Plants harbour a diverse fungal community with complex symbiotic interactions and significant rol... more Plants harbour a diverse fungal community with complex symbiotic interactions and significant roles in host physiology. However, the cues that steer the composition and structure of this community are poorly understood. Trees are useful models for assessing these factors because their large size and long lifespan give these ecosystems time and space to evolve and mature. Investigation of well-characterised pathosystems such as Dutch elm disease (DED) can reveal links between endomycobiome and pathogens. We examined the endophytic mycobiome across the aerial part of a landmark elm tree to identify structural patterns within plant hosts, highlighting not only commonalities but also the effect of local infections in some branches of the crown. We used a common garden trial of trees with varying levels of genotypic susceptibility to DED to identify associations between susceptibility and endomycobiome. Three families of yeasts were linked to higher DED tolerance: Buckleyzymaceae, Herpot...
Background: Bioinformatic software for RNA-seq analysis has high computational requirement in ter... more Background: Bioinformatic software for RNA-seq analysis has high computational requirement in terms of CPU number, RAM size, and processor characteristics. Specifically, de novo transcriptome assembly demands large computational infrastructure due to the massive data size, and the complexity of the algorithms employed. Comparative studies about the quality of the transcriptome yielded by de novo assemblers have been previously published, lacking, however, a hardware efficiency-oriented approach to help selecting the assembly hardware platform in a cost-efficient way. Objective: We tested the performance of two popular de novo transcriptome assemblers, Trinity and SOAPdenovo-Trans (SDNT) in terms of cost-efficiency and quality to assess limitations, and provide troubleshooting and guidelines to run transcriptome assemblies efficiently. Method: We built virtual machines with different hardware characteristics (CPU number, RAM size) in the Amazon Elastic Compute Cloud of the Amazon Web...
Drought-induced reduction of leaf gas exchange entails a complex regulation of the plant leaf met... more Drought-induced reduction of leaf gas exchange entails a complex regulation of the plant leaf metabolism. We used a combined molecular and physiological approach to understand leaf photosynthetic and respiratory responses of 2-year-old Quercus ilex seedlings to drought. Mild drought stress resulted in glucose accumulation while net photosynthetic CO2 uptake (Pn ) remained unchanged, suggesting a role of glucose in stress signaling and/or osmoregulation. Simple sugars and sugar alcohols increased throughout moderate-to-very severe drought stress conditions, in parallel to a progressive decline in Pn and the quantum efficiency of photosystem II; by contrast, minor changes occurred in respiration rates until drought stress was very severe. At very severe drought stress, 2-oxoglutarate dehydrogenase complex gene expression significantly decreased, and the abundance of most amino acids dramatically increased, especially that of proline and γ-aminobutyric acid (GABA) suggesting enhanced p...
Wilt diseases caused by vascular pathogens include some of the most damaging stresses affecting t... more Wilt diseases caused by vascular pathogens include some of the most damaging stresses affecting trees. Dutch elm disease (DED), caused by the fungus Ophiostoma novo-ulmi, destroyed most of North American and European elm populations in the 20th century. The highly susceptible English elm, also known as Atinian clone, suffered the highest mortality rates during the last pandemic event, probably due to its lack of genetic diversity. To study the DED pathosystem, we inoculated English elm ramets with O. novo-ulmi and evaluated xylem anatomy, molecular response, and disease symptoms. The high DED susceptibility of the clone was linked to xylem structure. The transcript levels changed significantly for 1,696 genes during O. novo-ulmi invasion. Genes covering different steps of the plant immune system were identified, many of which showed homology with Arabidopsis thaliana genes involved in systemic acquired resistance. Induction of several pathogenesis-related proteins and repression of ...
Abstract Castanea sativa Mill. and C. crenata Lieb. and Zucc. store 11S globulins as major seed p... more Abstract Castanea sativa Mill. and C. crenata Lieb. and Zucc. store 11S globulins as major seed proteins while Quercus ilex L. and Q. robur L., also members of the Fagaceae family, accumulate glutelins. The structure of the 11S Castanea globulins, which is similar to the ...
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.
We have carried out a candidate-gene-based association genetic study in Pinus pinaster Aiton and ... more We have carried out a candidate-gene-based association genetic study in Pinus pinaster Aiton and evaluated the predictive performance for genetic merit gain of the most significantly associated genes and single nucleotide polymorphisms (SNPs). We used a second generation 384-SNP array enriched with candidate genes for growth and wood properties to genotype mother trees collected in 20 natural populations covering most of the European distribution of the species. Phenotypic data for total height, polycyclism, root-collar diameter and biomass were obtained from a replicated provenance-progeny trial located in two sites with contrasting environments (Atlantic vs Mediterranean climate). General linear models identified strong associations between growth traits (total height and polycyclism) and four SNPs from the korrigan candidate gene, after multiple testing corrections using false discovery rate. The combined genomic breeding value predictions assessed for the four associated korriga...
