Water status dynamics and drought tolerance of juvenile European beech, Douglas fir and Norway spruce trees as dependent on neighborhood and nitrogen supply.

To increase the resilience of forests to drought and other hazards, foresters are increasingly planting mixed stands. This requires knowledge about the drought response of tree species in pure and mixed-culture neighborhoods. In addition, drought frequently interacts with continued atmospheric nitrogen (N) deposition. To disentangle these factors for European beech, Norway spruce and Douglas fir, we conducted a replicated 3-factorial sapling growth experiment with three moisture levels, (high, medium, and low), two N levels (high and ambient), and pure and mixed-culture neighborhoods. We measured biomass, stomatal conductance (GS), shoot water potential (at predawn: ΨPD, midday, and turgor loss point: ΨTLP), branch xylem embolism resistance (Ψ50) and minimum epidermal conductance (Gmin). The three species differed most with respect to Gmin (10-fold higher in beech than in the conifers), hydroscape area (larger in beech), and the time elapsed to reach stomatal closure (TΨGS90) and ΨTLP (TTLP; shorter in beech), while Ψ50 and ΨTLP were remarkably similar. Neighborhood (pure vs mixed-culture) influenced biomass production, water status and hydraulic traits, notably GS (higher in Douglas fir, but lower in spruce and beech, in mixtures than pure culture), hydraulic safety margin (smaller for beech in mixtures), and TΨGS90 and TTLP (shorter for spruce in mixture). High N generally increased GS, but no consistent N effects on leaf water status and hydraulic traits were detected, suggesting that neighbor identity had a larger effect on plant water relations than N availability. We conclude that both tree neighborhood and N availability modulate the drought response of beech, spruce, and Douglas fir. Species mixing can alleviate the drought stress of some species, but often by disadvantaging other species. Thus, our study suggests that stabilizing and building resilience of production forests against a drier and warmer climate may depend primarily on the right species choice; species mixing can support the agenda.

Coordinated hydraulic traits influence the two phases of time to hydraulic failure in five temperate tree species differing in stomatal stringency.

Worldwide, forests are increasingly exposed to extreme droughts causing tree mortality. Because of the complex nature of the mechanisms involved, various traits have been linked to tree drought responses with contrasting results. This may be due to species-specific strategies in regulating water potential, a process that unfolds in two distinct phases: a first phase until stomatal closure, and a second phase until reaching lethal xylem hydraulic thresholds. We conducted dry-down experiments with five broadleaved temperate tree species differing in their degree of isohydry to estimate the time to stomatal closure (tsc) and subsequent time to critical hydraulic failure (tcrit). We measured various traits linked to tree drought responses, such as the water potentials at turgor loss point (Ptlp), stomatal closure (Pgs90), and 12%, 50% and 88% loss of xylem hydraulic conductance (P12, P50, P88), hydraulic capacitance (C), minimum leaf conductance (gmin), hydroscape area (HSA) and hydraulic safety margins (HSM). We found that Pgs90 followed previously recorded patterns of isohydry and was associated with HSA. Species ranked from more to less isohydric in the sequence Acer pseudoplatanus < Betula pendula < Tilia cordata < Sorbus aucuparia < Fagus sylvatica. Their degree of isohydry was associated with leaf safety (Ptlp and gmin), drought avoidance (C) and tsc, but decoupled from xylem safety (HSM and P88) and tcrit. Regardless of their stomatal stringency, species with wider HSM and lower P88 reached critical hydraulic failure later. We conclude that the duration of the first phase is determined by stomatal regulation, while the duration of the second phase is associated with xylem safety. Isohydry is thus linked to water use rather than to drought survival strategies, confirming the proposed use of HSA as a complement to HSM for describing plant drought responses before and after stomatal closure.

Plasticity of wood and leaf traits related to hydraulic efficiency and safety is linked to evaporative demand and not soil moisture in rubber (Hevea brasiliensis).

