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At least 145 records · Page 8

Transcriptome architecture of the three main lineages of agrobacteria

ABSTRACT Agrobacteria are a diverse, polyphyletic group of prokaryotes with multipartite genomes capable of transferring DNA into the genomes of host plants, making them an essential tool in plant biotechnology. Despite their utility in plant transformation, genome-wide transcriptional regulation is not well understood across the three main lineages of agrobacteria. Transcription start sites (TSSs) are a necessary component of gene expression and regulation. In this study, we used differential RNA-seq and a TSS identification algorithm optimized on manually annotated TSS, then validated with existing TSS to identify thousands of TSS with nucleotide resolution for representatives of each lineage. We extend upon the 356 TSSs previously reported in Agrobacterium fabrum C58 by identifying 1,916 TSSs. In addition, we completed genomes and phenotyping of Rhizobium rhizogenes C16/80 and Allorhizobium vitis T60/94, identifying 2,650 and 2,432 TSSs, respectively. Parameter optimization was crucial for an accurate, high-resolution view of genome and transcriptional dynamics, highlighting the importance of algorithm optimization in genome-wide TSS identification and genomics at large. The optimized algorithm reduced the number of TSSs identified internal and antisense to the coding sequence on average by 90.5% and 91.9%, respectively. Comparison of TSS conservation between orthologs of the three lineages revealed differences in cell cycle regulation of ctrA as well as divergence of transcriptional regulation of chemotaxis-related genes when grown in conditions that simulate the plant environment. These results provide a framework to elucidate the mechanistic basis and evolution of pathology across the three main lineages of agrobacteria. IMPORTANCE Transcription start sites (TSSs) are fundamental for understanding gene expression and regulation. Agrobacteria, a group of prokaryotes with the ability to transfer DNA into the genomes of host plants, are widely used in plant biotechnology. However, the genome-wide transcriptional regulation of agrobacteria is not well understood, especially in less-studied lineages. Differential RNA-seq and an optimized algorithm enabled identification of thousands of TSSs with nucleotide resolution for representatives of each lineage. The results of this study provide a framework for elucidating the mechanistic basis and evolution of pathology across the three main lineages of agrobacteria. The optimized algorithm also highlights the importance of parameter optimization in genome-wide TSS identification and genomics at large.

59 BASIC BIOLOGICAL SCIENCES↗

Regulatory Coordination of Photophysical, Photochemical, and Biochemical Reactions in the Photosynthesis of Land Plants

Balance among the sequential photophysical, photochemical, and biochemical reactions of photosynthesis is needed for converting fleeting energy in light to stable energy in chemical bonds. Any imbalance acts as either a bottleneck for limiting photosynthetic efficiency or an agent for inducing structural and functional damage to photosynthetic apparatus. Not only must each reaction be carefully regulated, but regulatory processes must also be coordinated across the reactions. However, regulations of different stages of photosynthesis have rarely been studied jointly. Non-photochemical quenching (NPQ) and stomatal conductance (g s ) are key regulators of photophysical and biochemical reactions, respectively. Existing evidence suggests that the redox state of plastoquinone regulates g s and that the photochemical reactions are partially regulated by the ultrastructural dynamics of thylakoids induced by osmotic water fluxes in chloroplasts of land plants. To examine how these regulations are coordinated and feedback to each other, we simultaneously measured NPQ and gs and inferred the redox state of plastoquinone and the light-induced thylakoid swelling/shrinking on numerous C 3 and C 4 species. For all species measured, NPQ and gs covary with the redox states of the electron transport chain, particularly plastoquinone, and increase as thylakoid swelling is inferred. NPQ has the maximal sensitivity at the light intensity at which thylakoid is inferred to be fully swollen. Our findings suggest that plant energy and water use strategies are intimately linked by evolution, and studying the regulations of different photosynthetic stages as a whole can lead to new insights of the functioning of photosynthetic machinery in dynamic environments.

