Quercus Genetics: Insights into the Past, Present, and Future of Oaks

Backs, Janet Rizner; Ashley, Mary V.

doi:10.3390/f12121628

Cited by 6 publications

(8 citation statements)

References 8 publications

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“…distributed throughout the Northern Hemisphere to Malaysia and Colombia (Kew Royal Botanic Garden: https://powo.science.kew.org/results?q=Quercus ). Playing an important role in human life since the prehistoric period, oaks are the most important woody species in terms of diversity, ecological dominance, and economic value, being a source of a wide variety of goods and services for humans and animals ( Leroy et al., 2020 ; Backs and Ashley, 2021 ). Among them Q. suber and Q. ilex are the dominant species in natural forest ecosystems over a large area of the Western Mediterranean Basin, and in the agrosilvopastoral Spanish “dehesa” ( Olea and San Miguel-Ayanz, 2006 ; De Rigo and Gaudullo, 2016 ; Surová et al., 2017 ).…”

Section: Proteomics Survey (2012-2022): Where Are We Now?mentioning

confidence: 99%

Proteomics research in forest trees: A 2012-2022 update

et al. 2023

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This review is a compilation of proteomic studies on forest tree species published in the last decade (2012-2022), mostly focused on the most investigated species, including Eucalyptus, Pinus, and Quercus. Improvements in equipment, platforms, and methods in addition to the increasing availability of genomic data have favored the biological knowledge of these species at the molecular, organismal, and community levels. Integration of proteomics with physiological, biochemical and other large-scale omics in the direction of the Systems Biology, will provide a comprehensive understanding of different biological processes, from growth and development to responses to biotic and abiotic stresses. As main issue we envisage that proteomics in long-living plants will thrive light on the plant responses and resilience to global climate change, contributing to climate mitigation strategies and molecular breeding programs. Proteomics not only will provide a molecular knowledge of the mechanisms of resilience to either biotic or abiotic stresses, but also will allow the identification on key gene products and its interaction. Proteomics research has also a translational character being applied to the characterization of the variability and biodiversity, as well as to wood and non-wood derived products, traceability, allergen and bioactive peptides identification, among others. Even thought, the full potential of proteomics is far from being fully exploited in forest tree research, with PTMs and interactomics being reserved to plant model systems. The most outstanding achievements in forest tree proteomics in the last decade as well as prospects are discussed.

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Section: Proteomics Survey (2012-2022): Where Are We Now?mentioning

confidence: 99%

Proteomics research in forest trees: A 2012-2022 update

et al. 2023

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“…The genus Quercus (family Fagaceae, common name oak) emerged during global warming 55 million years ago [ 9 ], and is one of the largest genera of flowering woody plants, evergreen or deciduous, that produces acorn fruits; it dominates so-called oak forests and woodlands, natural or modified ecosystems, and constitutes a source of biodiversity [ 10 ]. The genus Quercus is one of the most relevant clades in the Northern Hemisphere in terms of number of species and ecological dominance [ 11 ]; in fact, the Plants of the World Online database [ 12 ] contains 460 Quercus spp. distributed throughout the Northern Hemisphere to Malaysia and Colombia.…”

Section: Quercus Ilex the Dominant Forest Tree Species In T...mentioning

confidence: 99%

“…Oaks have played an important role in human life since the prehistoric period and throughout different civilizations, being a source of a wide variety of goods and services, from wood for fuel and construction to food for human and animal consumption [ 13 ]. Despite being one of the most important woody species in terms of diversity, ecological dominance, and economic value [ 11 ], their molecular biology is scarcely known, and oaks can be considered, in general terms, an orphan of molecular studies, with some exceptions. Among those, it is worth mentioning Quercus robur L., considered the model within the genus, Quercus lobata Née, Quercus suber L. and Q. ilex , with this last species constituting our object of study for the past 20 years [ 8 ].…”

