Vers l'élaboration d'un modèle de construction des parois secondaires des fibres de bois chez le peuplier

Trees are able to grow high et survive many years thanks to their wood properties. Wood delivers three major functions in trees : (i) water conduction, (ii) mechanical support et (iii) nutrient storage. In Angiosperm trees, vessels, fibers et parenchyma rays are respectively assigned to these functions, each of them following their own development scheme. Cell wall composition et structure varies greatly depending on cell type, developmental stage et environmental conditions. This complexity therefore represents a hindrance to study the molecular mechanisms of wood formation. However, this can be circumvented by the development of cell-specific approaches.This work aims at characterizing fiber development, focusing on their secondary cell wall, developing cell-specific methods et integrative analysis at the cell level. Development of ATR-FTIR hyperspectral imaging enabled to finely characterize differences in cell wall composition between cell types in a tree et within cell types in different types of wood. Transcriptomics data obtained by RNA-Seq of microdissected fibers et rays gave rise to major differences in the transcriptome of these two cell types. Combining both kind of result led to the identification of key players in fibers development. Hence, this work opens up new research hypothesis, which could lead to a better understanding of the molecular mechanisms underlying wood fiber development, including from a dynamic perspective.Les arbres atteignent des hauteurs et des durées de vie considérables grâce aux propriétés remarquables de leur bois. En effet, le bois remplit trois fonctions principales : (i) la conduction de la sève brute de la racine au houppier, (ii) le soutien mécanique de la masse toujours en augmentation de l'arbre en croissance et (iii) le stockage de réserves temporaires, capitales pour la pérennité de l'arbre. Chez les angiospermes, les vaisseaux, les fibres et les rayons parenchymateux sont, respectivement, affiliés à ces fonctions. Chacune de ces cellules possède son propre schéma de développement. Par ailleurs, la composition et la structure des parois de ces cellules varient considérablement en fonction des stades de développement et des conditions environnementales. Cette complexité représente donc un frein à l’étude des mécanismes moléculaires de la formation du bois. Cette difficulté peut être contournée par le développement d’approches à l’échelle cellulaire.La thèse présentée ici vise à une caractérisation du développement des fibres, plus particulièrement de leurs parois secondaires, par le déploiement d’outils de caractérisation à l’échelle cellulaire et d’une analyse intégrative à cette échelle. Le développement d’une méthode de caractérisation des parois à l’échelle cellulaire, l’imagerie hyperspectrale en ATR-FTIR, a permis une analyse fine des différences entre types cellulaires au sein d’un arbre et entre types de bois pour un même type cellulaire. L’étude de données transcriptomiques obtenues par RNA-Seq de fibres et rayons micro disséqués a, elle, permis d’identifier des différences transcriptionnelles entre ces deux types cellulaires. La combinaison de ces deux résultats a permis d’identifier des acteurs semblant majeurs dans le développement des fibres de bois. Ce travail de thèse ouvre donc des perspectives de recherche permettant de mieux comprendre les mécanismes moléculaires associés à la formation des fibres de bois

Radiative Scale Height and Shadows in Protoplanetary Disks

International audiencePlanets form in young circumstellar disks called protoplanetary disks. However, it is still difficult to catch planet formation in situ. Nevertheless, from recent ALMA/SPHERE data, encouraging evidence of the direct and indirect presence of embedded planets has been identified in disks around young stars: co-moving point sources, gravitational perturbations, rings, cavities, and emission dips or shadows cast on disks. The interpretation of these observations needs a robust physical framework to deduce the complex disk geometry. In particular, protoplanetary disk models usually assume the gas pressure scale height given by the ratio of the sound speed over the azimuthal velocity H/r = cs/vk. By doing so, radiative pressure fields are often ignored, which could lead to a misinterpretation of the real vertical structure of such disks. We follow the evolution of a gaseous disk with an embedded Jupiter-mass planet through hydrodynamical simulations, computing the disk scale height including radiative pressure, which was derived from a generalization of the stellar atmosphere theory. We focus on the vertical impact of the radiative pressure in the vicinity of circumplanetary disks, where temperatures can reach ≳1000 K for an accreting planet and radiative forces can overcome gravitational forces from the planet. The radiation pressure effects create a vertical, optically thick column of gas and dust at the protoplanet location, casting a shadow in scattered light. This mechanism could explain the peculiar illumination patterns observed in some disks around young stars such as HD 169142 where a moving shadow has been detected or the extremely high aspect ratio H/r ∼ 0.2 observed in systems like AB Aur and CT Cha

ATR-FTIR Microspectroscopy Brings a Novel Insight Into the Study of Cell Wall Chemistry at the Cellular Level

