María Verónica Arana

Premise: Third‐generation sequencing has revolutionized genomics, enabling in‐depth analysis of genome sequence, structure, and epigenetic features. Yet, extracting high‐quality DNA for long‐read sequencing remains a bottleneck—particularly in non‐model plants, such as mature trees growing in natural environments, which often contain abundant endogenous compounds that hinder extraction and downstream applications. Methods and Results: We developed an optimized, robust, and cost‐effective DNA extraction protocol that yields high‐quality DNA suitable for Oxford Nanopore Technologies and PacBio sequencing. Validation across diverse taxa—including six Nothofagus species, gymnosperms endemic to Andean–Patagonian forests, exotic conifers of commercial value, and model plants—demonstrated consistently high DNA purity (A ₂₆₀ /A ₂₈₀ > 1.8, A ₂₆₀ /A ₂₃₀ > 2.0) and fragment sizes ≥30 kbp. Downstream sequencing confirmed suitability for applications requiring long, intact molecules and base modification detection. Conclusions: Compared to commercial kits and standard protocols, this approach achieved superior DNA integrity and yield without specialized equipment, offering an accessible solution for researchers working with challenging plant species.

Nothofagus pumilio , or lenga beech, is a widespread and locally‐adapted tree species endemic to South America's Patagonia region. Its diverse populations span a 2000‐km‐long range in the Andes Mountains, which is already experiencing adverse effects from climate change. Here the Andes contain two uncorrelated temperature and precipitation gradients, which offers a unique opportunity to evaluate how gradients drive local adaptation and conversely how changes in these gradients could lead to future maladaptation risk. We predicted climate maladaptation risk for N. pumilio populations with genomic offset. Our dataset includes 493 adult trees in 20 natural forest sites across the distribution range that were sampled with a paired‐site study design, which creates the opportunity to also investigate genomic offset patterns at small spatial scales. Local climate data for both current and future projected conditions were extracted from the CHELSA online repository. We used 490 putatively‐adaptive single nucleotide polymorphisms, that is, those associated with chosen climatic gradients, and assessed genomic offset using two methods: LFMM ‘genetic.gap’ and Gradient Forest. We projected risk at sampled sites and spatially across the full Argentina species distribution range, considering three possible emission scenarios and two future time periods within the 21st century, using Ensemble Means calculated from CMIP6 projections. Contrary to our expectations, our results predict a complex mosaic of heightened maladaptation risk across the landscape, with particularly high values in northern treeline and southern valley populations, across all investigated scenarios. This suggests a more complicated pattern of risk than uniformly increased risk along elevation or latitude clines. Using external evidence, we contextualize our genomic offset results and investigate possible species' responses, including how maladaptation risk could impact Patagonian forests in the future.

Arabidopsis is regarded as the gold standard among plant systems because it has generated knowledge with translational potential across various disciplines. Nevertheless, the influence of less-explored fields within the Arabidopsis community, such as ecology and evolutionary ecology, has yet to be synthesized to emphasize their contributions to other plant disciplines. This essay summarizes current eco-evolutionary knowledge in Arabidopsis and highlights its potential to enrich the insights made by the Arabidopsis community as well as others working with other plant model and non-model systems. We underline the value of accession-based approaches but also highlight the importance for developing population-based approaches to understand how and where evolutionary change begins. Furthermore, we focus on the evolutionary value of phenotypic plasticity as necessary to comprehend the response of organisms to environmental changes. We also elaborate on conceptual and technical challenges to transcriptomic studies conducted in field conditions that evaluate gene function and gene effect on integrated phenotypes in natural environments. Overall, we believe that the development of joint eco-evolutionary and genetic research in Arabidopsis can help other plant species to develop as model systems, but the Arabidopsis community should also look at the advances of other emerging plant model systems.