Section: Quercus Ilex the Dominant Forest Tree Species In T...mentioning

confidence: 99%

Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How

Maldonado‐Alconada

Castillejo

Rey

et al. 2022

IJMS

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The holm oak (Quercus ilex L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, “dehesa.” It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the basis of the economy in rural areas. Currently, there is renewed interest in its use for dietary diversification and sustainable food production. It is part of cultural richness, both economically (tangible) and environmentally (intangible), and must be preserved for future generations. However, a worrisome degradation of the species and associated ecosystems is occurring, observed in an increase in tree decline and mortality, which requires urgent action. Breeding programs based on the selection of elite genotypes by molecular markers is the only plausible biotechnological approach. To this end, the authors’ group started, in 2004, a research line aimed at characterizing the molecular biology of Q. ilex. It has been a challenging task due to its biological characteristics (long life cycle, allogamous, high phenotypic variability) and recalcitrant nature. The biology of this species has been characterized following the central dogma of molecular biology using the omics cascade. Molecular responses to biotic and abiotic stresses, as well as seed maturation and germination, are the two main objectives of our research. The contributions of the group to the knowledge of the species at the level of DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, and metabolomics are discussed here. Moreover, data are compared with those reported for Quercus spp. All omics data generated, and the genome of Q. ilex available, will be integrated with morphological and physiological data in the systems biology direction. Thus, we will propose possible molecular markers related to resilient and productive genotypes to be used in reforestation programs. In addition, possible markers related to the nutritional value of acorn and derivate products, as well as bioactive compounds (peptides and phenolics) and allergens, will be suggested. Subsequently, the selected molecular markers will be validated by both genome-wide association and functional genomic analyses.

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“…It is one of the most important clades of woody angiosperms in the Northern hemisphere in terms of species diversity, ecological dominance, and economic value (Backs and Ashley, 2021), and has been part of our life, culture, and subsistence since ancient times (Leroy et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…Holm oak ( Quercus ilex L.) is included in the 640 recorded species in the “Plants of the World Online” database within the genus Quercus (de Rigo and Caudullo, 2016; Kew Royal Botanic Gardens; https://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:325819-2#bibliography). It is one of the most important clades of woody angiosperms in the Northern hemisphere in terms of species diversity, ecological dominance, and economic value (Backs and Ashley, 2021), and has been part of our life, culture, and subsistence since ancient times (Leroy et al, 2020). Moreover, it is a priority species for afforestation due to its high adaptability to semi-arid climate conditions, drought tolerance (Barbeta and Peñuelas, 2016), and plastic response to varying edaphic conditions (Laureano et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

A first draft genome of Holm oak (Quercus ilexL.), the most representative species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem “dehesa”

Rey

Labella-Ortega

Guerrero‐Sanchez

et al. 2022

Preprint

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The holm oak (Quercus ilex L.) is the most representative species of the Mediterranean Basin and the agrosilvopastoral Spanish dehesa ecosystem. Being part of our life, culture, and subsistence since ancient times, it has great environmental and economic importance. More recently, there has been a renewed interest in using the Q. ilex acorn as a functional food due to its nutritional and nutraceutical properties. However, the holm oak and its related ecosystems are threatened by different factors, with oak decline syndrome and climate change being the most worrying on the short and medium term. Breeding programs informed by selection of elite genotypes seems to be the only plausible biotechnological solution to rescue populations under threat. To achieve this and other downstream analyses, we need a high-quality Q. ilex reference genome. Here, we introduce the first draft genome assembly of Q. ilex using long-read sequencing (PacBio). The assembled nuclear haploid genome has 530 contigs totaling 842.2 Mbp (N50 = 3.3 Mbp), of which 448.7 Mb (53%) are repetitive sequences. We annotated 39,443 protein-coding genes and Benchmarking Universal Single-Copy Orthologs analysis detected 412 out of 425 expected complete and single-copy genes (94.80%) within the Q. ilex genome. The chloroplast genome size was 142.3 Kbp with 149 protein-coding genes successfully annotated. This first draft should allow for the validation of -omics data as well as the identification and functional annotation of genes related to phenotypes of interest such as those associated to resilience against oak decline syndrome and climate change, higher acorn productivity and nutraceutical value.

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Quercus Genetics: Insights into the Past, Present, and Future of Oaks

Abstract: The genus Quercus comprises over 400 species found across the Northern Hemisphere [...]

Cited by 6 publications

References 8 publications

Proteomics research in forest trees: A 2012-2022 update

Proteomics research in forest trees: A 2012-2022 update

Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How

A first draft genome of Holm oak (Quercus ilexL.), the most representative species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem “dehesa”

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