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Premise: Density-dependent pollinator visitation can lead to density-dependent mating patterns and within-population genetic structure. In Gymnadenia conopsea, individuals in low-density patches receive more self pollen than individuals in high-density patches, suggesting higher relatedness at low density. Ongoing fragmentation is also expected to cause more local matings, potentially leading to biparental inbreeding depression. Methods: To evaluate whether relatedness decreases with local density, we analyzed 1315 SNP loci in 113 individuals within two large populations. We quantified within-population genetic structure in one of the populations, recorded potential habitat barriers, and visualized gene flow using estimated effective migration surfaces (EEMS). We further estimated the magnitude of biparental inbreeding depression that would result from matings restricted to within 5 m. Results: There was no significant relationship between local density and relatedness in any population. We detected significant fine-scale genetic structure consistent with isolation by distance, with positive kinship coefficients at distances below 10 m. Kinship coefficients were low, and predicted biparental inbreeding depression resulting from matings within the closest 5 m was a modest 1–3%. The EEMS suggested that rocks and bushes may act as barriers to gene flow within a population. Conclusions: The results suggest that increased self-pollen deposition in sparse patches does not necessarily cause higher selfing rates or that inbreeding depression results in low establishment success of inbred individuals. The modest relatedness suggests that biparental inbreeding depression is unlikely to be an immediate problem following fragmentation of large populations. The results further indicate that habitat structure may contribute to governing fine-scale genetic structure in G. conopsea.

The nomenclature and taxonomy of Acarospora molybdina is revised using morphological and molecular data. The new combination Myriospora molybdina is proposed and Acarospora hysgina is recognized as a distinct species while A. brunneola is reduced to synonymy with A. hysgina. In its new circumscription M. molybdina is an arctic species, in Scandinavia only occurring in northernmost Norway. Further localities are reported from Greenland, Russia, Svalbard and the USA (Alaska). Acarospora hysgina is the correct name for a species distributed along the west coast of Sweden and Norway, formerly thought to belong to A. molybdina. Localities are also reported from Canada (New Brunswick), Greenland and the USA (Maine). The following names are lectotypified: Acarospora brunneola, A. molybdina var. confusa, Lecanora ereutica beta microcyclos, Parmelia ereutica, P. hysgina and P. molybdina.

Subarctic regions are warming faster than other parts of the globe, and warming is expected to impact carbon (C) assimilation and its allocation into plant biomass and soluble sugars in plant tissues. We analyzed the concentration of soluble sugars (fructose, glucose, and sucrose) in fine roots and rhizomes for three dominant species: Anthoxanthum odoratum, Equisetum spp., and Ranunculus acris. We also examined the concentration and pool of soluble sugars at the plant community level with the aim to investigate the impact of soil warming duration [medium-term (11 years, MTW) vs. long-term (> 60 years, LTW)] and magnitude on soluble sugars in geothermally warmed subarctic grasslands. Among three species, R. acris exhibited the highest concentration of soluble sugars in both fine roots and rhizomes. Comparing total soluble sugar (TSS) between fine roots and rhizomes, rhizomes exhibited a higher concentration in A. odoratum and Equisetum. spp., whereas fine roots had a higher concentration in R. acris. Soil warming did not affect TSS in E. spp. and R. acris, while in A. odoratum, it increased TSS in fine roots and rhizomes in MTW and only in fine roots in LTW. At the plant community level in MTW, soil warming did not affect the soluble sugar concentration in fine roots. However, it increased the TSS and sucrose concentration in rhizomes, which positively correlated with the abundance of grasses. The TSS pool in fine roots decreased with soil warming in MTW, mainly due to a decline in fine root biomass that described 70 % of the decline in the TSS pool. Also, in LTW, soil warming decreased the TSS pool in fine roots, but 74 % of the decline was mainly driven by decreased soluble sugar concentration, specifically that of sucrose, and not by the change in fine root biomass. The decrease in sucrose concentration in fine roots in LTW was related to a decrease in the abundance of A. odoratum. We highlight the species-specific and organ-specific differences in soluble suga

Seasonal dynamics of root growth play an important role in large-scale ecosystem processes; they are largely governed by growth regulatory compounds and influenced by environmental conditions. Yet, our knowledge about physiological drivers of root growth is mostly limited to laboratory-based studies on model plant species. We sampled root tips of Eriophorum vaginatum and analyzed their auxin concentrations and meristem lengths biweekly over a growing season in situ in a subarctic peatland, both in surface soil and at the permafrost thawfront. Auxin concentrations were almost five times higher in surface than in thawfront soils and increased over the season, especially at the thawfront. Surprisingly, meristem length showed an opposite pattern and was almost double in thawfront compared with surface soils. Meristem length increased from peak to late season in the surface soils but decreased at the thawfront. Our study of in situ seasonal dynamics in root physiological parameters illustrates the potential for physiological methods to be applied in ecological studies and emphasizes the importance of in situ measurements. The strong effect of root location and the unexpected opposite patterns of meristem length and auxin concentrations likely show that auxin actively governs root growth to ensure a high potential for nutrient uptake at the thawfront.

Most animal pollination results from plant–insect interactions, but how we perceive these interactions may differ with the sampling method adopted. The two most common methods are observations of visits by pollinators to plants and observations of pollen loads carried by insects. Each method could favour the detection of different species and interactions, and pollen load observations typically reveal more interactions per individual insect than visit observations. Moreover, while observations concern plant and insect individuals, networks are frequently analysed at the level of species. Although networks constructed using visitation and pollen-load data have occasionally been compared in relatively specialised, bee-dominated systems, it is not known how sampling methodology will affect our perception of how species (and individuals within species) interact in a more generalist system. Here we use a Diptera-dominated high-Arctic plant–insect community to explore how sampling approach shapes several measures of species' interactions (focusing on specialisation), and what we can learn about how the interactions of individuals relate to those of species. We found that species degrees, interaction strengths, and species motif roles were significantly correlated across the two method-specific versions of the network. However, absolute differences in degrees and motif roles were greater than could be explained by the greater number of interactions per individual provided by the pollen-load data. Thus, despite the correlations between species roles in networks built using visitation and pollen-load data, we infer that these two perspectives yield fundamentally different summaries of the ways species fit into their communities. Further, individuals' roles generally predicted the species' overall role, but high variability among individuals means that species' roles cannot be used to predict those of particular individuals. These findings emphasize the importance of adopting

