Biology subjects

Aubry, S.

Publications and source records attributed to Aubry, S..

6 recordsLinked to original sources

bioRxiv2026

Future-proofing agrobiodiversity: climate and niche-aware conservation planning using reinforcement learning.

Despite substantial global commitments to expand protected-area networks, the strategic allocation of limited resources remains challenging. Spatial conservation planning helps identify priority regions that maximise conservation benefits per unit area. Yet, they also tend to neglect two fundamental aspects of conservation: climate-driven range shifts and the representation of environmentally distinct populations within species. Here, we propose a continental-scale conservation planning framework that explicitly accounts for both processes through novel routines implemented in the conservation planning software CAPTAIN. We apply this framework to European crop wild relatives (CWR), for which niche coverage is a focal priority, as it underpins their potential to support agricultural adaptation to future environmental stressors through breeding programs. Comparative analyses on a subset of 186 CWR associated with five focal crops show that accounting for range shifts and niche coverage leads to substantially different conservation priorities from those obtained with a baseline model based on current distributions only. These additions reduced the number of non-protected species by 64%, increased the average protected distribution range by 43%, increased mean niche coverage from 75.8% to 84.5% and reduced the number of species with less than half of their niche protected from 35 to 10. Applied to a more comprehensive checklist of 1,140 European CWRs, the final framework identifies continental-scale priority areas representing 93.5% of these taxa and includes 94.4% of its critically endangered species. Our results highlight the importance of incorporating both temporal dynamics and within-species environmental representation when designing conservation strategies under climate change. RepositoryThe repository will be made publicly accessible after publication at doi: https://10.5281/zenodo.19855597

ecology↗

bioRxiv2023

Detection of genetically modified organisms using highly multiplexed amplicon sequencing

The circulation of products based on genetically modified (GM) organisms is highly regulated by some governments having implemented strict rules on the breeding, planting, marketing, labelling, and trading of such products. To ensure compliance, accurate detection methods for GM events are necessary, along with assurance that GM material falls within relevant threshold levels. The increasing complexity and potential of undocumented GM are a growing challenge for genetic screening. In this study, we developed and assessed a highly multiplexed amplicon sequencing assay for the detection of GM events based on a microfluidics platform and next-generation sequencing (NGS). To probe GM events comprehensively, we designed a total of 230 new amplicons to cover flanking, promoter, junction and coding sequences of GM sequences. In addition, we designed and implemented parallel amplification of ribosomal and chloroplast markers to define crop species identity from potentially mixed samples. Using reference GM material of 11 crop species and multiple amplicons, we successfully detected the presence of 10 known modifications per GM event. We also find that reported flanking sequences of GM events may not be all useful for diagnostic. We assessed the assays potential to detect GM events in mixed samples as well as in highly diluted DNA. Finally, we performed a prospective search of potentially undocumented GM events in plant material. Our microfluidics-based amplicon GM detection approach fills important gaps in detecting potentially undocumented and complex GM events by recovering a wide range of specific amplicon sequences for evaluation. Integrating highly parallel amplicon assays in GM screening efforts should be an effective complement to aid post-market monitoring and regulatory compliance efforts.

genomics↗

bioRxiv2022

Importance of agriculture for Crop Wild Relatives conservation in Switzerland

Crop Wild Relatives are a subset of the global plant diversity that is often neglected, as not the primary focus for conservationists or plant breeders. However, a relatively large portion of the wild flora, up to 60% in Switzerland for example, do share genetic relationships with cultivated species and therefore can be considered as Crop Wild Relatives. Their conservation appears simultaneously a challenge to conservation programmes but also a considerable levy to mobilize other sectors, like agriculture, to contribute to the conservation of biodiversity at large. Here, we provide a comprehensive checklist of Swiss Crop Wild Relatives representing 2,226 taxa, of which 285 prioritised taxa, referred to as "Crop wild relatives Of Concern", were designated. Following a taxa-specific ecogeographic analysis, we analysed the extent to which CWR of concern are already contained in existing protected areas as well as their distribution in the agricultural area. Prioritised Crop Wild Relatives species richness was compared to modelled species richness to identify potential conservation gaps. About a fifth of CWR of concern is not significantly better protected than a random species by existing protected areas. However, 28.8 % and 15.5 % of these taxa are more frequently distributed in agricultural and summer grazing areas respectively than random expectations. A clear deficit of species richness for these Crop Wild Relatives of concern was inferred on low lands, possibly related to a lower sampling effort. We further identified a network of 39 sites that contains all taxa of Swiss CWR of concern and that could be used as a primary conservation infrastructure. More generally, our results could be generalized to other countries and support better consideration of CWR in agriculture areas, an important "reservoir" for expanding specific measures of conservation that are crucial to meet the future global goals of diversity conservation frameworks.

