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Metabolic profiling of grape berries infected with powdery mildew.
No full textThis dataset contains the normalized responses of profiled volatile and polar metabolites from control and infected berries with powdery mildew
Transcriptomic Leaf Profiling Reveals Differential Responses of the Two Most Traded Coffee Species to Elevated [CO2]
No full textAs atmospheric [CO2] continues to rise to unprecedented levels, understanding its impact on plants is imperative to improve crop performance and sustainability under future climate conditions. In this context, transcriptional changes promoted by elevated CO2 (eCO2) were studied in genotypes from the two major traded coffee species: the allopolyploid Coffea arabica (Icatu) and its diploid parent, C. canephora (CL153). While Icatu expressed more genes than CL153, a higher number of differentially expressed genes were found in CL153 as a response to eCO2. Although many genes were found to be commonly expressed by the two genotypes under eCO2, unique genes and pathways differed between them, with CL153 showing more enriched GO terms and metabolic pathways than Icatu. Divergent functional categories and significantly enriched pathways were found in these genotypes, which altogether supports contrasting responses to eCO2. A considerable number of genes linked to coffee physiological and biochemical responses were found to be affected by eCO2 with the significant upregulation of photosynthetic, antioxidant, and lipidic genes. This supports the absence of photosynthesis down-regulation and, therefore, the maintenance of increased photosynthetic potential promoted by eCO2 in these coffee genotypes
PHENO Reference MIAPPE templates
No full textThis dataset includes both reference MIAPPE files (.xlsx) used in PHENO (https://brapi.biodata.pt/) and PHENO documentation (https://pheno-docs.readthedocs.io/en/latest/)
Morpho-physiological changes imposed by water deficit in cork oak saplings
No full textCork oak half-sibling acorns from two field-grown mother trees (Alcochete, Portugal, Lat. 38.747491; Long. -8.931877) were collected in November 2018. Viable acorns were selected and cleaned by submergence in tap water, transferred to a water bath at 45 ºC for 2 h and dried in a 30 ºC chamber for 24 h. Acorns were stored in plastic bags at 4 ºC in the dark until further use. In January 2019, acorns were sown on a mixture of sand and vermiculite (1:1) in 700 mL pots (1 per pot) and maintained under a 12 h photoperiod (light intensity 400 μmol m-2 s-1) at 25 ºC, with regular watering. After two months, saplings were transferred to 7 L pots containing a mixture of soil and sand (1:1) and grown from March 2019 to September 2020 (assay-1) in a greenhouse (Oeiras, Portugal, Lat. 38.696189, Long. -9.320762). During the first year of growth all plants were kept under well-watered (WW) conditions (300 mL H2O/day) for optimal growth. In March 2020, saplings were divided into two groups that were subjected to WW conditions (control) or water deficit (WD), imposed by 4 weeks of water withholding followed by 20 weeks of deficit irrigation (300 mL H2O /week). A total of 57 plants were included in each group. Soil water content (SWC) was followed during the experiment and calculated according to (Sapeta et al., 2013). After stress imposition, stem diameter (1 cm above the root collar) and main stem height were measured monthly. A replicate assay (assay-2) was conducted with cork oak saplings sown in January 2021. In this case, drought stress was applied as mentioned above, from March 2022 to August 2022. These plants were used to measure photosynthesis efficiency using chlorophyll fluorescence. The effect of drought on photosynthesis was evaluated in assay-2 by rapid photosynthetic light curves using a MINI-PAM-II fluorometer (Heinz-Walz, Germany). This analysis was conducted in stems and leaves at day 0, 56, 100 and 120 after stress imposition. In detail, chlorophyll a fluorescence was measured in dark-adapted young leaves and stem sections (1 cm above root collar) subjected to increasing (every 20 seconds) photosynthetic active radiation (PAR, 3 – 470 μmol photons m-2 s-1).