Nitrogen can be taken up by trees in the form of nitrate, ammonium and amino acids, but the influence of the different forms on tree growth and development is poorly understood in angiosperm species like Populus. We studied the effects of both organic and inorganic forms of nitrogen on growth and wood formation of hybrid aspen trees in experimental conditions that allowed growth under four distinct steady-state nitrogen levels. Increased nitrogen availability had a positive influence on biomass accumulation and the radial dimensions of both xylem vessels and fibers, and a negative influence on wood density. An optimal level of nitrogen availability was identified where increases in biomass accumulation outweighed decreases in wood density. None of these responses depended on the source of nitrogen except for shoot biomass accumulation, which was stimulated more by treatments complemented with nitrate than by ammonium alone or the organic source arginine. The most striking difference between the nitrogen sources was the effect on lignin composition, whereby the abundance of H-type lignin increased only in the presence of nitrate. The differential effect of nitrate is possibly related to the well-known role of nitrate as a signaling compound. RNA-sequencing revealed that while the lignin-biosynthetic genes did not significantly (FDR <0.01) respond to added NO3- , the expression of several laccases, catalysing lignin polymerization, was dependent on N-availability. These results reveal a unique role of nitrate in wood formation and contribute to the knowledge basis for decision-making in utilizing hybrid aspen as a bioresource.

Plants tightly control growth of their lateral organs, which led to the concept of apical dominance. However, outgrowth of the dormant lateral primordia is sensitive to the plant's nutritional status, resulting in an immense plasticity in plant architecture. While the impact of hormonal regulation on apical dominance is well characterized, the prime importance of sugar signaling to unleash lateral organ formation has just recently emerged. Here, we aimed to identify transcriptional regulators, which control the trade-off between growth of apical versus lateral organs. Making use of locally inducible gain-of-function as well as single and higher-order loss-of-function approaches of the sugar-responsive S1-basic-leucine-zipper (S1-bZIP) transcription factors, we disclosed their largely redundant function in establishing apical growth dominance. Consistently, comprehensive phenotypical and analytical studies of S1-bZIP mutants show a clear shift of sugar and organic nitrogen (N) allocation from apical to lateral organs, coinciding with strong lateral organ outgrowth. Tissue-specific transcriptomics reveal specific clade III SWEET sugar transporters, crucial for long-distance sugar transport to apical sinks and the glutaminase GLUTAMINE AMIDO-TRANSFERASE 1_2.1, involved in N homeostasis, as direct S1-bZIP targets, linking the architectural and metabolic mutant phenotypes to downstream gene regulation. Based on these results, we propose that S1-bZIPs control carbohydrate (C) partitioning from source leaves to apical organs and tune systemic N supply to restrict lateral organ formation by C/N depletion. Knowledge of the underlying mechanisms controlling plant C/N partitioning is of pivotal importance for breeding strategies to generate plants with desired architectural and nutritional characteristics.

Quinoa is an agriculturally important crop species originally domesticated in the Andes of central South America. One of its most important phenotypic traits is seed colour. Seed colour variation is determined by contrasting abundance of betalains, a class of strong antioxidant and free radicals scavenging colour pigments only found in plants of the order Caryophyllales. However, the genetic basis for these pigments in seeds remains to be identified. Here we demonstrate the application of machine learning (extreme gradient boosting) to identify genetic variants predictive of seed colour. We show that extreme gradient boosting outperforms the classical genome-wide association approach. We provide re-sequencing and phenotypic data for 156 South American quinoa accessions and identify candidate genes potentially controlling betalain content in quinoa seeds. Genes identified include novel cytochrome P450 genes and known members of the betalain synthesis pathway, as well as genes annotated as being involved in seed development. Our work showcases the power of modern machine learning methods to extract biologically meaningful information from large sequencing data sets.

By-products of metal corrosion, when coming into contact with organic matter, have the capacity to preserve it from decay. A pilot study was conducted aiming to explore the potential and limitations of plant remains preserved in by-products of metal corrosion for archaeobotanical research. The organic remains considered come from the surface/immediate proximity of the metal funerary artefacts of two ancient cemeteries—Varna and Messambria, Eastern Bulgaria. Metal corrosion by-products were observed and sampled, under a low magnification stereo microscope. Subsequently, the plant macrofossils recognised were analysed under reflected light and a scanning electron microscope (SEM). Additionally, pollen was extracted from the metal corrosion by-products, using standard acetolysis. The analyses from the graves of both cemeteries allowed identification of textiles and plant fibres, as well as wood (Cornus sp., Pinus sp., Viburnum sp.). At Varna cemetery epidermis fragments of Juncus sp. were recognized, while at Messambria necropolis fruits of almond were found. The pollen analysis from Varna points to use of flowers in the ritual (Daphne tetrads were recorded) and shows a notably open landscape with 77% non-arboreal pollen (NAP). The palynological analysis from the Messambria necropolis revealed the use of flowers in the burial ritual indicated by clusters of Vitis, Cistus and Rosaceae pollen. The surrounding vegetation was dominated by open oak woodland and open habitats (43% NAP) with a strong presence of anthropogenic indicators. The outcome of the study proved to be promising for reconstructing details of the burial rituals including associated plant materials, as well as the surrounding plant habitats during the functioning of the cemeteries.

As part of a taxonomic reassessment of species that were classified in Berkheya series Rigidae in the most recent monograph of Berkheya, the type material for Berkheya rigida and its putative heterotypic synonyms is reassessed. The original material for the basionym, Stobaea rigida, is heterospecific. Therefore, a second-step lectotype is designated consistent with predominant usage of the name Berkheya rigida. The name Apuleia rigida and its replacement name Stobaea gaertneri apply to a conspicuously radiate species and are excluded from the synonymy of Berkheya rigida. The morphological variability of Berkheya rigida is discussed.

MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in both plants and animals. They are thought to have evolved convergently in these lineages and hypothesized to have played a role in the evolution of multicellularity. In line with this hypothesis, miRNAs have so far only been described in few unicellular eukaryotes. Here, we investigate the presence and evolution of miRNAs in Amoebozoa, focusing on species belonging to Acanthamoeba, Physarum and dictyostelid taxonomic groups, representing a range of unicellular and multicellular lifestyles. miRNAs that adhere to both the stringent plant and animal miRNA criteria were identified in all examined amoebae, expanding the total number of protists harbouring miRNAs from 7 to 15. We found conserved miRNAs between closely related species, but the majority of species feature only unique miRNAs. This shows rapid gain and/or loss of miRNAs in Amoebozoa, further illustrated by a detailed comparison between two evolutionary closely related dictyostelids. Additionally, loss of miRNAs in the Dictyostelium discoideum drnB mutant did not seem to affect multicellular development and, hence, demonstrates that the presence of miRNAs does not appear to be a strict requirement for the transition from uni- to multicellular life.

Aim: The microclimate and light conditions on the forest floor are strongly modified by tree canopies. Therefore, we need to better consider the micro-environment when quantifying trait–environment relationships for forest understorey plants. Here, we quantify relationships between micro-environmental conditions and plant functional traits at the community level, including intraspecific trait variation, and their relationship with microclimate air temperature, light and soil properties. Location: Deciduous temperate forests across Europe. Time period: 2018. Major taxa studied: Herbaceous vegetation. Methods: We sampled 225 plots across 15 regions along four complementary gradients capturing both macro- and microclimatic conditions including latitude, elevation, forest management and distance to forest edges. We related the community-weighted mean of five plant functional traits (plant height, specific leaf area [SLA], plant carbon [C], plant nitrogen [N] and plant C:N ratio) across 150 vascular plant species to variation in local microclimate air temperature, light and soil properties. We tested the effect of accounting for intraspecific variation in trait–environment relationships and performed variation partitioning to identify major drivers of trait variation. Results: Microclimate temperature, light availability and soil properties were all important predictors of community-weighted mean functional traits. When light availability and variation in temperature were higher, the herb community often consisted of taller plants with a higher C:N ratio. In more productive environments (e.g. with high soil nitrogen availability), the community was dominated by individuals with resource-acquisitive traits: high SLA and N but low C:N. Including intraspecific trait variation increased the strength of the trait–micro-environment relationship, and increased the importance of light availability. Main conclusions: The trait–environment relationships were much stronger when the

High concentrations of sodium (Na+), chloride (Cl-), calcium (Ca2+), and sulphate (SO42-) are frequently found in saline soils. Crop plants cannot successfully develop and produce because salt stress impairs the uptake of Ca2+, potassium (K+), and water into plant cells. Different intracellular and extracellular ionic concentrations change with salinity, including those of Ca2+, K+, and protons. These cations serve as stress signaling molecules in addition to being essential for ionic homeostasis and nutrition. Maintaining an appropriate K+:Na+ ratio is one crucial plant mechanism for salt tolerance, which is a complicated trait. Another important mechanism is the ability for fast extrusion of Na+ from the cytosol. Ca2+ is established as a ubiquitous secondary messenger, which transmits various stress signals into metabolic alterations that cause adaptive responses. When plants are under stress, the cytosolic-free Ca2+ concentration can rise to 10 times or more from its resting level of 50-100 nanomolar. Reactive oxygen species (ROS) are linked to the Ca2+ alterations and are produced by stress. Depending on the type, frequency, and intensity of the stress, the cytosolic Ca2+ signals oscillate, are transient, or persist for a longer period and exhibit specific signatures. Both the influx and efflux of Ca2+ affect the length and amplitude of the signal. According to several reports, under stress Ca2+ alterations can occur not only in the cytoplasm of the cell but also in the cell walls, nucleus, and other cell organelles and the Ca2+ waves propagate through the whole plant. Here, we will focus on how wheat and other important crops absorb Na+, K+, and Cl- when plants are under salt stress, as well as how Ca2+, K+, and pH cause intracellular signaling and homeostasis. Similar mechanisms in the model plant Arabidopsis will also be considered. Knowledge of these processes is important for understanding how plants react to salinity stress and for the development of toler

Background and Aims Organelle genomes are usually maternally inherited in angiosperms. However, biparental inheritance has been observed, especially in hybrids resulting from crosses between divergent genetic lineages. When it concerns the plastid genome, this exceptional mode of inheritance might rescue inter-lineage hybrids suffering from plastid–nuclear incompatibilities. Genetically differentiated lineages of Silene nutans exhibit strong postzygotic isolation owing to plastid–nuclear incompatibilities, highlighted by inter-lineage hybrid chlorosis and mortality. Surviving hybrids can exhibit variegated leaves, which might indicate paternal leakage of the plastid genome. We tested whether the surviving hybrids inherited the paternal plastid genome and survived thanks to paternal leakage. Methods We characterized the leaf phenotype (fully green, variegated or white) of 504 surviving inter-lineage hybrids obtained from a reciprocal cross experiment among populations of four genetic lineages (W1, W2, W3 and E1) of S. nutans from Western Europe and genotyped 560 leaf samples (both green and white leaves for variegated hybrids) using six lineage-specific plastid single nucleotide polymorphisms. Key Results A high proportion of the surviving hybrids (≤98 %) inherited the paternal plastid genome, indicating paternal leakage. The level of paternal leakage depended on cross type and cross direction. The E1 and W2 lineages as maternal lineages led to the highest hybrid mortality and to the highest paternal leakage from W1 and W3 lineages in the few surviving hybrids. This was consistent with E1 and W2 lineages, which contained the most divergent plastid genomes. When W3 was the mother, more hybrids survived, and no paternal leakage was detected. Conclusions By providing a plastid genome potentially more compatible with the hybrid nuclear background, paternal leakage has the potential to rescue inter-lineage hybrids from plastid–nuclear incompatibilities. This phenomenon mi