Wood is a complex tissue that fulfills three major functions in trees: water conduction, mechanical support and nutrient storage. In Angiosperm trees, vessels, fibers and parenchyma rays are respectively assigned to these functions. Cell wall composition and structure strongly varies according to cell type, developmental stages and environmental conditions. This complexity can therefore hinder the study of the molecular mechanisms of wood formation, underlying the construction of its properties. However, this can be circumvented thanks to the development of cell-specific approaches and microphenotyping. Here, we present a non-destructive microphenotyping method based on attenuated total reflectance–Fourier transformed infrared (ATR-FTIR) microspectroscopy. We applied this technique to three types of poplar wood: normal wood of staked trees (NW), tension and opposite wood of artificially tilted trees (TW, OW). TW is produced by angiosperm trees in response to mechanical strains and is characterized by the presence of G fibers, exhibiting a thick gelatinous extralayer, named G-layer, located in place of the usual S2 and/or S3 layers. By contrast, OW located on the opposite side of the trunk is totally deprived of fibers with G-layers. We developed a workflow for hyperspectral image analysis with both automatic pixel clustering according to cell wall types and identification of differentially absorbed wavenumbers (DAWNs). As pixel clustering failed to assign pixels to ray S-layers with sufficient efficiency, the IR profiling and identification of DAWNs were restricted to fiber and vessel cell walls. As reported elsewhere, this workflow identified cellulose as the main component of the G-layers, while the amount in acetylated xylans and lignins were shown to be reduced. These results validate ATR-FTIR technique for in situ characterization of G layers. In addition, this study brought new information about IR profiling of S-layers in TW, OW and NW. While OW and NW exhibited similar profiles, TW fibers S-layers combined characteristics of TW G-layers and of regular fiber S-layers. Unexpectedly, vessel S-layers of the three kinds of wood showed significant differences in IR profiling. In conclusion, ATR-FTIR microspectroscopy offers new possibilities for studying cell wall composition at the cell level

Imagerie ATR-FTIR : phénotypage à l’échelle de la paroi dans le modèle bois de tension de peuplier

International audienceLes arbres atteignent des hauteurs et des durées de vie considérables grâce aux propriétés remarquables de leur bois. En effet, le bois remplit trois fonctions principales : (1) la conduction de l’eau de la racine au houppier, (2) le soutien mécanique de la masse toujours en augmentation de l’arbre en croissance et (3) le stockage de réserves temporaires, capitales pour la pérennité de l’arbre. Chez les angiospermes, les vaisseaux, les fibres et les rayons parenchymateux sont, respectivement, affiliés à ces fonctions [1]. La composition et la structure des parois de ces cellules varient considérablement en fonction des stades de développement et des conditions environnementales. Par exemple, en réponse à des contraintes mécaniques, les angiospermes produisent un bois dit de tension qui se caractérise par la présence d’une couche surnuméraire dans les parois des fibres, appelée couche G, et composée exclusivement de cellulose et de polysaccharides non-cellulosiques [2-3]. Le bois est donc un assemblage complexe des parois secondaires des fibres et vaisseaux, interconnectés aux cellules vivantes de rayons. Afin de s’affranchir de cette grande complexité, les mécanismes moléculaires de la formation du bois doivent être préférentiellement étudiés au niveau cellulaire.Ici, nous présentons le développement d’une méthode de microphénotypage non destructrice basée sur la microspectroscopie ATR-FTIR. Nous avons appliqué cette technique sur du bois de peupliers inclinés pour induire la formation de bois de tension. Grâce aux analyses d’images hyperspectrales obtenues, nous avons montré que(i) les couches G sont principalement composées de cellulose et de polysaccharides non cellulosiques,(ii) les lignines des parois cellulaires des vaisseaux sont plus riches en unités G alors que celles des fibres sont plus riches en unités S.Ces résultats sont conformes aux études antérieures [3-6], avec une résolution spatiale cinq fois plus élevée. Nous avons enfin pu étudier avec précision la composition des parois de fibres de bois de tension hors couche G et de rayons, jusqu’alors peu étudiées.En résumé, la microspectroscopie ATR-FTIR offre de nouvelles possibilités pour l’étude de la composition de la paroi cellulaire à l’échelle de la cellule