The efficiency of Photosystem (PS) II (ΦPSII) was calculated using the formula ΦPSII = (Fm’-Fs)/Fm’ (Genty et al., 1989), where Fs and Fm’ represent steady state and maximum fluorescence, respectively. Electron transport rate (ETR) was calculated using ETR = ΦPSII x PAR x 0.5 x 0.84, where 0.84 is the assumed light absorbance of the leaf, and 0.5 the fraction of light absorbed by PSII (Genty et al., 1989)
Nematodes quantification and classification on soil extracts with five different mulch types in a Vaccinium virgatum plantation
No full textEvaluation of nematodes abundance on soil extracts with five different mulch types where blueberry plants (Vaccinium virgatum cv. ‘Centra Blue’) have grown. Nematodes were quantified and classified into phytoparasites, bacteriophages, fungivores, omnivores and predator
Next-Generation Proteomics Reveals a Greater Antioxidative Response to Drought in Coffea arabica Than in Coffea canephora
No full textDrought is a major threat to coffee, compromising the quality and quantity of its production. We have analyzed the core proteome of 18 Coffea canephora cv. Conilon Clone 153 and C. arabica cv. Icatu plants and assessed their responses to moderate (MWD) and severe (SWD) water deficits. Label-free quantitative shotgun proteomics identified 3000 proteins in both genotypes, but less than 0.8% contributed to ca. 20% of proteome biomass. Proteomic changes were dependent on the severity of drought, being stronger under SWD and with an enrolment of different proteins, functions, and pathways than under MWD. The two genotypes displayed stress-responsive proteins under SWD, but only C. arabica showed a higher abundance of proteins involved in antioxidant detoxification activities. Overall, the impact of MWD was minor in the two genotypes, contrary to previous studies. In contrast, an extensive proteomic response was found under SWD, with C. arabica having a greater potential for acclimation/resilience than C. canephora. This is likely supported by a wider antioxidative response and an ability to repair photosynthetic structures, being crucial to develop new elite genotypes that assure coffee supply under water scarcity levels
TRACE-RICE: physico-chemical_data_INIAV
No full textWithin the scope of the TRACE-RICE project, this study performed at INIAV research institute (Portugal) aims to characterize and discriminate between 22 rice varieties, which are mostly commercialized within the Mediterranean region. With this purpose, quality data was obtained from 22 samples of different rice varieties (originated from Portugal, Spain, France, Italy, Pakistan and Egypt)
Protein Isoelectric Points
No full textDataset containing the isoelectric points for ~120K proteins, taken from PDB (https://www.rcsb.org/) and processed via pyPKA (https://pypka.org/) and deposited in pKPDB (https://pypka.org/pKPDB/). Determined from the theoretical titration curve accounting for the individual pKa values of all titrable residues of each protein
Replication Data for: New insights into adaptation and population structure of cork oak using genotyping by sequencing (Filtered SNPs)
No full textThis dataset contains the filtered SNP files (.vcf and .loci format) from GBS reads assembled in ipyrad for used in the title study
Understanding the Impact of Drought in Coffea Genotypes: Transcriptomic Analysis Supports a Common High Resilience to Moderate Water Deficit but a Genotype Dependent Sensitivity to Severe Water Deficit
No full textWater scarcity is the most significant factor limiting coffee production, although some cultivars can still have important drought tolerance. This study analyzed leaf transcriptomes of two coffee cultivars with contrasting physiological responses, Coffea canephora cv. CL153 and Coffea. arabica cv. Icatu, subjected to moderate (MWD) or severe water deficits (SWD). We found that MWD had a low impact compared with SWD, where 10% of all genes in Icatu and 17% in CL153 reacted to drought, being mainly down-regulated upon stress. Drought triggered a genotype-specific response involving the up-regulation of reticuline oxidase genes in CL153 and heat shock proteins in Icatu. Responsiveness to drought also included desiccation protectant genes, but primarily, aspartic proteases, especially in CL153. A total of 83 Transcription Factors were found engaged in response to drought, mainly up-regulated, especially under SWD. Together with the enrollment of 49 phosphatases and 272 protein kinases, results suggest the involvement of ABA-signaling processes in drought acclimation. The integration of these findings with complementing physiological and biochemical studies reveals that both genotypes are more resilient to moderate drought than previously thought and suggests the existence of post-transcriptional mechanisms modulating the response to drought