The predicted increase of drought intensity in South-East Asia has raised concern about the sustainability of rubber (Hevea brasiliensis Müll. Arg.) cultivation. In order to quantify the degree of phenotypic plasticity in this important tree crop species, we analysed a set of wood and leaf traits related to the hydraulic safety and efficiency in PB260 clones from eight small-holder plantations in Jambi province, Indonesia, representing a gradient in local microclimatic and edaphic conditions. Across plots, branch embolism resistance (P50) ranged from -2.14 to -2.58 MPa. The P50 and P88 values declined, and the hydraulic safety margin increased, with an increase in the mean annual vapour pressure deficit (VPD). Among leaf traits, only the changes in specific leaf area were related to the differences in evaporative demand. These variations of hydraulic trait values were not related to soil moisture levels. We did not find a trade-off between hydraulic safety and efficiency, but vessel density (VD) emerged as a major trait associated with both safety and efficiency. The VD, and not vessel diameter, was closely related to P50 and P88 as well as to specific hydraulic conductivity, the lumen-to-sapwood area ratio and the vessel grouping index. In conclusion, our results demonstrate some degree of phenotypic plasticity in wood traits related to hydraulic safety in this tropical tree species, but this is only in response to the local changes in evaporative demand and not soil moisture. Given that VPD may increasingly limit plant growth in a warmer world, our results provide evidence of hydraulic trait changes in response to a rising evaporative demand.

Leaf physiological and morphological constraints of water-use efficiency in C3 plants.

The increasing evaporative demand due to climate change will significantly affect the balance of carbon assimilation and water losses of plants worldwide. The development of crop varieties with improved water-use efficiency (WUE) will be critical for adapting agricultural strategies under predicted future climates. This review aims to summarize the most important leaf morpho-physiological constraints of WUE in C3 plants and identify gaps in knowledge. From the carbon gain side of the WUE, the discussed parameters are mesophyll conductance, carboxylation efficiency and respiratory losses. The traits and parameters affecting the waterside of WUE balance discussed in this review are stomatal size and density, stomatal control and residual water losses (cuticular and bark conductance), nocturnal conductance and leaf hydraulic conductance. In addition, we discussed the impact of leaf anatomy and crown architecture on both the carbon gain and water loss components of WUE. There are multiple possible targets for future development in understanding sources of WUE variability in plants. We identified residual water losses and respiratory carbon losses as the greatest knowledge gaps of whole-plant WUE assessments. Moreover, the impact of trichomes, leaf hydraulic conductance and canopy structure on plants' WUE is still not well understood. The development of a multi-trait approach is urgently needed for a better understanding of WUE dynamics and optimization.

Root and branch hydraulic functioning and trait coordination across organs in drought-deciduous and evergreen tree species of a subtropical highland forest.

Vessel traits are key in understanding trees' hydraulic efficiency, and related characteristics like growth performance and drought tolerance. While most plant hydraulic studies have focused on aboveground organs, our understanding of root hydraulic functioning and trait coordination across organs remains limited. Furthermore, studies from seasonally dry (sub-)tropical ecosystems and mountain forests are virtually lacking and uncertainties remain regarding potentially different hydraulic strategies of plants differing in leaf habit. Here, we compared wood anatomical traits and specific hydraulic conductivities between coarse roots and small branches of five drought-deciduous and eight evergreen angiosperm tree species in a seasonally dry subtropical Afromontane forest in Ethiopia. We hypothesized that largest vessels and highest hydraulic conductivities are found in roots, with greater vessel tapering between roots and equally-sized branches in evergreen angiosperms due to their drought-tolerating strategy. We further hypothesized that the hydraulic efficiencies of root and branches cannot be predicted from wood density, but that wood densities across organs are generally related. Root-to-branch ratios of conduit diameters varied between 0.8 and 2.8, indicating considerable differences in tapering from coarse roots to small branches. While deciduous trees showed larger branch xylem vessels compared to evergreen angiosperms, root-to-branch ratios were highly variable within both leaf habit types, and evergreen species did not show a more pronounced degree of tapering. Empirically determined hydraulic conductivity and corresponding root-to-branch ratios were similar between both leaf habit types. Wood density of angiosperm roots was negatively related to hydraulic efficiency and vessel dimensions; weaker relationships were found in branches. Wood density of small branches was neither related to stem nor coarse root wood densities. We conclude that in seasonally dry subtropical forests, similar-sized coarse roots hold larger xylem vessels than small branches, but the degree of tapering from roots to branches is highly variable. Our results indicate that leaf habit does not necessarily influence the relationship between coarse root and branch hydraulic traits. However, larger conduits in branches and a low carbon investment in less dense wood may be a prerequisite for high growth rates of drought-deciduous trees during their shortened growing season. The correlation of stem and root wood densities with root hydraulic traits but not branch wood points toward large trade-offs in branch xylem towards mechanical properties.