59 BASIC BIOLOGICAL SCIENCES↗

The Marchantia polymorpha pangenome reveals ancient mechanisms of plant adaptation to the environment

Plant adaptation to terrestrial life started 450 million years ago and has played a major role in the evolution of life on Earth. The genetic mechanisms allowing this adaptation to a diversity of terrestrial constraints have been mostly studied by focusing on flowering plants. Here, we gathered a collection of 133 accessions of the model bryophyte Marchantia polymorpha and studied its intraspecific diversity using selection signature analyses, a genome-environment association study and a pangenome. We identified adaptive features, such as peroxidases or nucleotide-binding and leucine-rich repeats (NLRs), also observed in flowering plants, likely inherited from the first land plants. The M. polymorpha pangenome also harbors lineage-specific accessory genes absent from seed plants. We conclude that different land plant lineages still share many elements from the genetic toolkit evolved by their most recent common ancestor to adapt to the terrestrial habitat, refined by lineage-specific polymorphisms and gene family evolution.

59 BASIC BIOLOGICAL SCIENCES↗

Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis

The colonization of land and the diversification of terrestrial plants is intimately linked to the evolutionary history of their symbiotic fungal partners. Extant representatives of these fungal lineages include mutualistic plant symbionts, the arbuscular mycorrhizal (AM) fungi in Glomeromycota and fine root endophytes in Endogonales (Mucoromycota), as well as fungi with saprotrophic, pathogenic and endophytic lifestyles. These fungal groups separate into three monophyletic lineages but their evolutionary relationships remain enigmatic confounding ancestral reconstructions. Their taxonomic ranks are currently fluid. In this study, we recognize these three monophyletic linages as phyla, and use a balanced taxon sampling and broad taxonomic representation for phylogenomic analysis that rejects a hard polytomy and resolves Glomeromycota as sister to a clade composed of Mucoromycota and Mortierellomycota. Low copy numbers of genes associated with plant cell wall degradation could not be assigned to the transition to a plant symbiotic lifestyle but appears to be an ancestral phylogenetic signal. Both plant symbiotic lineages, Glomeromycota and Endogonales, lack numerous thiamine metabolism genes but the lack of fatty acid synthesis genes is specific to AM fungi. Many genes previously thought to be missing specifically in Glomeromycota are either missing in all analyzed phyla, or in some cases, are actually present in some of the analyzed AM fungal lineages, e.g. the high affinity phosphorus transporter Pho89. Based on a broad taxon sampling of fungal genomes we present a well-supported phylogeny for AM fungi and their sister lineages. We show that among these lineages, two independent evolutionary transitions to mutualistic plant symbiosis happened in a genomic background profoundly different from that known from the emergence of ectomycorrhizal fungi in Dikarya. These results call for further reevaluation of genomic signatures associated with plant symbiosis.

59 BASIC BIOLOGICAL SCIENCES↗

Role of Fe in long-range ordered Ni 2 Cr precipitates in Ni-Cr-Fe model alloys during isothermal aging

The precipitation of new phases during long-term service at elevated temperatures is a concern for the thermal stability of engineering alloys. In Ni-Cr-based alloys, e.g., Alloy 690, the formation of long-range ordered Ni 2 Cr causes embrittlement and may impact the lifetime of nuclear power plant components. In this work, we quantify the formation and evolution of Ni 2 Cr precipitation in eleven Ni-Cr-Fe model alloys with 0, 5, 7, and 10wt % Fe contents, and with Ni/Cr atomic ratios of 1.8, 2.0, 2.2, 2.4. These alloys were isothermally aged up to 10,000h at temperatures between 330 and 475°C. The alloys were characterized by synchrotron-based x-ray diffraction and Vickers hardness testing to quantify Ni 2 Cr precipitate size, and the impact of precipitate size on the mechanical properties as a function of Fe content. After 10,000 h of aging at 475°C and 418°C, the formation of Ni 2 Cr was observed in all alloys with 0 and 5wt % Fe. After 10,000h of aging at 418°C, Ni 2 Cr precipitates were also observed in the 7wt % Fe containing Ni/Cr=2.0 sample. Further, no clear evidence of Ni 2 Cr was observed in any of the 10wt % Fe samples at any time and temperature combination. We find that the face-centered cubic matrix lattice contraction and Vickers hardness are correlated with the Ni 2 Cr formation. The greatest change in hardness and lattice contraction occurs in stoichiometric alloys (Ni/Cr=2.0) with 0wt % Fe at 475°C. The rate of change in the material properties for the 5wt % Fe alloys is reduced, however the magnitude of changes is similar to 0wt % Fe alloys. A precipitation hardening model developed for Ni-Cr alloys based on critical resolved shear stress with weakly coupled dislocations shows a clear link between Ni 2 Cr precipitate size and hardness. This trend held across all alloys with Ni 2 Cr formation regardless of Fe concentration. This important structure-property relationship can potentially help define Ni-Cr-Fe-based component lifetimes directly through an understanding of how Ni 2 Cr formation impacts mechanical properties as a function of Fe content.