This thesis has focused on the evolutionary history of Isoetes (Isoetales, Lycopsida), its phylogeny, megaspore morphology and evolutionary path through deep time. With a broadened sampling of species to include more of the worldwide diversity of the genus compared to previous work an unexpected sister to the rest of the genus was found. Isoetes wormaldii Sim is a critically endangered species from the southeastern Cape region in South Africa, which grows in ponds and slow-moving streams. There are only a few, small populations, and they are very sensitive to habitat changes. The rest of Isoetes is divided into five major clades, which show complex and not readily understandable biogeographic patterns, and by which processes the species came to live in their current locations in the world is often a conundrum. The age of the extant Isoetes is intriguing as it could potentially explain some of the baffling geographic distributions. Analyses based on whole chloroplast genomes and nuclear cistrons found that the choice of clock model and which genome dataset the dating analysis is based on matter greatly when trying to date the genus as the results were highly inconsistent. The solution to the dating analysis woes might be dependent on finding new bases, e.g., fossil evidence, for age calibrations which would require the morphology of Isoetes to be better understood. Our study of megaspore morphology found substantial differences among species of Isoetes in both ornamentation and surface texture/structure. While no major clade within the genus could be unambiguously defined by their spore morphology there are some characteristics of smaller clades and patterns of ornamentation and surface texture across the phylogeny. Our tentative hypothesis is that a pustulate megaspore ornamentation and a cobwebby texture are ancestral features in the megaspore of Isoetes.

Climate is assumed to strongly influence species distribution and abundance. Although the performance of many organisms is influenced by the climate in their immediate proximity, the climate data used to model their distributions often have a coarse spatial resolution. This is problematic because the local climate experienced by individuals might deviate substantially from the regional average. This problem is likely to be particularly important for sessile organisms like plants and in environments where small-scale variation in climate is large. To quantify the effect of local temperature on vital rates and population growth rates, we used temperature values measured at the local scale (in situ logger measures) and integral projection models with demographic data from 37 populations of the forest herb Lathyrus vernus across a wide latitudinal gradient in Sweden. To assess how the spatial resolution of temperature data influences assessments of climate effects, we compared effects from models using local data with models using regionally aggregated temperature data at several spatial resolutions (≥1 km). Using local temperature data, we found that spring frost reduced the asymptotic population growth rate in the first of two annual transitions and influenced survival in both transitions. Only one of the four regional estimates showed a similar negative effect of spring frost on population growth rate. Our results for a perennial forest herb show that analyses using regionally aggregated data often fail to identify the effects of climate on population dynamics. This emphasizes the importance of using organism-relevant estimates of climate when examining effects on individual performance and population dynamics, as well as when modeling species distributions. For sessile organisms that experience the environment over small spatial scales, this will require climate data at high spatial resolutions.

The genetic control underlying natural variation in lignin content and composition in trees is not fully understood. We performed a systems genetic analysis to uncover the genetic regulation of lignin biosynthesis in a natural ‘SwAsp’ population of aspen (Populus tremula) trees. We analyzed gene expression by RNA sequencing (RNA-seq) in differentiating xylem tissues, and lignin content and composition using Pyrolysis-GC-MS in mature wood of 268 trees from 99 genotypes. Abundant variation was observed for lignin content and composition, and genome-wide association study identified proteins in the pentose phosphate pathway and arabinogalactan protein glycosylation among the top-ranked genes that are associated with these traits. Variation in gene expression and the associated genetic polymorphism was revealed through the identification of 312 705 local and 292 003 distant expression quantitative trait loci (eQTL). A co-expression network analysis suggested modularization of lignin biosynthesis and novel functions for the lignin-biosynthetic CINNAMYL ALCOHOL DEHYDROGENASE 2 and CAFFEOYL-CoA O-METHYLTRANSFERASE 3. PHENYLALANINE AMMONIA LYASE 3 was co-expressed with HOMEOBOX PROTEIN 5 (HB5), and the role of HB5 in stimulating lignification was demonstrated in transgenic trees. The systems genetic approach allowed linking natural variation in lignin biosynthesis to trees´ responses to external cues such as mechanical stimulus and nutrient availability.

The plant endoplasmic reticulum (ER) contacts heterotypic membranes at membrane contact sites (MCSs) through largely undefined mechanisms. For instance, despite the well-established and essential role of the plant ER-chloroplast interactions for lipid biosynthesis, and the reported existence of physical contacts between these organelles, almost nothing is known about the ER-chloroplast MCS identity. Here we show that the Arabidopsis ER membrane-associated VAP27 proteins and the lipid-binding protein ORP2A define a functional complex at the ER-chloroplast MCSs. Specifically, through in vivo and in vitro association assays, we found that VAP27 proteins interact with the outer envelope membrane (OEM) of chloroplasts, where they bind to ORP2A. Through lipidomic analyses, we established that VAP27 proteins and ORP2A directly interact with the chloroplast OEM monogalactosyldiacylglycerol (MGDG), and we demonstrated that the loss of the VAP27-ORP2A complex is accompanied by subtle changes in the acyl composition of MGDG and PG. We also found that ORP2A interacts with phytosterols and established that the loss of the VAP27-ORP2A complex alters sterol levels in chloroplasts. We propose that, by interacting directly with OEM lipids, the VAP27-ORP2A complex defines plant-unique MCSs that bridge ER and chloroplasts and are involved in chloroplast lipid homeostasis.

The present study evaluated the repercussions of magnetopriming on the root system architecture of soybean plants subjected to arsenic toxicity using synchrotron radiation source based micro-computed tomography (SR-µCT). This will be used evey where as abbreviation for the technique for three-dimensional imaging. Seeds of soybean were exposed to the static magnetic field (SMF) of strength (200 mT) for 1h prior to sowing. Magnetoprimed and non-primed seeds were grown for 1 month in a soil-sand mixture containing four different levels of sodium arsenate (0, 5, 10, and 50 mg As kg−1 soil). The results showed that arsenic adversely affects the root growth in non-primed plants by reducing their root length, root biomass, root hair, size and number of root nodules, where the damaging effect of As was observed maximum at higher concentrations (10 and 50 mg As kg−1 soil). However, a significant improvement in root morphology was detected in magnetoprimed plants where SMF pretreatment enhanced the root length, root biomass, pore diameter of cortical cells, root hair formation, lateral roots branching, and size of root nodules and girth of primary roots. Qualitative analysis of x-ray micro-CT images showed that arsenic toxicity damaged the epidermal and cortical layers of the root as well as reduced the pore diameter of the cortical cells. However, the diameter of cortical cells pores in magnetoprimed plants was observed higher as compared to plants emerged from non-primed seeds at all level of As toxicity. Thus, the study suggested that magnetopriming has the potential to attenuate the toxic effect of As and could be employed as a pre-sowing treatment to reduce the phytotoxic effects of metal ions in plants by improving root architecture and root tolerance index. This study is the very first exploration of the potential benefits of magnetopriming in mitigating the toxicity of metals (As) in plant roots utilizing the micro-CT technique.

