Salvia hispanica L. (chia) is a plant of the Lamiaceae family native to Central America, is mainly grown in southwestern France, with a preference for the ORURO® variety. Chia seeds contain over 30 % oil and 19 % protein. They are rich in omega-3 (ω3) and omega-6 (ω6) fatty acids, with a favorable ω3/ ω6 ratio, making them a valuable source of nutrients. Chia seeds store nutrients in lipid droplets and protein bodies. During germination, these nutrients are mobilized to support seedling growth. This study explores how germination can enhance the quality of chia seed reserves for food applications. Thus, we examined the biochemical and metabolic changes during germination leading to the breakdown and mobilization of seed reserves. Using proteomics and lipidomics, we monitored changes in storage proteins and lipids during chia seed germination. Our findings revealed significant molecular remodeling, suggesting that germination may enhances chia's nutritional value for human consumption.

Branched broomrape (Phelipanche ramosa (L.) Pomel), an obligate parasitic weed with a wide host range, is known for its devasting effects on many crops worldwide. Soil fungi, notably Fusarium sp., are described as pathogenic to broomrape, while the hypothesis of the phytotoxicity of fusaric acid produced by F. verticillioides for parasitic weeds of the genus Orobanche has been proposed. Using image analysis and untargeted metabolomics, this study investigated fungal metabolites phytotoxic for P. ramosa and produced by the F. venenatum MIAE02836 strain, isolated from symptomatic broomrapes and identified as a promising candidate for broomrape biocontrol. Phytotoxicity tests of crude extracts from the fungus alone or in interaction with broomrape on P. ramosa microcalli and quantification of necrosis by image analysis confirmed the phytotoxic potential of F. venenatum MIAE02836 metabolites towards the early developmental stages of P. ramosa. Data analysis of a non-targeted metabolomics approach revealed numerous metabolites produced by F. venenatum MIAE02836. Four of them, accumulated during interaction with the parasitic plant, are known for their phytotoxic potential: maculosin, cyclo(Leu-Phe), phenylalanyl-D-histidine and anguidine. These results suggest that combining image acquisition of the microcalli screening test and untargeted metabolomic approach is an interesting and relevant method to characterize phytotoxic fungal metabolites.

The extracellular space in plant tissues, known as the apoplast, remains one of the least characterized cellular compartments. The apoplastic fluid (APF), akin to mammalian extracellular fluid, serves as the primary interface between pathogens and their host. It allows the exchange of signalling molecules, coordinates host cell responses, and enables the circulation of pathogen effectors that modulate the immune response. We describe here the first multi-omics analysis of the APF content just 6 h after the onset of A. thaliana infection with B. cinerea , a fast-killing necrotrophic fungus. By varying plant nitrogen nutrition, known to affect both plant defenses and pathogen virulence, we identify candidates that do not stand out under optimal conditions. Our analysis uncovers novel nitrogen-dependent mechanisms that regulate both basal and early induced apoplastic immunity, revealing the presence of previously unidentified, potentially protective apoplastic metabolites as well as the intercellular transport of nuclear proteins, thereby offering new insights into early apoplastic immune responses.

The analysis of metabolic profiles using high resolution mass spectrometry (MS) data gives deep insights into the biological processes. In metabolomics, MS generates a large number of features that represent metabolites. However, identifying specific metabolites from these features can be challenging. One of the major bottlenecks in the metabolomics field is the identification of MS features, which is a prerequisite for any biochemical interpretation. By identifying similarities and differences within a family, evaluating MS features at the metabolite family level can help assign functional roles to individual MS features. This data can help interpret metabolic pathways and processes within a biological system. For the assignment of metabolite families to MS features, it is very important to have good quality, reliable, and diverse spectral libraries. We initiated a global effort to collect high-resolution MS/MS spectra of metabolites from all biological origins, including mammals, microorganisms, and plants. The mFAM-MS/MS Collection delivers valuable training data to assign machine-readable classified information on the unknown metabolites. The mFam Consortium used a standardized metadata template and has developed a globally curated MS/MS spectral library of 7,872 spectra with 2,126 unique metabolites. This library was compiled from 47 datasets contributed by 25 laboratories and leverages 12 instrument types, including QTOF, Orbitrap, and Ion Mobility systems. It comprises 4,646 spectra in positive mode and 3,226 in negative mode. This standardized resource significantly enhances metabolite identification capabilities, supports the development of machine learning-based annotation tools, and accelerates the discovery of novel metabolites. All spectra are available under the collective contributor label mFam in the MassBank system, including the web interface and the 2025.10 data release available at GitHub and Zenodo.

Summary: The extracellular space in plant tissues, known as the apoplast, remains one of the least characterized cellular compartments. The apoplastic fluid, akin to mammalian extracellular fluid, serves as the primary interface between pathogens and their host. It allows the exchange of signalling molecules, coordinates host cell responses and enables the circulation of pathogen effectors that modulate the immune response. We describe here a comprehensive multi‐omics analysis of the apoplastic washing fluids content just 6 h after the onset of Arabidopsis thaliana infection with Botrytis cinerea , a fast‐killing necrotrophic fungus. By varying plant nitrogen nutrition, known to affect both plant defenses and pathogen virulence, we identify candidates that do not stand out under optimal conditions. Our analysis uncovers novel nitrogen‐dependent mechanisms that regulate both basal and early induced apoplastic immunity, revealing the presence of previously unidentified, potentially protective apoplastic metabolites as well as RAN GTPase, a nuclear protein, thereby offering new insights into early apoplastic immune responses.