36 MATERIALS SCIENCE↗

Generation of a chromosome-scale genome assembly of the insect-repellent terpenoid-producing Lamiaceae species, Callicarpa americana

Plants exhibit wide chemical diversity due to the production of specialized metabolites that function as pollinator attractants, defensive compounds, and signaling molecules. Lamiaceae (mints) are known for their chemodiversity and have been cultivated for use as culinary herbs, as well as sources of insect repellents, health-promoting compounds, and fragrance. We report the chromosome-scale genome assembly of Callicarpa americana L. (American beautyberry), a species within the early-diverging Callicarpoideae clade of Lamiaceae, known for its metallic purple fruits and use as an insect repellent due to its production of terpenoids. Using long-read sequencing and Hi-C scaffolding, we generated a 506.1-Mb assembly spanning 17 pseudomolecules with N50 contig and N50 scaffold sizes of 7.5 and 29.0 Mb, respectively. In all, 32,164 genes were annotated, including 53 candidate terpene synthases and 47 putative clusters of specialized metabolite biosynthetic pathways. Our analyses revealed 3 putative whole-genome duplication events, which, together with local tandem duplications, contributed to gene family expansion of terpene synthases. Kolavenyl diphosphate is a gateway to many of the bioactive terpenoids in C. americana; experimental validation confirmed that CamTPS2 encodes kolavenyl diphosphate synthase. Syntenic analyses with Tectona grandis L. f. (teak), a member of the Tectonoideae clade of Lamiaceae known for exceptionally strong wood resistant to insects, revealed 963 collinear blocks and 21,297 C. americana syntelogs. Access to the C. americana genome provides a road map for rapid discovery of genes encoding plant-derived agrichemicals and a key resource for understanding the evolution of chemical diversity in Lamiaceae.