Chlorophyll is essential in photosynthesis, converting sunlight into chemical energy in plants, algae, and certain bacteria. Its structure, featuring a porphyrin ring enclosing a central magnesium ion, varies in forms like chlorophyll a, b, c, d, and f, allowing light absorption at a broader spectrum. With a 20-carbon phytyl tail (except for chlorophyll c), chlorophyll is anchored to proteins. Previous findings suggested the presence of chlorophyll with a modified farnesyl tail in thermophilic cyanobacteria Thermosynechoccocus vestitus. In our Arabidopsis thaliana PSII cryo-EM map, specific chlorophylls showed incomplete phytyl tails, suggesting potential farnesyl modifications. However, further high-resolution mass spectrometry (HRMS) analysis in A. thaliana and T. vestitus did not confirm the presence of any farnesyl tails. Instead, we propose the truncated tails in PSII models may result from binding pocket flexibility rather than actual modifications.

Marine heatwaves (MHWs) caused by anthropogenic climate change are becoming a key driver of change at the ecosystem level. Thermal conditions experienced by marine organisms across their distribution, particularly towards the equator, are likely to approach their physiological limits, resulting in extensive mortality and subsequent changes at the population level. Populations at the margins of their species’ distribution are thought to be more sensitive to climate-induced environmental pressures than central populations, but our understanding of variability in fitness-related physiological traits in trailing versus leading-edge populations is limited. In a laboratory simulation study, we tested whether two leading (Iceland) and two trailing (Spain) peripheral populations of the intertidal macroalga Corallina officinalis display different levels of maximum potential quantum efficiency (Fv/Fm) resilience to current and future winter MHWs scenarios. Our study revealed that ongoing and future local winter MHWs will not negatively affect leading-edge populations of C. officinalis, which exhibited stable photosynthetic efficiency throughout the study. Trailing edge populations showed apositive though non-significant trend in photosynthetic efficiency throughout winter MHWs exposure. Poleward and equatorward populations did not produce significantly different results, with winter MHWs having no negative affect on Fv/Fm of either population. Additionally, we found no long-term regional or population-level influence of a winter MHWs on this species’ photosynthetic efficiency. Thus, we found no statistically significant difference in thermal stress responses between leading and trailing populations. Nonetheless, C. officinalis showed a trend towards higher stress responses in southern than northern populations. Because responses rest on a variety of local population traits, they are difficult to predict based solely on thermal pressures.

BBXs are B-Box zinc finger proteins that can act as transcription factors and regulators of protein complexes. Several BBX proteins play important roles in plant development. Two Arabidopsis thaliana microProteins belonging to the BBX family, named miP1a and miP1b, homotypically interact with and modulate the activity of other BBX proteins, including CONSTANS, which transcriptionally activates the florigen, FLOWERING LOCUS T. Arabidopsis plants overexpressing miP1a and miP1b showed delayed flowering. In tomato, the closest homologs of miP1a and miP1b are the microProteins SlBBX16 and SlBBX17. This study was aimed at investigating whether the constitutive expression of SlBBX16/17 in Arabidopsis and tomato impacted reproductive development. The heterologous expression of the two tomato microProteins in Arabidopsis caused a delay in the flowering transition; however, the effect was weaker than that observed when the native miP1a/b were overexpressed. In tomato, overexpression of SlBBX17 prolonged the flowering period; this effect was accompanied by downregulation of the flowering inhibitors Self Pruning (SP) and SP5G. SlBBX16 and SlBBX17 can hetero-oligomerize with TCMP-2, a cystine-knot peptide involved in flowering pattern regulation and early fruit development in tomato. The increased expression of both microProteins also caused alterations in tomato fruit development: we observed in the case of SlBBX17 a decrease in the number and size of ripe fruits as compared to WT plants, while for SlBBX16, a delay in fruit production up to the breaker stage. These effects were associated with changes in the expression of GA-responsive genes.

Metacaspases are cysteine proteases present in plants, fungi and protists. While the association of metacaspases with cell death is studied in a range of organisms, their native substrates are largely unknown. Here, we explored the in vivo proteolytic landscape of the two metacaspases, CrMCA-I and CrMCA-II, present in the green freshwater alga Chlamydomonas reinhardtii, using mass spectrometry-based degradomics approach, during control conditions and salt stress. Comparison between the cleavage events of CrMCA-I and CrMCA-II in metacaspase mutants revealed unique cleavage preferences and substrate specificity. Degradome analysis demonstrated the relevance of the predicted metacaspase substrates to the physiology of C. reinhardtii cells and its adaptation during salt stress. Functional enrichment analysis indicated an involvement of CrMCA-I in the catabolism of carboxylic acids, while CrMCA-II plays an important role in photosynthesis and translation. Altogether, our findings suggest distinct cellular functions of the two metacaspases in C. reinhardtii during salt stress response.

