Biology subjects

Sork, V.

Publications and source records attributed to Sork, V..

3 recordsLinked to original sources

bioRxiv2026

CHH methylation is recruited to gene-proximal transposable elements during repeated drought stress

Long-lived trees must continually adjust to environmental change and face sustained climatic shifts over their lifetimes. One increasingly important challenge is the rising frequency of drought caused by climate change. Environmentally responsive DNA methylation is widespread in plants, but whether it contributes to gene expression during environmental stress remains unclear, particularly in long-lived trees. Here, we integrated long read methylomes and transcriptomes from valley oak (Quercus lobata) seedlings exposed to repeated drought and well-watered treatments. Repeated drought induced a reproducible DNA methylation response that repeatedly targeted the same genomic regions despite turnover of individual methylated sites. These repeatedly targeted regions were transposable elements (TEs) located near genes. Genes adjacent to CHH-methylated TEs were enriched for core drought-response pathways, including abscisic acid signaling, osmotic adjustment and cell-wall remodeling, and remained transcriptionally activated under drought. However, higher CHH methylation levels were associated with progressively smaller transcriptional responses, suggesting that environmentally responsive DNA methylation influences how strongly drought-response genes are activated rather than simply switching them on or off. At the same time, greater CHH methylation was associated with continued repression of nearby TEs, suggesting that this response may simultaneously regulate gene activity while maintaining genome stability. Together, these findings identify a reproducible genome-regulatory response associated with repeated environmental stress in a long-lived tree. By repeatedly targeting the same genomic regions despite turnover of individual sites, this response provides a framework for how long-lived trees repeatedly adjust gene expression while maintaining genome stability during environmental change.

evolutionary biology↗

bioRxiv2025

Drought tolerance is associated with constitutive gene expression, not plasticity, across California oak species

O_LIDrought is a major stressor for plants globally. Variation in gene expression patterns across species can provide critical evidence for the genomic basis of drought tolerance. C_LIO_LIWe paired comparative transcriptomics with functional trait measurements to identify genomic mechanisms associated with drought tolerance across six species from three oak clades in California, including a pair of species within each clade representing relatively mesic or xeric environments. We tested how plastic and constitutive gene expression patterns varied among species with contrasting drought tolerance traits. We also tested whether gene expression responses were decoupled from phylogenetic history, suggesting they have evolved multiple times as adaptations to species climate niches. C_LIO_LISpecies with drought-tolerant traits exhibited lower levels of gene expression plasticity during leaf dehydration than drought-sensitive species, but showed signatures of positive selection on constitutive gene expression. Drought-sensitive species across clades converged in their patterns of plastic gene expression during dehydration, diverging from their more closely related drought tolerant species, suggesting that repeated evolution has shaped plastic gene expression responses to drought. C_LIO_LIDrought-tolerant oak species have evolved constitutive gene expression alongside drought tolerant functional traits, while drought-sensitive oak species have evolved similar plastic gene expression responses to drought. C_LI

evolutionary biology↗

bioRxiv2024

Comparison of conservation strategies for California Channel Island Oak (Quercus tomentella) using climate suitability predicted from genomic data

Management strategies, such as assisted gene flow, could increase resilience to climate change in tree populations. Knowledge of evolutionary history and genetic structure of species is needed to assess the risks and benefits of different strategies. Quercus tomentella, or Island Oak, is a rare oak restricted to six Channel Islands in California, USA, and Baja California, Mexico. Previous work has shown that Island Oaks on each island are genetically differentiated, but it is unclear whether assisted gene flow could enable populations to tolerate future climates. We performed whole-genome sequencing on Island Oak individuals and Q. chrysolepis, a closely related species that hybridizes with Island Oak (127 total), to characterize genetic structure and introgression across its range and assess the relationship between genomic variation and climate. We introduce and assess three potential management strategies with different trade-offs between conserving historic genetic structure and enabling populations to survive changing climates: the status quo approach; ecosystem preservation approach, which conserves the trees and their associated biodiversity; and species preservation approach, which conserves the species. We compare the impact of these approaches on predicted maladaptation to climate using Gradient Forest. We also introduce a climate suitability index to identify optimal pairs of seed sources and planting sites for approaches involving assisted gene flow. We found one island (Santa Rosa) that could benefit from the ecosystem preservation approach and also serve as a species preservation site. Overall, we find that both the ecosystem and species preservation approaches will do better than the status quo approach. If preserving Island Oak ecosystems is the goal, assisted migration into multiple sites could produce adapted populations. If the goal is to preserve a species, the Santa Rosa population would be suitable. This case study both illustrates viable conservation strategies for Island Oak and introduces a framework for tree conservation.

evolutionary biology↗