Ambient and substrate energy influence decomposer diversity differentially across trophic levels.

The species-energy hypothesis predicts increasing biodiversity with increasing energy in ecosystems. Proxies for energy availability are often grouped into ambient energy (i.e., solar radiation) and substrate energy (i.e., non-structural carbohydrates or nutritional content). The relative importance of substrate energy is thought to decrease with increasing trophic level from primary consumers to predators, with reciprocal effects of ambient energy. Yet, empirical tests are lacking. We compiled data on 332,557 deadwood-inhabiting beetles of 901 species reared from wood of 49 tree species across Europe. Using host-phylogeny-controlled models, we show that the relative importance of substrate energy versus ambient energy decreases with increasing trophic levels: the diversity of zoophagous and mycetophagous beetles was determined by ambient energy, while non-structural carbohydrate content in woody tissues determined that of xylophagous beetles. Our study thus overall supports the species-energy hypothesis and specifies that the relative importance of ambient temperature increases with increasing trophic level with opposite effects for substrate energy.

Addressing controversies in the xylem embolism resistance-vessel diameter relationship.

Although xylem embolism is a key process during drought-induced tree mortality, its relationship to wood anatomy remains debated. While the functional link between bordered pits and embolism resistance is known, there is no direct, mechanistic explanation for the traditional assumption that wider vessels are more vulnerable than narrow ones. We used data from 20 temperate broad-leaved tree species to study the inter- and intraspecific relationship of water potential at 50% loss of conductivity (P50 ) with hydraulically weighted vessel diameter (Dh ) and tested its link to pit membrane thickness (TPM ) and specific conductivity (Ks ) on species level. Embolism-resistant species had thick pit membranes and narrow vessels. While Dh was weakly associated with TPM , the P50 -Dh relationship remained highly significant after accounting for TPM . The interspecific pattern between P50 and Dh was mirrored by a link between P50 and Ks , but there was no evidence for an intraspecific relationship. Our results provide robust evidence for an interspecific P50 -Dh relationship across our species. As a potential cause for the inconsistencies in published P50 -Dh relationships, our analysis suggests differences in the range of trait values covered, and the level of data aggregation (species, tree or sample level) studied.

Enhancing the structural diversity between forest patches-A concept and real-world experiment to study biodiversity, multifunctionality and forest resilience across spatial scales.

Intensification of land use by humans has led to a homogenization of landscapes and decreasing resilience of ecosystems globally due to a loss of biodiversity, including the majority of forests. Biodiversity-ecosystem functioning (BEF) research has provided compelling evidence for a positive effect of biodiversity on ecosystem functions and services at the local (α-diversity) scale, but we largely lack empirical evidence on how the loss of between-patch ß-diversity affects biodiversity and multifunctionality at the landscape scale (γ-diversity). Here, we present a novel concept and experimental framework for elucidating BEF patterns at α-, ß-, and γ-scales in real landscapes at a forest management-relevant scale. We examine this framework using 22 temperate broadleaf production forests, dominated by Fagus sylvatica. In 11 of these forests, we manipulated the structure between forest patches by increasing variation in canopy cover and deadwood. We hypothesized that an increase in landscape heterogeneity would enhance the ß-diversity of different trophic levels, as well as the ß-functionality of various ecosystem functions. We will develop a new statistical framework for BEF studies extending across scales and incorporating biodiversity measures from taxonomic to functional to phylogenetic diversity using Hill numbers. We will further expand the Hill number concept to multifunctionality allowing the decomposition of γ-multifunctionality into α- and ß-components. Combining this analytic framework with our experimental data will allow us to test how an increase in between patch heterogeneity affects biodiversity and multifunctionality across spatial scales and trophic levels to help inform and improve forest resilience under climate change. Such an integrative concept for biodiversity and functionality, including spatial scales and multiple aspects of diversity and multifunctionality as well as physical and environmental structure in forests, will go far beyond the current widely applied approach in forestry to increase resilience of future forests through the manipulation of tree species composition.

Anatomical adjustments of the tree hydraulic pathway decrease canopy conductance under long-term elevated CO2.