Long non-coding RNAs (lncRNAs) play essential roles in various biological processes, such as chromatin remodeling, post-transcriptional regulation, and epigenetic modifications. Despite their critical functions in regulating plant growth, root development, and seed dormancy, the identification of plant lncRNAs remains a challenge due to the scarcity of specific and extensively tested identification methods. Most mainstream machine learning-based methods used for plant lncRNA identification were initially developed using human or other animal datasets, and their accuracy and effectiveness in predicting plant lncRNAs have not been fully evaluated or exploited. To overcome this limitation, we retrained several models, including CPAT, PLEK, and LncFinder, using plant datasets and compared their performance with mainstream lncRNA prediction tools such as CPC2, CNCI, RNAplonc, and LncADeep. Retraining these models significantly improved their performance, and two of the retrained models, LncFinder-plant and CPAT-plant, alongside their ensemble, emerged as the most suitable tools for plant lncRNA identification. This underscores the importance of model retraining in tackling the challenges associated with plant lncRNA identification. Finally, we developed a pipeline (Plant-LncPipe) that incorporates an ensemble of the two best-performing models and covers the entire data analysis process, including reads mapping, transcript assembly, lncRNA identification, classification, and origin, for the efficient identification of lncRNAs in plants. The pipeline, Plant-LncPipe, is available at: https://github.com/xuechantian/Plant-LncRNA-pipline.

Due to their sessile nature, plants must precisely time and coordinate their physiological processes with daily and seasonal changes in the environment. In this PhD thesis, I explored the interaction between an internal timekeeper, or circadian clock, and hormonal regulation, and how it may control plant growth and adaptation in the model species Arabidopsis thaliana (Arabidopsis) and hybrid aspen (Populus tremula x P. tremuloides). Our research showed how the circadian clock component ZEITLUPE (ZTL) regulates abscisic acid (ABA)-mediated stomatal closure, indicating its central role in environmental adaptation. We investigated the effects of manipulating gibberellin (GA) metabolism in hybrid aspen by the strategic expression of the Arabidopsis GIBBERELLIN20-OXIDASE1 gene, using a clock-controlled promoter. This approach struck a delicate balance between enhanced growth and seasonal adaptation and showed potential for increased tree performance through biotechnological means. Our studies on the circadian clock components LATE ELONGATED HYPOCOTYL (LHY) and EARLY BIRD (EBI) in hybrid aspen suggested their involvement in regulating GA metabolism and overall plant growth. Taken together, these findings improve our understanding of how plants regulate growth and respond to environmental stresses and help to provide solutions for enhancing plant resilience and productivity.

Forestry in Sweden largely relies on planting genetically improved seedlings after clear-cutting, and high survival and early growth of planted seedlings is vital for stand establishment, economic viability, and carbon sequestration. Norway spruce (Picea abies) and Scots pine (Pinus sylvestris) are the two most important tree species in Swedish forest stands and both are associated with a variety of ectomycorrhizal fungi. While seedlings are generally not fertilized at outplanting, previous results have shown that fertilization with arginine phosphate can increase root growth and seedling survival. However, it is not clear how this affects fungal community composition on the roots of growing seedlings. In a planting experiment sampled after one and two growing seasons, we found that planting position had the largest effects both on seedling performance and on fungal community composition and provide insight into the early stages of fungal community succession on planted Norway spruce and Scots pine seedlings. Fungal taxa present on seedlings before planting persisted on seedling roots, while some degree of novel colonization by site indigenous taxa was observed. Fertilization modified the relative abundance of some fungal taxa but did not lead to significant changes in overall community composition. In terms of seedling performance, ammonium nitrate led to increased mortality while arginine phosphate improved root growth.

Insect herbivores can inflict substantial costs on plant reproductive success. Seed herbivory impacts directly by reducing the number of seeds and therefore the dispersal and reproductive potential of the plant. Fig trees, Ficus, provide keystone resources for tropical forests. The pollinating fig wasps develop inside figs, so consumption of unripe figs results in trees not only losing seeds but also their pollen dispersers. Selection to defend figs should therefore be strong. Seed herbivory is understudied in tropical forests and most data has been collected from fallen fruits. Here we use canopy sampling to identify fig-consuming larvae in central Panama and quantify both their consequences for the fig trees' reproductive success and the defensive value that ants provide against these larvae. Field surveys of 46 crops from nine fig species revealed that larvae could destroy up to 80% of figs on a tree. From seven Ficus species we barcoded (using COI) 51 individual fig consuming larvae (mainly Lepidoptera) that grouped into seven molecular operational taxonomic units. Lepidopteran larvae formed two feeding strategies, either stationary within a fig or tunneling between figs. Within the context of our study, stationary larvae were specialists whereas tunneling larvae were either specialists or generalists found on different Ficus species. Trees with ants had significantly fewer figs consumed by larvae (9% +/- 17% (mean +/- SD) for trees with azteca ants and 16% +/- 24% for trees with other ants) than did trees without ants (51% +/- 27%). Our results corroborate earlier findings that hosting ants can be an effective defensive mechanism for trees against seed herbivores or other antagonistic insects. Our study contributes to a wider body of research around the networks of insects associated with figs that highlights the importance of a multitrophic approach for understanding mutualism stability and persistence in the face of antagonism.

The Violaceae family is rich in metal-tolerant species and species producing cyclic peptides (cyclotides) that are linked to the resistance to biotic factors. Plants that inhabit areas polluted with heavy metals have developed various mechanisms of tolerance. To test the role of cyclotides in protection against abiotic factors, including heavy metals, cell suspension cultures of Viola species/genotypes (V. lutea ssp. westfalica, V. tricolor, V. arvensis, and V. uliginosa), representing different levels of tolerance to heavy metals (from the most tolerant-MET to the least tolerant populations/species-NMET), were used. The relative abundances of the cyclotides in the control, untreated cell suspensions of all the selected species/genotypes, and cells treated with Zn or Pb (200 mu M or 2000 mu M) for 24 h or 72 h were determined via MALDI-MS. Transmission electron microscopy with X-ray microanalysis was used to detect putative co-localization of the cyclotides with Zn or Pb in the cells of V. tricolor treated with the highest concentration of heavy metals for 72 h. Cyclotide biosynthesis was dependent on the type of heavy metal and its concentration, time of treatment, plant species, and population type (MET vs. NMET). It was positively correlated with the level of tolerance of particular Viola species. The increased production of cyclotides was observed in the cells of metallophyte species, mostly in Zn-treated cells. The nonmetallophyte-V. uliginosa presented a decrease in the production of cyclotides independent of the dose and duration of the metal treatment. Cyclotides co-localized with Pb more evidently than with Zn, suggesting that cyclotides have heavy metal affinity. V. lutea ssp. westfalica transcriptome mining yielded 100 cyclotide sequences, 16 known and 84 novel named viwe 1-84. These findings support the hypothesis that cyclotides are involved in certain mechanisms of plant tolerance to heavy metals.