Summary: Plant survival in a warmer world requires the timely adjustment of biological processes to cyclical changes in the new environment. Circadian oscillators have been proposed to contribute to thermal adaptation and plasticity. However, the influence of temperature on circadian clock performance and its impact on plant behaviour in natural ecosystems are not well‐understood. We combined bioinformatics, molecular biology and ecophysiology to investigate the effects of increasing temperatures on the functioning of the circadian clock in two closely related tree species from Patagonian forests that constitute examples of adaptation to different thermal environments based on their altitudinal profiles. Nothofagus pumilio, the species from colder environments, showed a major rearrangement of its transcriptome and reduced ability to maintain rhythmicity at high temperatures compared with Nothofagus obliqua, which inhabits warmer zones. In altitude‐swap experiments, N. pumilio, but not N. obliqua, showed limited oscillator function in warmer zones of the forest, and reduced survival and growth. Our findings show that interspecific differences in the influence of temperature on circadian clock performance are associated with preferred thermal niches, and to thermal plasticity of seedlings in natural environments, highlighting the potential role of a resonating oscillator in ecological adaptation to a warming environment.

Plant survival in a warmer world requires the timely adjustment of biological processes to cyclical changes in the new environment. Circadian oscillators have been proposed to contribute to thermal adaptation and plasticity in plants, due to their ability to maintain periodicity in biological rhythms over a wide temperature range, promoting fitness. However, the influence of temperature and circadian clock performance on plant behaviour in natural ecosystems is not well understood. Here we used two co-occurring Nothofagus tree species from the Patagonian forests that are adapted to contrasting thermal environments derived from their different altitudinal profiles. We revealed that the upper thermal limits for accurate clock function are linked to the species’ thermal niches and contribute to seedling plasticity in natural environments. We computationally identified 24 circadian clock-related genes, which showed a high degree of structural conservation with clock genes from both annual and perennial species, and very similar patterns of gene expression to those of Arabidopsis thaliana . Warm temperatures produced a strong transcriptomic rearrangement, which affected the expression of clock-related genes and direct clock targets, evidencing the extent of clock functioning disruption by temperature. N. pumilio , the species from colder environments, showed reduced ability to keep rhythmicity at high temperatures compared to N. obliqua , which inhabits warmer zones. Accordingly, N. pumilio , but not N. obliqua , showed a limited oscillator function in warmer zones of the forest, reduced survival, and growth. Together, our results highlight the potential role of a resonating oscillator in ecological adaptation to a warming environment.

Societal Impact Statement: Forest trees tend to be strongly genetically adapted to their local environments, but climate change will probably subject trees to novel combinations of precipitation, temperature, and photoperiod. Local adaptation was investigated in the ecologically and economically important Patagonian tree species Nothofagus pumilio by characterizing its genetic diversity in relation to the varied environmental conditions across its range. These insights are useful for conservation and management decisions, for example by identifying suitable populations to establish seed source plantations for restoration and characterizing relationships with environmental drivers of selection to better understand how this species will respond to climate change.Summary: Nothofagus pumilio is a foundation tree species that inhabits a 2000‐km‐long range in the southern Andes, a region with two perpendicular environmental gradients: temperature and photoperiod (North–South), and precipitation (West–East). We investigated local adaptation patterns by searching for relationships between environmental clines and signatures of adaptation in candidate genes related to stress response, growth, and phenology. Using a paired site sampling design within a landscape genome analysis, we analyzed 493 adult N. pumilio trees in 20 sampling sites across the species' latitudinal range. We screened 47,336 single nucleotide polymorphism (SNP) loci in 1632 contigs (i.e., coding regions along the genome). Population structure and genetic diversity analyses preceded four genome scan analyses using genetic and environmental data. Population structure and genetic diversity are mainly oriented along the latitude axis. Genome scans identified 445 outlier SNPs, which are loci showing signatures of selection. Temperature and photoperiod variables were associated with notably more outliers than precipitation. However, the most frequent biological functions among genes were water deprivation response and cold response, suggesting that stress response is comprised of complex and polygenic traits that are affected by many environmental variables. Our findings suggest that N. pumilio shows signatures of local adaptation to extant climate conditions, including temperature, photoperiod, and precipitation. However, climate change is likely to alter existing relationships among environmental conditions to which this species is currently adapted. These changes may have unpredictable consequences for the species' future survival, adaptation potential, and the people who depend upon these forests.

