ABSTRACTThe periderm is basic for land plants due to its protective role during radial growth, wh... more ABSTRACTThe periderm is basic for land plants due to its protective role during radial growth, which is achieved by the polymers deposited in the cell walls. In most trees, like holm oak, the periderm is frequently replaced by subsequent internal periderms yielding a heterogeneous outer bark made of a mixture of periderms and phloem tissues, known as rhytidome. Exceptionally, cork oak forms a persistent or long-lived periderm which results in a homogeneous outer bark of thick phellem cell layers known as cork. Here we use the outer bark of cork oak, holm oak, and their natural hybrids’ to analyse the chemical composition, the anatomy and the transcriptome, and further understand the mechanisms underlying periderm development. The inclusion of hybrid samples showing rhytidome-type and cork-type barks is valuable to approach to cork and rhytidome development, allowing an accurate identification of candidate genes and processes. The present study underscores that biotic stress and cell...
Hybridization and introgression between cork oak (Quercus suber) and holm oak (Q. ilex) have trad... more Hybridization and introgression between cork oak (Quercus suber) and holm oak (Q. ilex) have traditionally been reckoned as undesirable processes, since hybrid individuals lack the profitable bark characteristics of cork oak. Nevertheless, a systematic and quantitative description of the bark of these hybrids at the microscopic level, based on a significant number of individuals, is not available to date. In this work we provide such a qualitative and quantitative description, identifying the most relevant variables for their classification. Hybrids show certain features intermediate between those of the parent species (such as phellem percentage in the outer bark, which was approximately 40% as a mean value for hybrids, 20% in holm oak and almost 99% in cork oak), as well as other unique features, such as the general suberization of inactive phloem (up to 25% in certain individuals), reported here for the first time. These results suggest a relevant hybridization-induced modificati...
The dataset contatins four SQLite3 databases of candidate marker loci from ddRADseq in <em>... more The dataset contatins four SQLite3 databases of candidate marker loci from ddRADseq in <em>Quercus suber</em>, <em>Quercus ilex </em>and their hybrids, corresponding to the data collected for the four filtering/imputation scenarios considered in the manuscript "ddRAD sequencing-based identification of species genomic boundaries and permeability in <em>Quercus ilex</em> and <em>Q. suber</em> hybrids" submitted to Frontiers in Plant Sciences. This work was funded by the project AGL2015-67495-C2-2-R (Spanish Ministry of Economy and Competitiveness).
Hybridization and its relevance is a hot topic in ecology and evolutionary biology. Interspecific... more 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 9,251 mar...
A noticeable proportion of low transcribed genes involved in wood formation in conifers may have ... more A noticeable proportion of low transcribed genes involved in wood formation in conifers may have been missed in previous transcriptomic studies. This could be the case for genes related to less abundant cell types, such as axial parenchyma and resin ducts, and genes related to juvenile wood. In this study, two normalized libraries have been obtained from the cambial zone of young individuals of Pinus canariensis C. Sm. ex DC, a species in which such cells are comparatively abundant. These two libraries cover earlywood (EW) and latewood (LW) differentiation, and reads have been de novo meta-assembled into one transcriptome. A high number of previously undescribed genes have been found. The transcriptional profiles during the growing season have been analyzed and several noticeable differences with respect to previous studies have been found. This work contributes to a more complete picture of wood formation in conifers. The genes and their transcription profiles described here provid...