ATR-FTIR imaging: phenotyping at the cell wall level in poplar wood

Trees are able to grow high and to live old thanks to the remarkable properties of their wood. As a matter of a fact, wood delivers three major functions: (1) water conduction from roots to crown, (2) support of the ever-increasing mass of the growing tree and (3) storage of temporary reserves, important for tree growth over the years. In angiosperm trees, different wood cell types are affected to each of these functions. Fibers are involved in tree mechanical support, vessels in water conduction and parenchyma rays in starch and/or lipid storage during the resting period. In addition, these cell types have distinct developmental programs. While fibers and vessels are early-dying cells, parenchyma rays stay alive longer. Therefore wood is a complex patchwork of cells and its structure results from the three-dimensional assembly of the cell walls of dead fibers and vessels, interconnected with still living parenchyma rays. This great complexity stands as an obstacle when studying wood formation and the construction of wood properties. However, this can be circumvented thanks to the development of cell-specific approaches. We developed a non-destructive method based on ATR-FTIR imaging on poplar wood sections. This technology enables to collect IR-absorbance spectra from small areas of cross-sections, which makes possible to differentiate between wood cell-types or even between the different cell wall layers from a single fiber. We first demonstrated that spectra taken from fiber cell walls on cross-sections differed from spectra obtained from wood powder. We also showed that ATR-FTIR imaging is able to discriminate the cell walls of fibers, vessels and rays. These findings are in accordance with other studies [1], but with an improved spatial resolution. ATR-FTIR microspectroscopy is thus a promising tool to finely characterize the cell wall of different wood cell types. This work has been partly supported by the OPeNSPeNU project (funded by the Centre Val de Loire Region

Genome assembly of the medicinal plant Voacanga thouarsii

International audienceAbstract The Apocynaceae tree Voacanga thouarsii, native to southern Africa and Madagascar, produces monoterpene indole alkaloids (MIA), which are specialized metabolites with a wide range of bioactive properties. Voacanga species mainly accumulates tabersonine in seeds making these species valuable medicinal plants currently used for industrial MIA production. Despite their importance, the MIA biosynthesis in Voacanga species remains poorly studied. Here, we report the first genome assembly and annotation of a Voacanga species. The combined assembly of Oxford Nanopore Technologies long-reads and Illumina short-reads resulted in 3,406 scaffolds with a total length of 1,354.26 Mb and an N50 of 3.04 Mb. A total of 33,300 protein coding genes were predicted and functionally annotated. These genes were then used to establish gene families and to investigate gene family expansion and contraction across the phylogenetic tree. A transposable element (TE) analysis showed the highest proportion of TE in V. thouarsii compared to all other MIA-producing plants. In a nutshell, this first reference genome of V. thouarsii will thus contribute to strengthen future comparative and evolutionary studies in MIA-producing plants leading to a better understanding of MIA pathway evolution. This will also allow the potential identification of new MIA biosynthetic genes for metabolic engineering purposes

The Madagascar palm genome provides new insights on the evolution of Apocynaceae specialized metabolism

International audienc

An updated version of the Madagascar periwinkle genome

This work was supported by EU Horizon 2020 research and innovation program [MIAMi project, grant number 814645; MKJ, SEO, VC]; ARD CVL Biopharmaceutical program of the Région Centre-Val de Loire [ETOPOCentre project, VC]; and ANR [project MIACYC – ANR-20-CE43-0010, VC].International audienceThe Madagascar periwinkle, Catharanthus roseus, belongs to the Apocynaceae family. This medicinal plant, endemic to Madagascar, produces many important drugs including the monoterpene indole alkaloids (MIA) vincristine and vinblastine used to treat cancer worldwide. Here, we provide a new version of the C. roseus genome sequence obtained through the combination of Oxford Nanopore Technologies long-reads and Illumina short-reads. This more contiguous assembly consists of 173 scaffolds with a total length of 581.128 Mb and an N50 of 12.241 Mb. Using publicly available RNAseq data, 21,061 protein coding genes were predicted and functionally annotated. A total of 42.87% of the genome was annotated as transposable elements, most of them being long-terminal repeats. Together with the increasing access to MIA-producing plant genomes, this updated version should ease evolutionary studies leading to a better understanding of MIA biosynthetic pathway evolutio

A systems biology approach uncovers a gene co-expression network associated with cell wall degradability in maize

Understanding the mechanisms triggering variation of cell wall degradability is a prerequisite to improving the energy value of lignocellulosic biomass for animal feed or biorefinery. Here, we implemented a multiscale systems approach to shed light on the genetic basis of cell wall degradability in maize. We demonstrated that allele replacement in two pairs of near-isogenic lines at a region encompassing a major quantitative trait locus (QTL) for cell wall degradability led to phenotypic variation of a similar magnitude and sign to that expected from a QTL analysis of cell wall degradability in the F271 × F288 recombinant inbred line progeny. Using DNA sequences within the QTL interval of both F271 and F288 inbred lines and Illumina RNA sequencing datasets from internodes of the selected near-isogenic lines, we annotated the genes present in the QTL interval and provided evidence that allelic variation at the introgressed QTL region gives rise to coordinated changes in gene expression. The identification of a gene co-expression network associated with cell wall-related trait variation revealed that the favorable F288 alleles exploit biological processes related to oxidation-reduction, regulation of hydrogen peroxide metabolism, protein folding and hormone responses. Nested in modules of co-expressed genes, potential new cell-wall regulators were identified, including two transcription factors of the group VII ethylene response factor family, that could be exploited to fine-tune cell wall degradability. Overall, these findings provide new insights into the regulatory mechanisms by which a major locus influences cell wall degradability, paving the way for its map-based cloning in maize