59 BASIC BIOLOGICAL SCIENCES↗

Plasma Wall Interaction with 3-D Plasma Boundaries

The interaction of the edge plasma and the material surfaces is one of the most critical challenges on the path to harness fusion power as new, fundamental energy source. This challenge typically combines the thrust to reach high density, low temperature (detached) plasmas in front of the divertor target plates as well as understanding the plasma material interaction (PMI) in particular in this regime. The combination of both research thrusts represents an extraordinarily challenging subject encompassing spatial scales spanning nanometers to meters in all states of matter and across a broad energy range. Modeling capabilities, which help to interpret data from nowadays experiments and enable extrapolation to future devices are urgently required. This is in particular true for toroidal magnetic confinement devices with three-dimensional (3D) plasma boundaries. Such plasma boundary geometries occur in tokamaks, when small amplitude magnetic perturbations are used to stabilize the unruly edge plasma or in stellarators, that are inherently 3D plasma confinement devices. In this project, the impact of 3D plasma boundaries on the plasma material interaction (PMI) was assessed. This work focused on plasma boundary conditions, in which high-density conditions at the material surfaces yield mitigation of the otherwise immense heat and particle loads that these materials would see. These so-called high recycling and eventually detached plasma regimes are of great interest for future reactor operation. In the project, key features that are unique to 3D boundaries were explored in comparison to canonically assumed axisymmetric plasma edge situations in tokamaks. In particular, the relevance of the 3D boundary situation in the extrapolation to the plasma boundary solution at ITER, the next step fusion energy experiment under construction as a multi-national, world-wide large-science experiment in southern France, has been explored. The EMC3-EIRENE plasma edge fluid and kinetic neutral transport code has been advanced to cope with the challenging and unprecedented conditions in the ITER boundary plasma including 3D fields that are planned to be used to suppress harmful edge instabilities, the so-called edge localized modes. This is a vital integration challenge for ITER and the results from this grant have provide a leading capability for this assessment. It was shown that the detachment process in a 3D edge solution for ITER follows the recycling regimes that are known from axisymmetric solutions, but that multiple plasma exhaust channels connected to the material surfaces are established which feature individual recycling characteristics. Because these channels touch the material surfaces in the divertor in a 3D geometry, the compatibility with the plasma material interaction (PMI), including erosion and impurity generation has been found to be an important part of the integration challenge. To address this, the fully 3D plasma material interaction code ERO2 has been adapted to these ITER specific geometries and a homogeneous mixing model was implemented, that allows to consider the mixing of Be and Was used at ITER in the PMI modeling. This model enhancement has been used to study non-local migration of Be in the JET ITER like wall configuration and it has been shown that with this model such complex migration processes in ITER relevant plasma shapes and with ITER relevant plasma boundary conditions can be addressed. The combined modeling approach using EMC3-EIRENE as a plasma boundary transport code and the ERO2 specialized PMI model will be an asset for the continued preparations of ITER operation as well as for Fusion Pilot Plant efforts that have emerged in the U.S. during the evolution of this grant. The predictive capability of this numerical tool has been validated at the DIII-D US national fusion facility. Here, dedicated plasma edge diagnostics were implemented to measure the impurity household around a 3D edge plasma during ELM suppression by 3D fields. Dedicated experiments with local material probes using these diagnostics and the state-of-the-art suite of boundary measurements at DIII-D have shown that the 3D perturbation of the plasma edge that is excreted by such 3D control fields yield a perturbation of the plasma boundary flux structure and hence also of the resulting PMI. The 3D boundary plasma is composed out of helical magnetic flux channels that intersect the divertor targets at an angle relative to the main guiding field, i.e., the toroidal magnetic field component of the tokamak. A similar effect has been measured as well on limiter surfaces during the startup campaign at the new stellarator experiment Wendelstein 7-X. These experiments ad initial analysis with the ERO plasma material interaction model, suggested that the place of erosion for a given particle from the surface and its re-deposition can be different in such 3D field geometries yielding potentially a significant level of net-erosion. This is not the case for axisymmetric solutions, where it was shown in the past that the eroded particles are effectively re-deposited into gaps produced by erosion at the same position and hence the net-erosion levels are small. For ITER, the quest to suppress the ELMs and at the same time maintain the integrity of the divertor is an issue, which these fundamental findings will help to resolve. The coupling of this work to the extrapolation in the ITER program has been addressed by both the PI and the lead numerical scientist being ITER Science Fellows in the duration of the contract and forward. A second focus in the exploration of 3D boundary effects on tokamaks and stellarators has been set on the measurement of helium exhaust features with such 3D fields. This is important because He represents the ash of the fusion process and needs to be exhausted. It was shown that 3D field application compatible with suppression of ELMs yields an increase of the helium exhaust performance. The ratio of the effective helium confinement time over the energy confinement time was reduced by almost 50% which demonstrated that the impact of helium accumulation in the plasma core with respect to the confinement of energy to sustain the fusion reaction is significantly improved with such 3D control fields. It was shown that this is the case for tokamaks as well as stellarators. At the Large helical Device in Japan, a similar enhancement of the helium exhaust features when small amplitude additional 3D fields were applied was measured. This is an important additional function of 3D field application and its impact on ITER is presently being studied in combination with investigations of helium exhaust in 3D field geometries of stellarator devices.

3D plasma edge transport↗

Temperature-Dependent Morphological Evolution during Corrosion of the Ni-20Cr Alloy in Molten Salt Revealed by Multiscale Imaging

Understanding the mechanisms leading to the degradation of alloys in molten salts at elevated temperatures is significant for developing several key energy generation and storage technologies, including concentrated solar and next-generation nuclear power plants. Specifically, the fundamental mechanisms of different types of corrosion leading to various morphological evolution characteristics for changing reaction conditions between the molten salt and alloy remain unclear. Here, in this work, the three-dimensional (3D) morphological evolution of Ni–20Cr in KCl–MgCl 2 is studied at 600 °C by combining in situ synchrotron X-ray and electron microscopy techniques. By further comparing different morphology evolution characteristics in the temperature range of 500–800 °C, the relative rates between diffusion and reaction at the salt–metal interface lead to different morphological evolution pathways, including intergranular corrosion and percolation dealloying. In this work, the temperature-dependent mechanisms of the interactions between metals and molten salts are discussed, providing insights for predicting molten salt corrosion in real-world applications.