plant biology↗

bioRxiv2021

Evolution of chlorophyll degradation is associated with plant transition to land

Colonization of land by green plants (Viridiplantae) some 500 million years ago was made possible by large metabolic and biochemical adaptations. Chlorophyll, the central pigment of photosynthesis, is highly photo-active. In order to mitigate deleterious effects of pigment accumulation, some plants have evolved a coordinated pathway to deal with chlorophyll degradation end-products, so-called phyllobilins. This pathway has been so far mostly unravelled in Arabidopsis thaliana. Here, large-scale comparative phylogenomic coupled to an innovative biochemical characterization strategy of phyllobilins allow a better understanding how such a pathway appeared in Viridiplantae. Our analysis reveals a stepwise evolution of the canonical pheophorbide a monooxygenase/phyllobilin pathway. It appears to have evolved gradually, first in chlorophytes chloroplasts, to ensure multicellularity by detoxifying chlorophyll catabolites, and in charophytes outside chloroplasts to allow adaptation of embryophytes to land. At least six out of the eight genes involved in the pathway were already present in the last common ancestor of green plants. This strongly suggests parallel evolution of distinct enzymes catalysing similar reactions in various lineages, particularly for the dephytylation step. Together, our study suggests that chlorophyll degradation accompanied the transition from water to land, and was therefore of great importance for plant diversification.

plant biology↗

bioRxiv2018

Pheophorbide a, a chlorophyll catabolite may regulate jasmonate signalling during dark-induced senescence in Arabidopsis

Chlorophyll degradation is one of the most visible landmarks of leaf senescence. During senescence, chlorophyll is degraded in the multi-step pheophorbide a oxygenase (PAO)/phyllobilin pathway, which is tightly regulated at the transcriptional level. This regulation allows a coordinated and efficient remobilisation of nitrogen towards sink organs. Taking advantage of combined transcriptome and metabolite analyses during dark-induced senescence of Arabidopsis thaliana mutants deficient in key steps of the PAO/phyllobilin pathway, we show an unanticipated role for one of the pathway intermediates, i.e. pheophorbide a. Both jasmonic acid-related gene expression and jasmonic acid precursors specifically accumulated in pao1, deficient in PAO. We propose that pheophorbide a, the last intact porphyrin intermediate of chlorophyll degradation and unique pathway bottleneck, has been recruited as a signalling molecule of the chloroplast metabolic status. Our work challenges the assumption that chlorophyll breakdown is merely a senescence output, but propose that the flux of pheophorbide a through the pathway acts in a feed-forward loop that remodels the nuclear transcriptome and controls the pace of chlorophyll degradation in senescing leaves.\n\nSummaryTranscriptome and metabolite profiles of key chlorophyll breakdown mutants reveal complex interplay between speed of chlorophyll degradation and jasmonic acid signalling\n\nFinancial sourcesThis work was supported by the European Union (Plant Fellow program), the Swiss National Foundation/ERA-NET (grant N{degrees} 163504) and the German Research Foundation (DFG, grant N{degrees} INST 186/822-1).

plant biology↗

bioRxiv2017

Discovery and reduction of nonspecific activities of the major herbicide-resistance gene BAR

Herbicide resistance is a major trait of genetically modified (GM) crops. Currently, resistance to phosphinothricin (also known as glufosinate) is the second most widespread genetically engineered herbicide-resistance trait in crops after glyphosate resistance1,2. Resistance to phosphinothricin in plants is achieved by transgenic expression of the bialaphos resistance (BAR) or phosphinothricin acetyltransferase (PAT) genes, which were initially isolated from the natural herbicide bialaphos-producing soil bacteria Streptomyces hygroscopicus and S. viridochromogenes, respectively3,4. Mechanistically, BAR and PAT encode phosphinothricin acetyltransferase, which transfers an acetyl group from acetyl coenzyme A (acetyl-CoA) to the -NH2 group of phosphinothricin, resulting in herbicide inactivation1. Although early in vitro enzyme assays showed that recombinant BAR and PAT exhibit substrate preference toward phosphinothricin over the 20 proteinogenic amino acids1, whether transgenic expression of BAR and PAT affects plant endogenous metabolism in vivo was not known. Combining metabolomics, plant genetics, and biochemical approaches, we show that transgenic BAR indeed converts two plant endogenous amino acids, aminoadipate and tryptophan, to their respective N-acetylated products in several plant species examined. We report the crystal structures of BAR, and further delineate structural basis for its substrate selectivity and catalytic mechanism. Through structure-guided protein engineering, we generated several BAR variants that display significantly reduced nonspecific activities compared to its wild-type counterpart. Our results demonstrate that transgenic expression of enzymes as a common strategy in modern biotechnology may render unintended metabolic consequences arisen from enzyme promiscuity. Understanding of such phenomena at the mechanistic level will facilitate better design of maximally insulated systems featuring heterologously expressed enzymes.

plant biology↗