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- Disclosing proteins in the leaves of cork oak plants associated with the immune response to Phytophthora cinnamomi inoculation in the roots: a long-term proteomics approachPublication . Coelho, Ana Cristina; Pires, Rosa; Schütz, Gabriela; Santa, Cátia; Manadas, Bruno; Pinto, Patricia ISThe pathological interaction between oak trees and Phytophthora cinnamomi has implications in the cork oak decline observed over the last decades in the Iberian Peninsula. During host colonization, the phytopathogen secretes effector molecules like elicitins to increase disease effectiveness. The objective of this study was to unravel the proteome changes associated with the cork oak immune response triggered by P. cinnamomi inoculation in a long-term assay, through SWATH-MS quantitative proteomics performed in the oak leaves. Using the Arabidopis proteome database as a reference, 424 proteins were confidently quantified in cork oak leaves, of which 80 proteins showed a p-value below 0.05 or a fold-change greater than 2 or less than 0.5 in their levels between inoculated and control samples being considered as altered. The inoculation of cork oak roots with P. cinnamomi increased the levels of proteins associated with protein-DNA complex assembly, lipid oxidation, response to endoplasmic reticulum stress, and pyridine-containing compound metabolic process in the leaves. In opposition, several proteins associated with cellular metabolic compound salvage and monosaccharide catabolic process had significantly decreased abundances. The most significant abundance variations were observed for the Ribulose 1,5-Bisphosphate Carboxylase small subunit (RBCS1A), Heat Shock protein 90-1 (Hsp90-1), Lipoxygenase 2 (LOX2) and Histone superfamily protein H3.3 (A8MRLO/At4G40030) revealing a pertinent role for these proteins in the host-pathogen interaction mechanism. This work represents the first SWATH-MS analysis performed in cork oak plants inoculated with P. cinnamomi and highlights host proteins that have a relevant action in the homeostatic states that emerge from the interaction between the oomycete and the host in the long term and in a distal organ.
- Using gradient Forest to predict climate response and adaptation in Cork oakPublication . Vanhove, Mathieu; Pina-Martins, Francisco; Coelho, Ana Cristina; Branquinho, Cristina; Costa, Augusta; Batista, Dora; Principe, Adriana; Sousa, Paulo; Henriques, Andre; Marques, Isabel; Belkadi, Bouchra; Knowles, L. Lacey; Paulo, Octavio S.Climate change is impacting locally adapted species such as the keystone tree species cork oak (Quercus suber L.). Quantifying the importance of environmental variables in explaining the species distribution can help build resilient populations in restoration projects and design forest management strategies. Using landscape genomics, we investigated the population structure and ecological adaptation of this tree species across the Mediterranean Basin. We applied genotyping by sequencing and derived 2,583 single nucleotide polymorphism markers genotyped from 81 individuals across 17 sites in the studied region. We implemented an approach based on the nearest neighbour haplotype 'coancestry' and uncovered a weak population structure along an east-west climatic gradient across the Mediterranean region. We identified genomic regions potentially involved in local adaptation and predicted differences in the genetic composition across the landscape under current and future climates. Variants associated with temperature and precipitation variables were detected, and we applied a nonlinear multivariate association method, gradient forest, to project these gene-environment relationships across space. The model allowed the identification of geographic areas within the western Mediterranean region most sensitive to climate change: south-western Iberia and northern Morocco. Our findings provide a preliminary assessment towards a potential management strategy for the conservation of cork oak in the Mediterranean Basin.
- Spectral analysis, biocompounds, and physiological assessment of Cork Oak leaves: unveiling the interaction with Phytophthora cinnamomi and beyondPublication . Guerra, Rui; Pires, Rosa; Brazio, António; Cavaco, Ana Margarida; Schütz, Gabriela; Coelho, Ana CristinaThe cork oak tree (Quercus suber L.) symbolizes the Montado landscape in Portugal and is a central element in the country’s social and economic history. In recent decades, the loss of thousands of cork oaks has been reported, revealing the ongoing decline of these agroforestry ecosystems. This emblematic tree of the Mediterranean Basin is host to the soil-born root pathogen Phytophthora cinnamomi, an active cork oak decline driver. In this framework, the early diagnosis of trees infected by the oomycete by non-invasive methods should contribute to the sustainable management of cork oak ecosystems, which motivated this work. Gas exchange and visible/near-infrared (400–1100 nm) reflectance spectroscopy measurements were conducted on leaves of both control and P. cinnamomi inoculated plants. These measurements were taken at 63, 78, 91, 126, and 248 days after inoculation. Additionally, at the end of the experiment, biochemical assays of pigments, sugars, and starch were performed. The spectroscopic measurements proved effective in distinguishing between control and inoculated plants, while the standard gas exchange and biochemistry data did not exhibit clear differences between the groups. The spectral data were examined both daily and globally, utilizing the PARAFAC method applied to a three-way array of samples × wavelengths × days. The separation of the two plant groups was attributed to variations in water content (4v (O−H)); shifts in the spectra red edge; and structural modifications in the epidermal layer and leaves’ mesophyll. These spectral signatures can assist in the field identification of cork oaks that are interacting with P. cinnamomi.
- Protein markers for the identification of cork oak plants infected with phytophthora cinnamomi by applying an (α, β)-k-feature set approachPublication . Coelho, Ana Cristina; Schütz, GabrielaCork oak decline in Mediterranean forests is a complex phenomenon, observed with remarkable frequency in the southern part of the Iberian Peninsula, causing the weakening and death of these woody plants. The defoliation of the canopy, the presence of dry peripheral branches, and exudations on the trunk are visible symptoms used for the prognosis of decline, complemented by the presence of Phytophthora cinnamomi identified in the rhizosphere of the trees and adjacent soils. Recently, a large proteomic dataset obtained from the leaves of cork oak plants inoculated and non-inoculated with P. cinnamomi has become available. We explored it to search for an optimal set of proteins, markers of the biological pattern of interaction with the oomycete. Thus, using published data from the cork oak leaf proteome, we mathematically modelled the problem as an α, β-k-Feature Set Problem to select molecular markers. A set of proteins (features) that represent dominant effects on the host metabolism resulting from pathogen action on roots was found. These results contribute to an early diagnosis of biochemical changes occurring in cork oak associated with P. cinnamomi infection. We hypothesize that these markers may be decisive in identifying trees that go into decline due to interactions with the pathogen, assisting the management of cork oak forest ecosystems.