Drought is the main selection agent in Mediterranean ecosystems and it is been suggested as an im... more Drought is the main selection agent in Mediterranean ecosystems and it is been suggested as an important evolutionary force responsible for population diversification in these environments. However, population divergence in quantitative traits can be driven by either directional natural selection, genetic drift or both. To investigate the roles of these forces on among-population divergence in ecophysiological traits related to drought tolerance (Δ13C, SLA, leaf size, Nmass), we compared molecular and quantitative genetic differentiation among thirteen cork oak (Quercus suber L.) populations spanning over a gradient of rainfall and temperature. Population differentiation for height, specific leaf area and leaf nitrogen content far exceeded the molecular differentiation measured by six nuclear microsatellites and was associated with the climatic gradient in among-year rainfall variation. These results suggest (1) these traits are subjected to directional selection and (2) the genetic differences among populations are partly due to adaptation to the rainfall unpredictability at the place of origin. By contrast, the low among population divergence found in stem diameter, annual growth and carbon isotopic discrimination (a surrogate for water use efficiency) and the weak association with the environmental gradient suggest low or no directional selection on these traits under dry conditions. Among-population differentiation for neutral markers was not a good predictor for differentiation regarding the quantitative traits studied here, but for leaf size. The observed correlation between the genetic differentiation for leaf size and that for molecular markers was exclusively due to the association between leaf size and microsatellite QpZAG46, which suggests a possible linkage between microsatellite QpZAG46 and genes encoding for leaf size
Summary Combined use of two newly designed PCR primers with already described rpl2 and trnH prime... more Summary Combined use of two newly designed PCR primers with already described rpl2 and trnH primers, yields amplification of three non-independent products from the hypervariable JLA region of eucalypt chloroplast. Polymorphism analysis of the resulting PCR markers is proved to be a time- and cost-efficient alternative to traditional cpDNA techniques as RFLP or sequencing for Eucalyptus globulus Labill. population genetics studies.
Axial system in gymnosperms wood is mostly constituted by tracheids, on which relay the transport... more Axial system in gymnosperms wood is mostly constituted by tracheids, on which relay the transport of water and nutrients and the mechanical support of aerial parts. However, it also includes a small proportion of parenchymatic cells, usually associated to resin ducts, mainly formed in the latewood. Few gymnosperm species, such as P. canariensis, show higher proportion of this tissue. These species display noticeable healing and even resprouting ability, probably associated to the abundance of axial parenchyma. In this work, we report the construction of EST (expressed sequence tag) libraries from developing xylem at the beginning of the growing season and during the summer, in order to identify candidate genes involved in the differentiation of the diverse cell types. Their expression patterns during the growing season have been analysed using microarrays.
Wounds stimulate diverse responses in plants, including mainly modifications in the differentiati... more Wounds stimulate diverse responses in plants, including mainly modifications in the differentiation fate of the injured and surrounding tissues, leading to the development of barriers against the attack of opportunistic pathogens and pests, healing or, in certain cases, regeneration of damaged organs or de novo generation of organs. The healing capacity is usually higher in angiosperms than gymnosperms. Specifically, re-sprouting is a relatively common feature in angiosperms, very important in post-fire recovery, after predation by herbivores, or even after logging. In conifers, resin from constitutive and traumatic channels covers the surface of the wound, preventing the entrance and development of fungi and other pathogens, but also impeding the eventual proliferation of immature xylem cells and the formation of a callus, as occurs in angiosperms. Thus, wounds in conifer stems must be sealed exclusively from the borders, presumably from vascular cambium, being a much slower proces...
Nowadays, there is a great amount of genomic and transcriptomic data available about forest speci... more Nowadays, there is a great amount of genomic and transcriptomic data available about forest species, including ambitious projects looking for complete sequencing and annotation of different gymnosperm genomes. Pinus canariensis is an endemic conifer of the Canary Islands with re-sprouting capability and resilience against fire and mechanical damage, as result of an adaptation to volcanic environments. Additionally, this species has a high proportion of axial parenchyma compared with other conifers, and this tissue connects with radial parenchyma allowing transport of reserves. The most internal tracheids stop accumulating water, and get filled of resins and polyphenols synthesized by the axial parenchyma; this is the so-called " torch-heartwood ", which avoids decay. This wood achieves very high prices due to its particular resistance to rot. These features make P. canariensis an interesting model species for the analysis of these developmental processes in conifers. In th...