During the course of terrestrial evolution, plants have developed complex networks that involve the coordination of phytohormone signalling pathways in order to adapt to an ever-changing environment. Transcription factors coordinate these responses by engaging in different protein complexes and exerting both positive and negative effects. ABA INSENSITIVE 5 (ABI5) binding proteins (AFPs), which are closely related to NOVEL INTERACTOR OF JAZ (NINJA)-like proteins, are known for their fundamental role in plants' morphological and physiological growth. Recent studies have shown that AFPs regulate several hormone-signalling pathways, including abscisic acid (ABA) and gibberellic acid (GA). Here, we review the genetic control of AFPs and their crosstalk with plant hormone signalling, and discuss the contributions of AFPs to plants’ growth and development.

Lichens are remarkable and classic examples of symbiotic organisms that have fascinated scientists for centuries. Yet, it has only been for a couple of decades that significant advances have focused on the diversity of their green algal and/or cyanobacterial photobionts. Cyanolichens, which contain cyanobacteria as their photosynthetic partner, include up to 10% of all known lichens and, as such, studies on their cyanobionts are much rarer compared to their green algal counterparts. For the unicellular cyanobionts, i.e. cyanobacteria that do not form filaments, these studies are even scarcer. Nonetheless, these currently include at least 10 different genera in the cosmopolitan lichen order Lichinales. An international consortium (International Network of CyanoBionts; INCb) will tackle this lack of knowledge. In this article, we discuss the status of current unicellular cyanobiont research, compare the taxonomic resolution of photobionts from cyanolichens with those of green algal lichens (chlorolichens), and give a roadmap of research on how to recondition the underestimated fraction of symbiotic unicellular cyanobacteria in lichens.

Fruit peel color is an important index of mango fruit quality. Therefore, increasing the anthocyanin accumulation and improving coloration in red mango are crucial for mango industry. The anthocyanin accumulation in mango is light-regulated. However, the effect of white light combined with different doses of UV-B on anthocyanin biosynthesis has not been clarified. Also lacking is a comprehensive analysis of responses of mango fruit peel to UV-B/white light treatments. In this study, green mature ‘Guifei’ mango fruits were subjected to white light combined with low (WL+UV-BL) or high dose UV-B (WL+UV-BH). Anthocyanin concentration, anthocyanin-related gene expression, reactive oxygen species (ROS), antioxidant, and plant hormone concentrations, and antioxidant enzyme activity were measured. The results showed that especially a WL+UV-BH regimen promoted anthocyanin formation in mango peel. Anthocyaninand light signal-related gene expression, ROS content, antioxidant enzyme activity, antioxidant concentrations, and total antioxidant capacity were also increased by UVB/ white light. Such treatments led to higher concentrations of jasmonic acid and cytokines, but decreased content of 1-aminocyclopropane-1-carboxylic acid and salicylic acids. Commercially, our findings may contribute to improving the commercial quality of mango. Scientifically, the present data sheds light on the mango fruit peelspecific molecular and physiological response network under UV-B/white light treatments., This study was supported by the National Key Research and Development Plan of China (grant number: 2023YFD2300801), National Natural Science Foundation of China (grant numbers: 32360736 and 32160678), the Major Science and Technology Plan of Hainan Province (grant number: ZDKJ2021014), Hainan Provincial Natural Science Foundation of China (grant number: 322RC568), Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University (grant number: XTCX2022NYC04), Scientific Research Foundation of Hainan University (grant number: KYQD(ZR)20053), and Hainan Provincial postgraduate innovative research project (grant number: Qhyb 2022-52).

Increasing environmental awareness and the carbon-storing capability of wood have amplified its relevance as a building material. The demand for high-quality wood species necessitates exploring alternative, underutilized wood sources due to limited forest areas and premium wood volume. Consequently, the veneer-based industry is considering lower-value hardwood species like grey alder (Alnus Incania), black alder (Alnus glutinosa), and aspen (Populus tremula) as substitutes for high-quality birch (Betula pendula). Initially less appealing due to their lower density and mechanical properties, these species show promise through densification, which enhances their density, strength, and hardness. This study aims to enhance plywood screw withdrawal capacity and surface hardness by densifying low-density wood species and using them in plywood face-veneer layers, or in all layers. The relationship between the wood density, surface hardness, and screw withdrawal capacity of plywood made of low-value species like aspen and black alder is examined. Experimental work with a pilot-scale veneer and plywood production line demonstrates improved surface hardness (65% and 93% for aspen and black alder, respectively) and screw withdrawal capacity (16% and 35% for aspen and black alder, respectively) in densified face veneer plywood. This research highlights the potential of densified low-value wood species to meet construction requirements, expanding their practical applications., Validerad;2024;Nivå 2;2024-07-24 (signyg);Funder: Estonian Research Council (PRG2213); Environmental Investment Center (RE.4.08.22-0012);Fulltext license: CC BY

Background: Gaseous phytohormone ethylene levels are directly influenced by the production of its immediate non-volatile precursor 1-aminocyclopropane-1-carboxylic acid (ACC). Owing to the strongly acidic character of the ACC molecule, its quantification has been difficult to perform. Here, we present a simple and straightforward validated method for accurate quantification of not only ACC levels, but also major members of other important phytohormonal classes – auxins, cytokinins, jasmonic acid, abscisic acid and salicylic acid from the same biological sample. Results: The presented technique facilitates the analysis of 15 compounds by liquid chromatography coupled with tandem mass spectrometry. It was optimized and validated for 10 mg of fresh weight plant material. The extraction procedure is composed of a minimal amount of necessary steps. Accuracy and precision were the basis for evaluating the method, together with process efficiency, recovery and matrix effects as validation parameters. The examined compounds comprise important groups of phytohormones, their active forms and some of their metabolites, including six cytokinins, four auxins, two jasmonates, abscisic acid, salicylic acid and 1-aminocyclopropane-1-carboxylic acid. The resulting method was used to examine their contents in selected Arabidopsis thaliana mutant lines. Conclusion: This profiling method enables a very straightforward approach for indirect ethylene study and explores how it interacts, based on content levels, with other phytohormonal groups in plants.

