involve specific regulation mechanisms that are unique to these species. However, to date, these mechanisms remain largely understudied, especially with approaches involving the use of high-throughput sequencing technology. In this study, the t ...[more]

PMID: 30042611

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Project description:BACKGROUND: Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management. RESULTS: We generated in excess of 7 million sequence reads, by pyrosequencing 21 normalized cDNA libraries derived from multiple Q. suber tissues and organs, developmental stages and physiological conditions. We deployed a stringent sequence processing and assembly pipeline that resulted in the identification of ~159,000 unigenes. These were annotated according to their similarity to known plant genes, to known Interpro domains, GO classes and E.C. numbers. The phylogenetic extent of this ESTs set was investigated, and we found that cork oak revealed a significant new gene space that is not covered by other model species or EST sequencing projects. The raw data, as well as the full annotated assembly, are now available to the community in a dedicated web portal at http://www.corkoakdb.org. CONCLUSIONS: This genomic resource represents the first trancriptome study in a cork producing species. It can be explored to develop new tools and approaches to understand stress responses and developmental processes in forest trees, as well as the molecular cascades underlying cork differentiation and disease response.

Project description:Purpose:Acetylcholinesterase (AChE) inhibitors are used to treat Alzheimer's patients because they enhance cholinergic neurotransmission. It is urgent to find new and efficient inhibitors from natural sources, highly bioavailable with low or no toxicity. The plant kingdom is extremely rich in a variety of compounds that are potent AChE inhibitors: flavonoids and other phenolic compounds have been recognized as promising Alzheimer's treatment agents. In this study, in vitro acetylcholinesterase inhibition, antioxidant activities, and total flavonoid and phenolic contents of ethanol-water extracts from Quercus suber cork and corkback were evaluated. Methods:The acetylcholinesterase activity was determined by a colorimetric assay based on Ellman's methodology. The Folin-Ciocalteu colorimetric method was used for total phenolic content determination and the aluminium chloride method for the determination of total flavonoid content. Antioxidant activity assays were performed using the DPPH and FRAP assays. Results:The acetylcholinesterase inhibitory activity from Q. suber cork and corkback ethanol-water extracts was as follows: 62% inhibition with corkback extracts over 0.5?mg/mL and around 49% inhibition in cork extracts over 1.0?mg/mL extracts' concentration. Regarding the DPPH radical scavenging activity, the concentrations of cork and corkback ethanol-water extracts required for 50% DPPH inhibition (IC50) were 3.2??g/mL and 4.0-5.2??g/mL. Corkback extracts are less effective than Trolox standard (3.2??g/mL) but cork extracts showed the same free radical scavenging activity compared to Trolox. Cork and corkback extracts have antioxidant power of 750.9-775.4?mg TEAC/g extract and 1051.2-2052.4?mg TEAC/g extract, respectively, which are significantly higher than the ones obtained with Trolox: 19.6-21.0?mg TEAC/g extract (cork assays) and 57.4-66.3?mg TEAC/g extract (corkback assays). The amounts of total phenolic (TPC) and flavonoid (TFC) compounds were 8.7-32.3?mg GAE/g and 4.8-10.7?mg CE/g dry mass for cork and 5.4-5.7?mg GAE/g and 42.5?mg CE/g dry mass for corkback extracts, respectively, using catechin (CE) and GAE (gallic acid) as standards. Conclusion:These findings demonstrate the remarkable potential of these extracts as valuable source of antioxidants with interesting acetylcholinesterase inhibitory activity.

Project description:Hybridization and its relevance is a hot topic in ecology and evolutionary biology. Interspecific gene flow may play a key role in species adaptation to environmental change, as well as in the survival of endangered populations. Despite the fact that hybridization is quite common in plants, many hybridizing species, such as Quercus spp., maintain their integrity, while precise determination of genomic boundaries between species remains elusive. Novel high throughput sequencing techniques have opened up new perspectives in the comparative analysis of genomes and in the study of historical and current interspecific gene flow. In this work, we applied ddRADseq technique and developed an ad hoc bioinformatics pipeline for the study of ongoing hybridization between two relevant Mediterranean oaks, Q. ilex and Q. suber. We adopted a local scale approach, analyzing adult hybrids (sensu lato) identified in a mixed stand and their open-pollinated progenies. We have identified up to 9,435 markers across the genome and have estimated individual introgression levels in adults and seedlings. Estimated contribution of Q. suber to the genome is higher, on average, in hybrid progenies than in hybrid adults, suggesting preferential backcrossing with this parental species, maybe followed by selection during juvenile stages against individuals with higher Q. suber genomic contribution. Most discriminating markers seem to be scattered throughout the genome, suggesting that a large number of small genomic regions underlie boundaries between these species. A noticeable proportion of the markers (26%) showed allelic frequencies in adult hybrids very similar to one of the parental species, and very different from the other; a finding that seems relevant for understanding the hybridization process and the occurrence of adaptive introgression. Candidate marker databases developed in this study constitute a valuable resource to design large scale re-sequencing experiments in Mediterranean sclerophyllous oak species and could provide insight in species boundaries and on adaptive introgression between Q. suber and Q. ilex.

Dataset Information

Characterization of the cork formation and production transcriptome in Quercus cerris?×?suber hybrids.

Publications

Characterization of the cork formation and production transcriptome in <i>Quercus cerris</i> × <i>suber</i> hybrids.

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