Summary: Climate change alters relationships among environmental conditions and thus has the potential to change the selection pressures acting on adaptive gene variants. Using a landscape genomic approach, we show that the southern beech species Nothofagus pumilio has notable genetic adaptations to climate along its 2000-kilometer-long range in the Andes. We screened 47,336 SNP loci in 1,632 contigs and found that high-latitude sampling sites have lower genetic diversity, likely due to greater impact of glacial oscillations at high latitudes. Using four genome scan methods, we identified 457 outlier SNPs that are either strongly differentiated among subpopulations or associated with environmental covariates related to temperature, day length, and precipitation. Temperature and day length parameters were associated with notably more outliers than precipitation (n = 133, 113, and 61 outliers, respectively), and almost half of all annotated outliers were related to stress response (n=38, 21%) or catabolism-metabolism (n=43, 24%). Our findings suggest that Nothofagus pumilio is an ideal Andean model of genetic adaptation to climate change because it is locally adapted to extant climate conditions, and shifting patterns among environmental parameters may be detrimental to its future survival and adaptation potential.

Inflorescence movements in response to natural gradients of sunlight are frequently observed in the plant kingdom and are suggested to contribute to reproductive success. Although the physiological and molecular bases of light‐mediated tropisms in vegetative organs have been thoroughly investigated, the mechanisms that control inflorescence orientation in response to light gradients under natural conditions are not well understood. In this work, we have used a combination of laboratory and field experiments to investigate light‐mediated re‐orientation of Arabidopsis thaliana inflorescences. We show that inflorescence phototropism is promoted by photons in the UV and blue spectral range (≤500 nm) and depends on multiple photoreceptor families. Experiments under controlled conditions show that UVR8 is the main photoreceptor mediating the phototropic response to narrowband UV‐B radiation, and phototropins and cryptochromes control the response to narrowband blue light. Interestingly, whereas phototropins mediate bending in response to low irradiances of blue, cryptochromes are the principal photoreceptors acting at high irradiances. Moreover, phototropins negatively regulate the action of cryptochromes at high irradiances of blue light. Experiments under natural field conditions demonstrate that cryptochromes are the principal photoreceptors acting in the promotion of the heliotropic response of inflorescences under full sunlight.

Global warming is predicted to exert negative impacts on plant growth due to the damaging effect of high temperatures on plant physiology. Revealing the genetic architecture underlying the heat stress response is therefore crucial for the development of conservation strategies, and for breeding heat-resistant plant genotypes. Here we investigated the transcriptional changes induced by heat in Nothofagus pumilio, an emblematic tree species of the sub-Antarctic forests of South America. Through the performance of RNA-seq of leaves of plants exposed to 20°C (control) or 34°C (heat shock), we generated the first transcriptomic resource for the species. We also studied the changes in protein-coding transcripts expression in response to heat. We found 5,214 contigs differentially expressed between temperatures. The heat treatment resulted in a down-regulation of genes related to photosynthesis and carbon metabolism, whereas secondary metabolism, protein re-folding and response to stress were up-regulated. Moreover, several transcription factor families like WRKY or ERF were promoted by heat, alongside spliceosome machinery and hormone signaling pathways. Through a comparative analysis of gene regulation in response to heat in Arabidopsis thaliana, Populus tomentosa and N. pumilio we provide evidence of the existence of shared molecular features of heat stress responses across angiosperms, and identify genes of potential biotechnological application.

Global warming is predicted to exert negative impacts on plant growth due to the damaging effect of high temperatures on plant physiology. Revealing the genetic architecture underlying the heat stress response is therefore crucial for the development of conservation strategies, and for breeding heat-resistant plant genotypes. Here we investigated the transcriptional changes induced by heat in Nothofagus pumilio , an emblematic tree species of the sub-Antarctic forests of South America. Through the performance of RNA-seq of leaves of plants exposed to 20°C (control) or 34°C (heat shock), we generated the first transcriptomic resource for the species. We also studied the changes in protein-coding transcripts expression in response to heat. We found 5,214 contigs differentially expressed between temperatures. The heat treatment resulted in a down-regulation of genes related to photosynthesis and carbon metabolism, whereas secondary metabolism, protein re-folding and response to stress were up-regulated. Moreover, several transcription factor families like WRKY or ERF were promoted by heat, alongside spliceosome machinery and hormone signaling pathways. Through a comparative analysis of gene regulation in response to heat in Arabidopsis thaliana, Populus tomentosa and N. pumilio we provide evidence of the existence of shared molecular features of heat stress responses across angiosperms, and identify genes of potential biotechnological application.