ABSTRACTThe periderm is basic for land plants due to its protective role during radial growth, wh... more ABSTRACTThe periderm is basic for land plants due to its protective role during radial growth, which is achieved by the polymers deposited in the cell walls. In most trees, like holm oak, the periderm is frequently replaced by subsequent internal periderms yielding a heterogeneous outer bark made of a mixture of periderms and phloem tissues, known as rhytidome. Exceptionally, cork oak forms a persistent or long-lived periderm which results in a homogeneous outer bark of thick phellem cell layers known as cork. Here we use the outer bark of cork oak, holm oak, and their natural hybrids’ to analyse the chemical composition, the anatomy and the transcriptome, and further understand the mechanisms underlying periderm development. The inclusion of hybrid samples showing rhytidome-type and cork-type barks is valuable to approach to cork and rhytidome development, allowing an accurate identification of candidate genes and processes. The present study underscores that biotic stress and cell...
Hybridization and introgression between cork oak (Quercus suber) and holm oak (Q. ilex) have trad... more Hybridization and introgression between cork oak (Quercus suber) and holm oak (Q. ilex) have traditionally been reckoned as undesirable processes, since hybrid individuals lack the profitable bark characteristics of cork oak. Nevertheless, a systematic and quantitative description of the bark of these hybrids at the microscopic level, based on a significant number of individuals, is not available to date. In this work we provide such a qualitative and quantitative description, identifying the most relevant variables for their classification. Hybrids show certain features intermediate between those of the parent species (such as phellem percentage in the outer bark, which was approximately 40% as a mean value for hybrids, 20% in holm oak and almost 99% in cork oak), as well as other unique features, such as the general suberization of inactive phloem (up to 25% in certain individuals), reported here for the first time. These results suggest a relevant hybridization-induced modificati...
The dataset contatins four SQLite3 databases of candidate marker loci from ddRADseq in <em>... more The dataset contatins four SQLite3 databases of candidate marker loci from ddRADseq in <em>Quercus suber</em>, <em>Quercus ilex </em>and their hybrids, corresponding to the data collected for the four filtering/imputation scenarios considered in the manuscript "ddRAD sequencing-based identification of species genomic boundaries and permeability in <em>Quercus ilex</em> and <em>Q. suber</em> hybrids" submitted to Frontiers in Plant Sciences. This work was funded by the project AGL2015-67495-C2-2-R (Spanish Ministry of Economy and Competitiveness).
Hybridization and its relevance is a hot topic in ecology and evolutionary biology. Interspecific... more 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 9,251 mar...
A noticeable proportion of low transcribed genes involved in wood formation in conifers may have ... more A noticeable proportion of low transcribed genes involved in wood formation in conifers may have been missed in previous transcriptomic studies. This could be the case for genes related to less abundant cell types, such as axial parenchyma and resin ducts, and genes related to juvenile wood. In this study, two normalized libraries have been obtained from the cambial zone of young individuals of Pinus canariensis C. Sm. ex DC, a species in which such cells are comparatively abundant. These two libraries cover earlywood (EW) and latewood (LW) differentiation, and reads have been de novo meta-assembled into one transcriptome. A high number of previously undescribed genes have been found. The transcriptional profiles during the growing season have been analyzed and several noticeable differences with respect to previous studies have been found. This work contributes to a more complete picture of wood formation in conifers. The genes and their transcription profiles described here provid...