36 MATERIALS SCIENCE↗

Nanopolysaccharide Builder: A User-Friendly Tool for Atomistic Models of Polysaccharide-Based Nanostructures

Here, we introduce Nanopolysaccharide Builder (NPB), a user-friendly software tool designed to construct polysaccharide nanostructures─mainly those based on cellulose, chitin, and chitosan─using experimental data or user-defined parameters. NPB enables the generation of cellulose and chitin allomorphs with customizable biochemical topologies and also facilitates the construction of large bundles that replicate nanostructures found in biological support systems, including plant cell walls and arthropod cuticles. The software outputs atomic Cartesian coordinates in Protein Data Bank (PDB) format and also provides atom connectivity files in PSF and PARM formats, ensuring seamless integration with major molecular dynamics (MD) engines such as NAMD, CHARMM, GROMACS, AMBER, OpenMM, and LAMMPS. Built on an interactive visualization framework, NPB features a graphical user interface (GUI) and supports both macOS and Linux operating systems. By enabling detailed atomic-scale studies of polysaccharide evolution in extracellular matrices and cell walls of algae, bacteria, fungi, and plants, NPB is poised to advance AI-guided research in sustainable chemical development and biomass utilization.

Wan, Zhangmin [Univ. of British Columbia, Vancouve↗

Architectural development of an ST fusion device

A recent U.S. National Academy study recommended the development of a next step Sustained High Power Density (SHPD) facility within the U.S. as an intermediate step in designing and building a Pilot Plant device. Several papers have been written describing the physics, design and engineering scoping analysis performed in developing this machine design. This paper places emphasis on the continued evolution of the architectural development of past activities to meet the requirements of an ST fusion pilot plant and power plant. The current effort centers on meeting basic physics and component requirements in a machine design that improves the chance of achieving fission level availability (95%) within an arrangement that promotes design simplicity, offsite construction with on-site modular assembly. As a prelude to both the SHPD and Pilot Plant, a scoping design of a 500MWe Spherical Tokamak Advanced Reactor (STAR) has been defined to investigate design options and physics scenarios that can successfully meet physics performance, engineering requirements and economic conditions of an ST power plant. Following a successful physics/engineering assessment, the STAR Power Plant design will be downsized to meet the specifications established in the design of a near term ST Pilot Plant

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

ZW sex chromosome structure in Amborella trichopoda

Sex chromosomes have evolved hundreds of times across the flowering plant tree of life; their recent origins in some members of this clade can shed light on the early consequences of suppressed recombination, a crucial step in sex chromosome evolution. Amborella trichopoda, the sole species of a lineage that is sister to all other extant flowering plants, is dioecious with a young ZW sex determination system. Here we present a haplotype-resolved genome assembly, including highly contiguous assemblies of the Z and W chromosomes. We identify a ~3-megabase sex-determination region (SDR) captured in two strata that includes a ~300-kilobase inversion that is enriched with repetitive sequences and contains a homologue of the Arabidopsis METHYLTHIOADENOSINE NUCLEOSIDASE (MTN1-2) genes, which are known to be involved in fertility. However, the remainder of the SDR does not show patterns typically found in non-recombining SDRs, such as repeat accumulation and gene loss. These findings are consistent with the hypothesis that dioecy is derived in Amborella and the sex chromosome pair has not significantly degenerated.