Chlorophyll fluorescence is a ubiquitous tool in basic and applied plant science research. Various standard commercial instruments are available for characterization of photosynthetic material like leaves or microalgae, most of which integrate the overall fluorescence signals above a certain cut-off wavelength. However, wavelength-resolved (fluorescence signals appearing at different wavelengths having different time dependent decay) signals contain vast information required to decompose complex signals and processes into their underlying components that can untangle the photo-physiological process of photosynthesis. Hence, to address this we describe an advanced chlorophyll fluorescence spectrometer - ChloroSpec - allowing three-dimensional simultaneous detection of fluorescence intensities at different wavelengths in a time-resolved manner. We demonstrate for a variety of typical examples that most of the generally used fluorescence parameters are strongly wavelength dependent. This indicates a pronounced heterogeneity and a highly dynamic nature of the thylakoid and the photosynthetic apparatus under actinic illumination. Furthermore, we provide examples of advanced global analysis procedures integrating this three-dimensional signal and relevant information extracted from them that relate to the physiological properties of the organism. This conveniently obtained broad range of data can make ChloroSpec a new standard tool in photosynthesis research.

Starch residue analysis was carried out on stone tools recovered from the bottom layer of the Anakena site on Rapa Nui (Easter Island). These deposits have been dated to AD 1000–1300 AD and so far, represent the earliest evidence of human settlement on this island. Twenty obsidian tools were analyzed. Analysis of 46 starch grains recovered from 20 obsidian tools from the earliest dated level of the Anakena site on Rapa Nui provides direct evidence for translocation of traditional crop plants at initial stages of the colonization of this island. The analysis of starch grains was based mainly on statistical methods for species identification but was complemented by visual inspection in some cases. Our results identify taxons previously unknown to have been cultivated on the island, such as breadfruit (Artocarpus altilis), Zingiber officinale (ginger), and starch grains of the Spondias dulcis and Inocarpus fagifer tropical trees. Additionally, starch grains of Colocasia esculenta (taro) and Dioscorea sp. (yam), both common species in Pacific agriculture, were identified. Furthermore, the presence of four American taxa Ipomoea batatas (sweet potato), Canna sp. (achira), Manihot esculenta (manioc), and Xanthosoma sp., was detected. The occurrence of Canna sp., M. esculenta, and Xanthosoma sp. starch grains suggests the translocation of previously not described South American cultivars into the Pacific. The detection of I. batatas from this site in Rapa Nui constitutes the earliest record of this cultigen in the Pacific. Our study provides direct evidence for translocation of a set of traditional Polynesian and South American crop plants at the initial stages of colonization in Rapa Nui.

Evolutionary radiation, a pivotal aspect of macroevolution, offers valuable insights into evolutionary processes. The genus Pinus is the largest genus in conifers with (Formula presented.) 90% of the extant species emerged in the Miocene, which signifies a case of rapid diversification. Despite this remarkable history, our understanding of the mechanisms driving radiation within this expansive genus has remained limited. Using exome capture sequencing and a fossil-calibrated phylogeny, we investigated the divergence history, niche diversification, and introgression among 13 closely related Eurasian species spanning climate zones from the tropics to the boreal Arctic. We detected complex introgression among lineages in subsection Pinus at all stages of the phylogeny. Despite this widespread gene exchange, each species maintained its genetic identity and showed clear niche differentiation. Demographic analysis unveiled distinct population histories among these species, which further influenced the nucleotide diversity and efficacy of purifying and positive selection in each species. Our findings suggest that radiation in the Eurasian pines was likely fueled by interspecific recombination and further reinforced by their adaptation to distinct environments. Our study highlights the constraints and opportunities for evolutionary change, and the expectations of future adaptation in response to environmental changes in different lineages.

A new species of Papaveraceae, Corydalis sunhangii, in the section Trachycarpae, is described and illustrated from Nyingchi City, Xizang, China. The new species has some resemblance to Corydalis kingdonis, but differs by radical leaves prominent, usually several, blade tripinnate (vs. insignificant, few, blade bi- to triternate); cauline leaf usually one, much smaller than radical leaves, usually situated in lower half of stem (vs. usually two, larger than radical leaves, concentrated in upper third of stem); racemes densely 13-35-flowered (vs. rather lax, 4-11-flowered); claw of lower petal shallowly saccate (vs. very prominently and deeply saccate); capsule oblong, with raised lines of dense papillae (vs. broadly obovoid, smooth). Phylogenetic analysis, based on 68 protein-coding plastid genes of 49 samples, shows that C. sunhangii is not closely related to any hitherto described species, which is consistent with our morphological analysis.

Phytophthora pseudosyringae is a self-fertile pathogen of woody plants, particularly associated with tree species from the genera Fagus, Notholithocarpus, Nothofagus and Quercus, which is found across Europe and in parts of North America and Chile. It can behave as a soil pathogen infecting roots and the stem collar region, as well as an aerial pathogen infecting leaves, twigs and stem barks, causing particular damage in the United Kingdom and western North America. The population structure, migration and potential outcrossing of a worldwide collection of isolates were investigated using genotyping-by-sequencing. Coalescent-based migration analysis revealed that the North American population originated from Europe. Historical gene flow has occurred between the continents in both directions to some extent, yet contemporary migration is overwhelmingly from Europe to North America. Two broad population clusters dominate the global population of the pathogen, with a subgroup derived from one of the main clusters found only in western North America. Index of association and network analyses indicate an influential level of outcrossing has occurred in this preferentially inbreeding, homothallic oomycete. Outcrossing between the two main population clusters has created distinct subgroups of admixed individuals that are, however, less common than the main population clusters. Differences in life history traits between the two main population clusters should be further investigated together with virulence and host range tests to evaluate the risk each population poses to natural environments worldwide.