Predicting gene expression responses to environment inArabidopsis thalianausing natural variation in DNA sequence DOI Creative Commons

Margarita Takou,

Emily S. Bellis, Jesse R. Lasky

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Апрель 28, 2024

Abstract The evolution of gene expression responses are a critical component adaptation to variable environments. Predicting how DNA sequence influences is challenging because the genotype phenotype map not well resolved for cis regulatory elements, transcription factor binding, interactions, and epigenetic features, mention these factors respond environment. We tested if flexible machine learning models could learn some underlying cis- map. this approach using cold-responsive transcriptome profiles in 5 diverse Arabidopsis thaliana accessions. first evidence that regulation plays role environmental response, finding 14 15 motifs were significantly enriched within up- down-stream regions differentially regulated genes (DEGs). next applied convolutional neural networks (CNNs), which de novo sequences predict response found CNNs predicted differential with moderate accuracy, predictions hindered by biological complexity large potential code. Overall, DEGs between specific environments can be based on variation sequences, although more information needs incorporated better may required.

Язык: Английский

A large-effect fitness trade-off across environments is explained by a single mutation affecting cold acclimation DOI
Gwonjin Lee, Brian J. Sanderson, Thomas James Ellis

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(6)

Опубликована: Янв. 30, 2024

Identifying the genetic basis of local adaptation and fitness trade-offs across environments is a central goal evolutionary biology. Cold acclimation an adaptive plastic response for surviving seasonal freezing, costs may be general mechanism in temperate zone species. Starting with locally adapted ecotypes

Язык: Английский

Процитировано

10
Fully Atomistic Molecular Dynamics Simulation of Ice Nucleation Near an Antifreeze Protein DOI Creative Commons
Yue Zhang, Ning Wei, Liwen Li

и другие.

Journal of the American Chemical Society, Год журнала: 2025, Номер unknown

Опубликована: Янв. 23, 2025

Heterogeneous ice nucleation is a widespread phenomenon in nature. Despite extensive research on near biological antifreeze proteins, probe for and growth processes at the atomic level still lacking. Herein, we present simulation evidence of heterogeneous process ice-binding surface (IBS) Tenebrio molitor protein (TmAFP). Our all-atomistic molecular dynamics simulations reveal detailed steps toward precritical nucleus formation from one-dimensional (1D) channel water to 2D nanolayer and, finally, 3D nucleus. Compared with homogeneous under same supercooling conditions, IBS TmAFP can markedly reduce critical size embryo lower free energy barrier, thereby favoring nucleation. Additionally, through artificial mutation selected functional groups IBS, gain deeper insights into how specific affect We highlight that carbonyl backbone play crucial role by providing fixed locations water. This function essential ensuring alignment between lattice structure.

Язык: Английский

Процитировано

1
Museum genomics reveals temporal genetic stasis and global genetic diversity in Arabidopsis thaliana DOI Creative Commons
Lúa López, Patricia L. M. Lang,

Stephanie Marciniak

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Фев. 7, 2025

Abstract Global patterns of population genetic variation through time offer a window into evolutionary processes that maintain diversity. Over time, lineages may expand or contract their distribution, causing turnover in composition. At individual loci, migration, drift, environmental change (among other processes) affect allele frequencies. Museum specimens widely distributed species unique the genetics understudied populations and changes over time. Here, we sequenced genomes 130 herbarium 91 new field collections Arabidopsis thaliana combined these with published genomes. We sought broader view genomic diversity across species, to test if composition is changing documented extensive previously uncharacterized range Africa, are under threat from anthropogenic climate change. Through did not find dramatic populations. Instead, found pattern every 100 years same magnitude seen when comparing Eurasian 185 km apart, potentially due combination drift selection. only mixed signals polygenic adaptation at phenology physiology QTL. genes conserved eudicots show altered levels directional frequency change, variable purifying background Our study highlights how museum can reveal dimensions wild evolving recent history.

Язык: Английский

Процитировано

0
Native Australian seedlings exhibit novel strategies to acclimate to repeated heatwave events DOI Creative Commons
Philippa R. Alvarez, Rosalie J. Harris, Alicia M. Cook

и другие.

Oecologia, Год журнала: 2025, Номер 207(6)

Опубликована: Май 15, 2025

Язык: Английский

Процитировано

0
Low frequency of the wild-type freezing-tolerance LsCBF7 allele among lettuce population suggests a negative selection during domestication and breeding DOI Creative Commons
Sunchung Park, Ainong Shi, Beiquan Mou

и другие.