59 BASIC BIOLOGICAL SCIENCES↗

The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence

To date, little is known about the evolution of fern genomes, with only two small genomes published from the heterosporous Salviniales. Here we assembled the genome of Alsophila spinulosa, known as the flying spider-monkey tree fern, onto 69 pseudochromosomes. The remarkable preservation of synteny, despite resulting from an ancient whole-genome duplication over 100 million years ago, is unprecedented in plants and probably speaks to the uniqueness of tree ferns. Our detailed investigations into stem anatomy and lignin biosynthesis shed new light on the evolution of stem formation in tree ferns. We identified a phenolic compound, alsophilin, that is abundant in xylem, and we provided the molecular basis for its biosynthesis. Finally, analysis of demographic history revealed two genetic bottlenecks, resulting in rapid demographic declines of A. spinulosa. The A. spinulosa genome fills a crucial gap in the plant genomic landscape and helps elucidate many unique aspects of tree fern biology.

59 BASIC BIOLOGICAL SCIENCES↗

Worldwide Population Genomics Reveal Long-Term Stability of the Mitochondrial Genome Architecture in a Keystone Marine Plant

Mitochondrial genomes (mitogenomes) of flowering plants are composed of multiple chromosomes. Recombination within and between the mitochondrial chromosomes may generate diverse DNA molecules termed isoforms. The isoform copy number and composition can be dynamic within and among individual plants due to uneven replication and homologous recombination. Nonetheless, despite their functional importance, the level of mitogenome conservation within species remains understudied. Whether the ontogenetic variation translates to evolution of mitogenome composition over generations is currently unknown. Here we show that the mitogenome composition of the seagrass Zostera marina is conserved among worldwide populations that diverged ca. 350,000 years ago. Using long-read sequencing, we characterized the Z. marina mitochondrial genome and inferred the repertoire of recombination-induced configurations. To characterize the mitochondrial genome architecture worldwide and study its evolution, we examined the mitogenome in Z. marina meristematic region sampled in 16 populations from the Pacific and Atlantic oceans. Our results reveal a striking similarity in the isoform relative copy number, indicating a high conservation of the mitogenome composition among distantly related populations and within the plant germline, despite a notable variability during individual ontogenesis. Our study supplies a link between observations of dynamic mitogenomes at the level of plant individuals and long-term mitochondrial evolution.

(sub)stoichiometric shifting↗

Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria

The fungal genus Armillaria contains necrotrophic pathogens and some of the largest terrestrial organisms that cause tremendous losses in diverse ecosystems, yet how they evolved pathogenicity in a clade of dominantly non-pathogenic wood degraders remains elusive. Here we show that Armillaria species, in addition to gene duplications and de novo gene origins, acquired at least 1,025 genes via 124 horizontal gene transfer events, primarily from Ascomycota. Horizontal gene transfer might have affected plant biomass degrading and virulence abilities of Armillaria, and provides an explanation for their unusual, soft rot-like wood decay strategy. Furthermore, combined multi-species expression data revealed extensive regulation of horizontally acquired and wood-decay related genes, putative virulence factors and two novel conserved pathogenicity-induced small secreted proteins, which induced necrosis in planta. Overall, this study details how evolution knitted together horizontally and vertically inherited genes in complex adaptive traits of plant biomass degradation and pathogenicity in important fungal pathogens.

60 APPLIED LIFE SCIENCES↗

Genomic Analysis Enlightens Agaricales Lifestyle Evolution and Increasing Peroxidase Diversity

Abstract As actors of global carbon cycle, Agaricomycetes (Basidiomycota) have developed complex enzymatic machineries that allow them to decompose all plant polymers, including lignin. Among them, saprotrophic Agaricales are characterized by an unparalleled diversity of habitats and lifestyles. Comparative analysis of 52 Agaricomycetes genomes (14 of them sequenced de novo) reveals that Agaricales possess a large diversity of hydrolytic and oxidative enzymes for lignocellulose decay. Based on the gene families with the predicted highest evolutionary rates—namely cellulose-binding CBM1, glycoside hydrolase GH43, lytic polysaccharide monooxygenase AA9, class-II peroxidases, glucose–methanol–choline oxidase/dehydrogenases, laccases, and unspecific peroxygenases—we reconstructed the lifestyles of the ancestors that led to the extant lignocellulose-decomposing Agaricomycetes. The changes in the enzymatic toolkit of ancestral Agaricales are correlated with the evolution of their ability to grow not only on wood but also on leaf litter and decayed wood, with grass-litter decomposers as the most recent eco-physiological group. In this context, the above families were analyzed in detail in connection with lifestyle diversity. Peroxidases appear as a central component of the enzymatic toolkit of saprotrophic Agaricomycetes, consistent with their essential role in lignin degradation and high evolutionary rates. This includes not only expansions/losses in peroxidase genes common to other basidiomycetes but also the widespread presence in Agaricales (and Russulales) of new peroxidases types not found in wood-rotting Polyporales, and other Agaricomycetes orders. Therefore, we analyzed the peroxidase evolution in Agaricomycetes by ancestral-sequence reconstruction revealing several major evolutionary pathways and mapped the appearance of the different enzyme types in a time-calibrated species tree.