The cause of reduced leaf-level transpiration under elevated CO2 remains largely elusive. Here, we assessed stomatal, hydraulic, and morphological adjustments in a long-term experiment on Aleppo pine (Pinus halepensis) seedlings germinated and grown for 22-40 months under elevated (eCO2; c. 860 ppm) or ambient (aCO2; c. 410 ppm) CO2. We assessed if eCO2-triggered reductions in canopy conductance (gc) alter the response to soil or atmospheric drought and are reversible or lasting due to anatomical adjustments by exposing eCO2 seedlings to decreasing [CO2]. To quantify underlying mechanisms, we analyzed leaf abscisic acid (ABA) level, stomatal and leaf morphology, xylem structure, hydraulic efficiency, and hydraulic safety. Effects of eCO2 manifested in a strong reduction in leaf-level gc (-55%) not caused by ABA and not reversible under low CO2 (c. 200 ppm). Stomatal development and size were unchanged, while stomatal density increased (+18%). An increased vein-to-epidermis distance (+65%) suggested a larger leaf resistance to water flow. This was supported by anatomical adjustments of branch xylem having smaller conduits (-8%) and lower conduit lumen fraction (-11%), which resulted in a lower specific conductivity (-19%) and leaf-specific conductivity (-34%). These adaptations to CO2 did not change stomatal sensitivity to soil or atmospheric drought, consistent with similar xylem safety thresholds. In summary, we found reductions of gc under elevated CO2 to be reflected in anatomical adjustments and decreases in hydraulic conductivity. As these water savings were largely annulled by increases in leaf biomass, we do not expect alleviation of drought stress in a high CO2 atmosphere.

Branch xylem vascular adjustments in European beech in response to decreasing water availability across a precipitation gradient.

Crucial for the climate adaptation of trees is a xylem anatomical structure capable of adjusting to changing water regimes. Although species comparisons across climate zones have demonstrated anatomical change in response to altered water availability and tree height, less is known about the adaptability of tree vascular systems to increasing water deficits at the intraspecific level. Information on the between-population and within-population variability of xylem traits helps assessing a species' ability to cope with climate change. We investigated the variability of wood anatomical and related hydraulic traits in terminal branches of European beech (Fagus sylvatica L.) trees across a precipitation gradient (520-890 mm year-1) and examined the influence of climatic water balance (CWB), soil water capacity (AWC), neighborhood competition (CI), tree height and branch age on these traits. Furthermore, the relationship between xylem anatomical traits and embolism resistance (P50) was tested. Within-population trait variation was larger than between-population variation. Vessel diameter, lumen-to-sapwood area ratio and potential conductivity of terminal branches decreased with decreasing CWB, but these traits were not affected by AWC, whereas vessel density increased with an AWC decrease. In contrast, none of the studied anatomical traits were influenced by variation in tree height (21-34 m) or CI. Branch age was highly variable (2-22 years) despite equal diameter and position in the flow path, suggesting different growth trajectories in the past. Vessel diameter decreased, and vessel density increased, with increasing branch age, reflecting negative annual radial growth trends. Although vessel diameter was not related to P50, vessel grouping index and lumen-to-sapwood area ratio showed a weak, though highly significant, positive relationship to P50. We conclude that the xylem anatomy of terminal tree-top branches in European beech is modified in response to increasing climatic aridity and/or decreasing soil water availability, independent of a tree height effect.

Mutually inclusive mechanisms of drought-induced tree mortality.

Unprecedented tree dieback across Central Europe caused by recent global change-type drought events highlights the need for a better mechanistic understanding of drought-induced tree mortality. Although numerous physiological risk factors have been identified, the importance of two principal mechanisms, hydraulic failure and carbon starvation, is still debated. It further remains largely unresolved how the local neighborhood composition affects individual mortality risk. We studied 9435 young trees of 12 temperate species planted in a diversity experiment in 2013 to assess how hydraulic traits, carbon dynamics, pest infestation, tree height and neighborhood competition influence individual mortality risk. Following the most extreme global change-type drought since record in 2018, one third of these trees died. Across species, hydraulic safety margins (HSMs) were negatively and a shift towards a higher sugar fraction in the non-structural carbohydrate (NSC) pool positively associated with mortality risk. Moreover, trees infested by bark beetles had a higher mortality risk, and taller trees a lower mortality risk. Most neighborhood interactions were beneficial, although neighborhood effects were highly species-specific. Species that suffered more from drought, especially Larix spp. and Betula spp., tended to increase the survival probability of their neighbors and vice versa. While severe tissue dehydration marks the final stage of drought-induced tree mortality, we show that hydraulic failure is interrelated with a series of other, mutually inclusive processes. These include shifts in NSC pools driven by osmotic adjustment and/or starch depletion as well as pest infestation and are modulated by the size and species identity of a tree and its neighbors. A more holistic view that accounts for multiple causes of drought-induced tree mortality is required to improve predictions of trends in global forest dynamics and to identify mutually beneficial species combinations.