Theoretical and Applied Genetics, Год журнала: 2024, Номер 137(6)

Опубликована: Май 18, 2024

Sustainable winter production in lettuce requires freezing tolerant varieties. This study identified a wild-type allele of LsCBF7 that could contribute to tolerance improvement lettuce. Lettuce is one the most consumed vegetables globally. While ideally grown 13-21 °C, its cultivation extends into milder climates. However, occasional temperatures can significantly reduce yields. Therefore, development freezing-tolerant varieties has become long-term goal breeding programs. Despite significance, our understanding remains limited. Plants have evolved coping mechanism against freezing, known as cold acclimation, whereby they increase when pre-exposed low nonfreezing temperatures. The CBF pathway well-known for central role acclimation. Previously, we 14 genes and discovered them, LsCBF7, had loss-of-function mutation. In this study, uncovered accessions from colder regions carried likely contributed increased tolerance, with 14% population carrying allele. Interestingly, wild (L. serriola) considered progenitor cultivated lettuce, was much more common, frequency 90%. finding suggests may undergone negative selection during domestication or Our data strongly indicate be linked early bolting, an undesirable trait which driven selection. shows promise improving it crucial decouple bolting fully harness potential breeding.

Язык: Английский

Процитировано

3
In situ diversification and adaptive introgression in Taiwanese Scutellaria DOI Open Access
Pei‐Wei Sun, Jui‐Tse Chang, Min‐Xin Luo

и другие.

Plant Biology, Год журнала: 2025, Номер unknown

Опубликована: Янв. 22, 2025

Abstract Island habitats provide unique opportunities to study speciation. Recent work indicates that both ex situ origination and in speciation contribute island species diversity. However, clear evidence of local adaptation endemic plant on islands requires in‐depth studies, which are scarce. This underscores the importance maintaining boundaries by examining how adaptive introgression, hybridization, genetic variation species. Multilocus genome scanning 51 nuclear genes was used investigate evolutionary relationships Scutellaria complex Taiwan assess role diversification generating high endemism Interspecies introgressions were detected phylogenetic networks ABBA‐BABA‐based analysis, suggesting ongoing or recent processes. Coalescent‐based simulation identified hybrid taiwanensis hsiehii , with hybridization between more than two parental Genotype‐environment association studies revealed influence climate, particularly precipitation‐ temperature‐related factors, contributed divergence Additionally, introgression related environmental pressures may have facilitated colonization new identified. research illustrates shaped histories this island‐endemic sheds light multifaceted mechanisms semi‐isolated islands.

Язык: Английский

Процитировано

0
Multiple independent MGR5 alleles contribute to a clinal pattern in leaf magnesium across the distribution of Arabidopsis thaliana DOI Creative Commons
Emmanuel Tergemina,

Shifa Ansari,

David E. Salt

и другие.

New Phytologist, Год журнала: 2025, Номер unknown

Опубликована: Март 24, 2025

Magnesium (Mg) is a crucial element in plants, particularly for photosynthesis. Mg homeostasis influenced by environmental and genetic factors, our understanding of its variation natural populations remains incomplete. We examine the leaf accumulation across distribution Arabidopsis thaliana, we investigate factors associated with levels. Using genome-wide association studies both widespread Eurasian population local-scale Cape Verde, identify Mg. validate main results, including effect size estimates, using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) mutagenesis. Our findings reveal significant between latitude origin. In Eurasia, find signal at nutrient-response regulator, RAPTOR1A, species range, that multiple alleles transporter, MAGNESIUM RELEASE 5 (MGR5), underlie contribute to observed latitudinal cline. Overall, results indicate spatial A. thaliana affected climatic resulting Further, they show an example allelic heterogeneity, which single locus trait formation phenotypic

Язык: Английский

Процитировано

0
Adaptation to soil type contributes little to local adaptation in an Italian and a Swedish ecotype of Arabidopsis thaliana on contrasting soils DOI Creative Commons
Thomas James Ellis, Jon Ågren

Biology Letters, Год журнала: 2024, Номер 20(9)

Опубликована: Сен. 1, 2024

Natural populations are subject to selection caused by a range of biotic and abiotic factors in their native habitats. Identifying these agents quantifying effects is key understanding how adapt local conditions. We performed factorial reciprocal-transplant experiment using locally adapted ecotypes

Язык: Английский

Процитировано

2
Genetic basis and trade-offs of cold acclimation DOI
Nigel G. Yoccoz

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(10)

Опубликована: Фев. 21, 2024

Язык: Английский

Процитировано

1
Adaptation to soil type contributes little to local adaptation in an Italian and a Swedish population ofArabidopsis thalianagrowing on contrasting soils DOI Creative Commons
Thomas James Ellis, Jon Ågren

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Апрель 28, 2024

Natural populations are subject to selection caused by a range of biotic and abiotic factors in their native habitats. Identifying these agents quantifying effects is key understanding how adapt local conditions. We performed fully factorial reciprocal transplant experiment using locally adapted accessions Arabidopsis thaliana at sites distinguish the contributions adaptation soil type climate. Overall adaptive differentiation was strong both sites. However, we found only very small differences strength on non-local soil, most constituted few percent overall differentiation. These results indicate that climatic conditions rather than primary driver between ecotypes.

Язык: Английский

Процитировано

1