59 BASIC BIOLOGICAL SCIENCES↗

Century-long timelines of herbarium genomes predict plant stomatal response to climate change

Abstract Dissecting plant responses to the environment is key to understanding whether and how plants adapt to anthropogenic climate change. Stomata, plants’ pores for gas exchange, are expected to decrease in density following increased CO 2 concentrations, a trend already observed in multiple plant species. However, it is unclear whether such responses are based on genetic changes and evolutionary adaptation. Here we make use of extensive knowledge of 43 genes in the stomatal development pathway and newly generated genome information of 191 Arabidopsis thaliana historical herbarium specimens collected over 193 years to directly link genetic variation with climate change. While we find that the essential transcription factors SPCH, MUTE and FAMA, central to stomatal development, are under strong evolutionary constraints, several regulators of stomatal development show signs of local adaptation in contemporary samples from different geographic regions. We then develop a functional score based on known effects of gene knock-out on stomatal development that recovers a classic pattern of stomatal density decrease over the past centuries, suggesting a genetic component contributing to this change. This approach combining historical genomics with functional experimental knowledge could allow further investigations of how different, even in historical samples unmeasurable, cellular plant phenotypes may have already responded to climate change through adaptive evolution.

Environmental Sciences & Ecology↗

Common origin of ornithine–urea cycle in opisthokonts and stramenopiles

Eukaryotic complex phototrophs exhibit a colorful evolutionary history. At least three independent endosymbiotic events accompanied by the gene transfer from the endosymbiont to host assembled a complex genomic mosaic. Resulting patchwork may give rise to unique metabolic capabilities; on the other hand, it can also blur the reconstruction of phylogenetic relationships. The ornithine–urea cycle (OUC) belongs to the cornerstone of the metabolism of metazoans and, as found recently, also photosynthetic stramenopiles. We have analyzed the distribution and phylogenetic positions of genes encoding enzymes of the urea synthesis pathway in eukaryotes. We show here that metazoan and stramenopile OUC enzymes share common origins and that enzymes of the OUC found in primary algae (including plants) display different origins. The impact of this fact on the evolution of stramenopiles is discussed here.

59 BASIC BIOLOGICAL SCIENCES↗

Physics-Informed Machine Learning-Aided System Space Discretization

Decision-making is the process of identifying and choosing alternatives based on an agreed-upon set of metrics and preferences established by the decision-maker. There are options to be considered during the decision-making process and each option offers a different trajectory and associated success profile in moving from a given system state to the desired system state. The decision-making process typically involves uncertainties associated with the current component and system states. In this sense, probabilistic risk assessment (PRA) can be an analytical method and tool for accomplishing the probabilistic aspect of the decision-making process. Dynamic PRA is an evolution of conventional PRA methodology in which driving forces on modeled plant elements and the element behaviors are explicitly modeled over time. In the recent past, risk assessment methodologies have evolved to address risk issues in a continuously evolving environment and a novel probabilistic dynamics framework in continuous time and state-space discretization forms has been proposed. While state-space discretization has shown its strength in both consequence and causal reasoning modes, several challenges, including the computational requirement and physically meaningful system state identification, exist. Conventional system space discretization has usually been done by either the equal width discretization method or a data-driven method. Those methods naturally possess challenges coming from the physical understanding of discretized system space (i.e., system state) and the trajectory moving from a given system state to another system state. The purpose of this paper is to present a physics-based and data-driven system state discretization method such that one can justify what the discretized system space implies and understand the state trajectory from the viewpoint of operational actions.

Kim, Junyung↗