Lack of hydraulic recovery as a cause of post-drought foliage reduction and canopy decline in European beech.

European beech (Fagus sylvatica) was among the most affected tree species during the severe 2018 European drought. It not only suffered from instant physiological stress but also showed severe symptoms of defoliation and canopy decline in the following year. To explore the underlying mechanisms, we used the Swiss-Canopy-Crane II site and studied in branches of healthy and symptomatic trees the repair of hydraulic function and concentration of carbohydrates during the 2018 drought and in 2019. We found loss of hydraulic conductance in 2018, which did not recover in 2019 in trees that developed defoliation symptoms in the year after drought. Reduced branch foliation in symptomatic trees was associated with a gradual decline in wood starch concentration throughout summer 2019. Visualization of water transport in healthy and symptomatic branches in the year after the drought confirmed the close relationship between xylem functionality and supported branch leaf area. Our findings showed that embolized xylem does not regain function in the season following a drought and that sustained branch hydraulic dysfunction is counterbalanced by the reduction in supported leaf area. It suggests acclimation of leaf development after drought to mitigate disturbances in canopy hydraulic function.

Soil water availability and branch age explain variability in xylem safety of European beech in Central Europe.

Xylem embolism resistance has been identified as a key trait with a causal relation to drought-induced tree mortality, but not much is known about its intra-specific trait variability (ITV) in dependence on environmental variation. We measured xylem safety and efficiency in 300 European beech (Fagus sylvatica L.) trees across 30 sites in Central Europe, covering a precipitation reduction from 886 to 522 mm year-1. A broad range of variables that might affect embolism resistance in mature trees, including climatic and soil water availability, competition, and branch age, were examined. The average P50 value varied by up to 1 MPa between sites. Neither climatic aridity nor structural variables had a significant influence on P50. However, P50 was less negative for trees with a higher soil water storage capacity, and positively related to branch age, while specific conductivity (Ks) was not significantly associated with either of these variables. The greatest part of the ITV for xylem safety and efficiency was attributed to random variability within populations. We conclude that the influence of site water availability on P50 and Ks is low in European beech, and that the high degree of within-population variability for P50, partly due to variation in branch age, hampers the identification of a clear environmental signal.

Plant PhysioSpace: a robust tool to compare stress response across plant species.

Generalization of transcriptomics results can be achieved by comparison across experiments. This generalization is based on integration of interrelated transcriptomics studies into a compendium. Such a focus on the bigger picture enables both characterizations of the fate of an organism and distinction between generic and specific responses. Numerous methods for analyzing transcriptomics datasets exist. Yet, most of these methods focus on gene-wise dimension reduction to obtain marker genes and gene sets for, for example, pathway analysis. Relying only on isolated biological modules might result in missing important confounders and relevant contexts. We developed a method called Plant PhysioSpace, which enables researchers to compute experimental conditions across species and platforms without a priori reducing the reference information to specific gene sets. Plant PhysioSpace extracts physiologically relevant signatures from a reference dataset (i.e. a collection of public datasets) by integrating and transforming heterogeneous reference gene expression data into a set of physiology-specific patterns. New experimental data can be mapped to these patterns, resulting in similarity scores between the acquired data and the extracted compendium. Because of its robustness against platform bias and noise, Plant PhysioSpace can function as an inter-species or cross-platform similarity measure. We have demonstrated its success in translating stress responses between different species and platforms, including single-cell technologies. We have also implemented two R packages, one software and one data package, and a Shiny web application to facilitate access to our method and precomputed models.

Hydraulic variability of three temperate broadleaf tree species along a water availability gradient in central Europe.