Drought is the main selection agent in Mediterranean ecosystems and it is been suggested as an im... more Drought is the main selection agent in Mediterranean ecosystems and it is been suggested as an important evolutionary force responsible for population diversification in these environments. However, population divergence in quantitative traits can be driven by either directional natural selection, genetic drift or both. To investigate the roles of these forces on among-population divergence in ecophysiological traits related to drought tolerance (Δ13C, SLA, leaf size, Nmass), we compared molecular and quantitative genetic differentiation among thirteen cork oak (Quercus suber L.) populations spanning over a gradient of rainfall and temperature. Population differentiation for height, specific leaf area and leaf nitrogen content far exceeded the molecular differentiation measured by six nuclear microsatellites and was associated with the climatic gradient in among-year rainfall variation. These results suggest (1) these traits are subjected to directional selection and (2) the genetic differences among populations are partly due to adaptation to the rainfall unpredictability at the place of origin. By contrast, the low among population divergence found in stem diameter, annual growth and carbon isotopic discrimination (a surrogate for water use efficiency) and the weak association with the environmental gradient suggest low or no directional selection on these traits under dry conditions. Among-population differentiation for neutral markers was not a good predictor for differentiation regarding the quantitative traits studied here, but for leaf size. The observed correlation between the genetic differentiation for leaf size and that for molecular markers was exclusively due to the association between leaf size and microsatellite QpZAG46, which suggests a possible linkage between microsatellite QpZAG46 and genes encoding for leaf size
Summary Combined use of two newly designed PCR primers with already described rpl2 and trnH prime... more Summary Combined use of two newly designed PCR primers with already described rpl2 and trnH primers, yields amplification of three non-independent products from the hypervariable JLA region of eucalypt chloroplast. Polymorphism analysis of the resulting PCR markers is proved to be a time- and cost-efficient alternative to traditional cpDNA techniques as RFLP or sequencing for Eucalyptus globulus Labill. population genetics studies.
Axial system in gymnosperms wood is mostly constituted by tracheids, on which relay the transport... more Axial system in gymnosperms wood is mostly constituted by tracheids, on which relay the transport of water and nutrients and the mechanical support of aerial parts. However, it also includes a small proportion of parenchymatic cells, usually associated to resin ducts, mainly formed in the latewood. Few gymnosperm species, such as P. canariensis, show higher proportion of this tissue. These species display noticeable healing and even resprouting ability, probably associated to the abundance of axial parenchyma. In this work, we report the construction of EST (expressed sequence tag) libraries from developing xylem at the beginning of the growing season and during the summer, in order to identify candidate genes involved in the differentiation of the diverse cell types. Their expression patterns during the growing season have been analysed using microarrays.
Wounds stimulate diverse responses in plants, including mainly modifications in the differentiati... more Wounds stimulate diverse responses in plants, including mainly modifications in the differentiation fate of the injured and surrounding tissues, leading to the development of barriers against the attack of opportunistic pathogens and pests, healing or, in certain cases, regeneration of damaged organs or de novo generation of organs. The healing capacity is usually higher in angiosperms than gymnosperms. Specifically, re-sprouting is a relatively common feature in angiosperms, very important in post-fire recovery, after predation by herbivores, or even after logging. In conifers, resin from constitutive and traumatic channels covers the surface of the wound, preventing the entrance and development of fungi and other pathogens, but also impeding the eventual proliferation of immature xylem cells and the formation of a callus, as occurs in angiosperms. Thus, wounds in conifer stems must be sealed exclusively from the borders, presumably from vascular cambium, being a much slower proces...
Nowadays, there is a great amount of genomic and transcriptomic data available about forest speci... more Nowadays, there is a great amount of genomic and transcriptomic data available about forest species, including ambitious projects looking for complete sequencing and annotation of different gymnosperm genomes. Pinus canariensis is an endemic conifer of the Canary Islands with re-sprouting capability and resilience against fire and mechanical damage, as result of an adaptation to volcanic environments. Additionally, this species has a high proportion of axial parenchyma compared with other conifers, and this tissue connects with radial parenchyma allowing transport of reserves. The most internal tracheids stop accumulating water, and get filled of resins and polyphenols synthesized by the axial parenchyma; this is the so-called " torch-heartwood ", which avoids decay. This wood achieves very high prices due to its particular resistance to rot. These features make P. canariensis an interesting model species for the analysis of these developmental processes in conifers. In th...
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