Plants harbour a diverse fungal community with complex symbiotic interactions and significant rol... more Plants harbour a diverse fungal community with complex symbiotic interactions and significant roles in host physiology. However, the cues that steer the composition and structure of this community are poorly understood. Trees are useful models for assessing these factors because their large size and long lifespan give these ecosystems time and space to evolve and mature. Investigation of well-characterised pathosystems such as Dutch elm disease (DED) can reveal links between endomycobiome and pathogens. We examined the endophytic mycobiome across the aerial part of a landmark elm tree to identify structural patterns within plant hosts, highlighting not only commonalities but also the effect of local infections in some branches of the crown. We used a common garden trial of trees with varying levels of genotypic susceptibility to DED to identify associations between susceptibility and endomycobiome. Three families of yeasts were linked to higher DED tolerance: Buckleyzymaceae, Herpot...
Background: Bioinformatic software for RNA-seq analysis has high computational requirement in ter... more Background: Bioinformatic software for RNA-seq analysis has high computational requirement in terms of CPU number, RAM size, and processor characteristics. Specifically, de novo transcriptome assembly demands large computational infrastructure due to the massive data size, and the complexity of the algorithms employed. Comparative studies about the quality of the transcriptome yielded by de novo assemblers have been previously published, lacking, however, a hardware efficiency-oriented approach to help selecting the assembly hardware platform in a cost-efficient way. Objective: We tested the performance of two popular de novo transcriptome assemblers, Trinity and SOAPdenovo-Trans (SDNT) in terms of cost-efficiency and quality to assess limitations, and provide troubleshooting and guidelines to run transcriptome assemblies efficiently. Method: We built virtual machines with different hardware characteristics (CPU number, RAM size) in the Amazon Elastic Compute Cloud of the Amazon Web...
Drought-induced reduction of leaf gas exchange entails a complex regulation of the plant leaf met... more Drought-induced reduction of leaf gas exchange entails a complex regulation of the plant leaf metabolism. We used a combined molecular and physiological approach to understand leaf photosynthetic and respiratory responses of 2-year-old Quercus ilex seedlings to drought. Mild drought stress resulted in glucose accumulation while net photosynthetic CO2 uptake (Pn ) remained unchanged, suggesting a role of glucose in stress signaling and/or osmoregulation. Simple sugars and sugar alcohols increased throughout moderate-to-very severe drought stress conditions, in parallel to a progressive decline in Pn and the quantum efficiency of photosystem II; by contrast, minor changes occurred in respiration rates until drought stress was very severe. At very severe drought stress, 2-oxoglutarate dehydrogenase complex gene expression significantly decreased, and the abundance of most amino acids dramatically increased, especially that of proline and γ-aminobutyric acid (GABA) suggesting enhanced p...
Wilt diseases caused by vascular pathogens include some of the most damaging stresses affecting t... more Wilt diseases caused by vascular pathogens include some of the most damaging stresses affecting trees. Dutch elm disease (DED), caused by the fungus Ophiostoma novo-ulmi, destroyed most of North American and European elm populations in the 20th century. The highly susceptible English elm, also known as Atinian clone, suffered the highest mortality rates during the last pandemic event, probably due to its lack of genetic diversity. To study the DED pathosystem, we inoculated English elm ramets with O. novo-ulmi and evaluated xylem anatomy, molecular response, and disease symptoms. The high DED susceptibility of the clone was linked to xylem structure. The transcript levels changed significantly for 1,696 genes during O. novo-ulmi invasion. Genes covering different steps of the plant immune system were identified, many of which showed homology with Arabidopsis thaliana genes involved in systemic acquired resistance. Induction of several pathogenesis-related proteins and repression of ...
Abstract Castanea sativa Mill. and C. crenata Lieb. and Zucc. store 11S globulins as major seed p... more Abstract Castanea sativa Mill. and C. crenata Lieb. and Zucc. store 11S globulins as major seed proteins while Quercus ilex L. and Q. robur L., also members of the Fagaceae family, accumulate glutelins. The structure of the 11S Castanea globulins, which is similar to the ...
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.
We have carried out a candidate-gene-based association genetic study in Pinus pinaster Aiton and ... more We have carried out a candidate-gene-based association genetic study in Pinus pinaster Aiton and evaluated the predictive performance for genetic merit gain of the most significantly associated genes and single nucleotide polymorphisms (SNPs). We used a second generation 384-SNP array enriched with candidate genes for growth and wood properties to genotype mother trees collected in 20 natural populations covering most of the European distribution of the species. Phenotypic data for total height, polycyclism, root-collar diameter and biomass were obtained from a replicated provenance-progeny trial located in two sites with contrasting environments (Atlantic vs Mediterranean climate). General linear models identified strong associations between growth traits (total height and polycyclism) and four SNPs from the korrigan candidate gene, after multiple testing corrections using false discovery rate. The combined genomic breeding value predictions assessed for the four associated korriga...
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Papers by Carmen Collada