Plant hydraulic traits are key for understanding and predicting tree drought responses. Information about the degree of the traits' intra-specific variability may guide the selection of drought-resistant genotypes and is crucial for trait-based modelling approaches. For the three temperate minor broadleaf tree species Acer platanoides, Carpinus betulus and Tilia cordata, we measured xylem embolism resistance (P50 ), leaf turgor loss point (PTLP ), specific hydraulic conductivity (KS ), Huber values (HVs), and hydraulic safety margins in adult trees across a precipitation gradient. We further quantified trait variability on different organizational levels (inter-specific to within-canopy variation), and analysed its relationship to climatic and soil water availability. Although we observed a certain intra-specific trait variability (ITV) in safety-related traits (P50 , PTLP ) with higher within-tree and between-tree than between populations variability, the magnitude was small compared to inter-specific differences, which explained 78.4% and 58.3% of the variance in P50 and PTLP , respectively. In contrast, efficiency-related traits (KS , HV) showed a high ITV both within populations and within the crowns of single trees. Surprisingly, the observed ITV of all traits was neither driven by climatic nor soil water availability. In conclusion, the high degree of conservatism in safety-related traits highlights their potential for trait-based modelling approaches.

Rapid hydraulic collapse as cause of drought-induced mortality in conifers.

Understanding the vulnerability of trees to drought-induced mortality is key to predicting the fate of forests in a future climate with more frequent and intense droughts, although the underlying mechanisms are difficult to study in adult trees. Here, we explored the dynamic changes of water relations and limits of hydraulic function in dying adults of Norway spruce (Picea abies L.) during the progression of the record-breaking 2018 Central European drought. In trees on the trajectory to drought-induced mortality, we observed rapid, nonlinear declines of xylem pressure that commenced at the early onset of xylem cavitation and caused a complete loss of xylem hydraulic conductance within a very short time. We also observed severe depletions of nonstructural carbohydrates, though carbon starvation could be ruled out as the cause of the observed tree death, as both dying and surviving trees showed these metabolic limitations. Our observations provide striking field-based evidence for fast dehydration and hydraulic collapse as the cause of drought-induced mortality in adult Norway spruce. The nonlinear decline of tree water relations suggests that considering the temporal dynamics of dehydration is critical for predicting tree death. The collapse of the hydraulic system within a short time demonstrates that trees can rapidly be pushed out of the zone of hydraulic safety during the progression of a severe drought. In summary, our findings point toward a higher mortality risk for Norway spruce than previously assumed, which is in line with current reports of unprecedented levels of drought-induced mortality in this major European tree species.

Pore constrictions in intervessel pit membranes provide a mechanistic explanation for xylem embolism resistance in angiosperms.

Embolism spreading in angiosperm xylem occurs via mesoporous pit membranes between vessels. Here, we investigate how the size of pore constrictions in pit membranes is related to pit membrane thickness and embolism resistance. Pit membranes were modelled as multiple layers to investigate how pit membrane thickness and the number of intervessel pits per vessel determine pore constriction sizes, the probability of encountering large pores, and embolism resistance. These estimations were complemented by measurements of pit membrane thickness, embolism resistance, and number of intervessel pits per vessel in stem xylem (n = 31, 31 and 20 species, respectively). The modelled constriction sizes in pit membranes decreased with increasing membrane thickness, explaining the measured relationship between pit membrane thickness and embolism resistance. The number of pits per vessel affected constriction size and embolism resistance much less than pit membrane thickness. Moreover, a strong relationship between modelled and measured embolism resistance was observed. Pore constrictions provide a mechanistic explanation for why pit membrane thickness determines embolism resistance, which suggests that hydraulic safety can be uncoupled from hydraulic efficiency. Although embolism spreading remains puzzling and encompasses more than pore constriction sizes, angiosperms are unlikely to have leaky pit membranes, which enables tensile transport of water.

Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing.

Expansions of short tandem repeats are genetic variants that have been implicated in several neuropsychiatric and other disorders, but their assessment remains challenging with current polymerase-based methods1-4. Here we introduce a CRISPR-Cas-based enrichment strategy for nanopore sequencing combined with an algorithm for raw signal analysis. Our method, termed STRique for short tandem repeat identification, quantification and evaluation, integrates conventional sequence mapping of nanopore reads with raw signal alignment for the localization of repeat boundaries and a hidden Markov model-based repeat counting mechanism. We demonstrate the precise quantification of repeat numbers in conjunction with the determination of CpG methylation states in the repeat expansion and in adjacent regions at the single-molecule level without amplification. Our method enables the study of previously inaccessible genomic regions and their epigenetic marks.