Biology subjects

Monroe, J. G.

Publications and source records attributed to Monroe, J. G..

16 recordsLinked to original sources

bioRxiv2026

Gene functional-state covariance reveals modular structure in the Arabidopsis thaliana dispensable genome

Classical multilocus theory predicts that selection acting on combinations of loci can maintain non-random associations among allelic states, causing selection to act on multilocus genotypes rather than individual alleles. Across eukaryotic species, pangenome studies have documented thousands of genes that vary in functional status between individuals, yet this variation is analyzed as if each gene evolves independently. Here we test for non-random association within the dispensable pangenome across 1,012 natural genotypes of Arabidopsis thaliana to better understand the structure and evolution of eukaryotic pangenomes. Genome-wide pairwise association testing of loss-of-function alleles across genotypes identified 150,033 significantly covarying gene pairs among 5,679 unique genes after controlling for kinship and population structure. Most associations were between genes on different chromosomes, and covarying gene pairs showed greater co-expression and functional similarity than expected by chance. Network analysis revealed a non-random higher-order architecture comprising stable functional communities with distinct biological functions and structured connectivity among communities. The enriched functions and connectivity of communities revealed a tight coupling of modules involving plant immunity, environmental response, and specialized metabolism, highlighting how these systems integrate and evolve in response to dynamic ecological pressures. Taken together, these results show that the dispensable genome has a complex higher-order structure driven by functionally interacting genes, and that variation in gene content provides a population-scale resource for investigating the organization and evolution of biological systems.

genomics↗

bioRxiv2025

Phylogenomic and comparative genome analysis of the Juglandaceae family reveals black walnut (Juglans nigra) as an ancient lineage of the Rhysocaryon section.

Accelerated climate change causes heatwaves, droughts, and severe freezes, posing threats to tree regeneration and to global biodiversity. Deeper genomic insights are crucial for breeding, conserving genetic resources, guiding management, and building resilience to these threats. Juglans, a globally distributed genus of timber and nut-producing trees, still has unresolved species relationships; comprehensive genomic data would clarify adaptation to rapid climate change and inform assisted migration strategies. We analyzed 20 Juglans species from North and South America and Asia using whole-genome data, chloroplast genome data, cold-hardiness gene families, and environmental variables related to freezing tolerance. Phylogenomic analyses indicate that black walnuts (J. nigra, section Rhysocaryon) may have diverged ~28.7 MYA (late Oligocene). J. nigra reveals higher nucleotide diversity with more genes than other Juglans, whereas J. hindsii clusters with Central/South American species, consistent with a more recent divergence within Rhysocaryon. As expected, Juglans species originating from mild-winter regions are distinct from those in cold-climate regions in genome-wide and cold-hardiness gene analyses, with introgression occurring mainly from temperate into tropical lineages. Juglans species from milder or warmer winters show CBF gene deletions, whereas cold-adapted species lack such gene deletions. These results support J. nigra as an ancient lineage within Rhysocaryon, consistent with subsequent colonization of Central/South America and longer evolutionary histories. Genome analyses further suggest Rhysocaryon is ancestral to Cardicaryon, Trachycaryon, and Dioscaryon. These findings illuminate the demographic history of the Juglans, particularly Rhysocaryon, and have direct implications for gene conservation, breeding, and assisted migration.

genomics↗

bioRxiv2025

Intron architecture predicts chromatin features in Arabidopsis thaliana

Introns are ubiquitous yet enigmatic features of eukaryotic genomes. They are reported to affect gene expression regulation but the mechanisms remain largely unresolved. Here we investigate the connections between intron architecture and chromatin features - histone marks, histone variants, DNA methylation, and gene expression patterns in Arabidopsis thaliana. We found that first intron positions predict active chromatin marks found near transcription start sites while the number of introns explains different chromatin marks enriched in the core of gene bodies in broadly expressed genes. Notably, gene body chromatin marks exhibit a positional gradient distribution across the ordinal position of exons and introns. We tested these relationships by comparing recent gene duplicates with diverged intron architectures, and confirmed that intron number is positively associated with H3K4me1, H3K36me3, H2A.X, meCG, and broad expression across tissues. Our results suggest two distinct mechanisms in which plant intron architecture may affect chromatin states and ultimately gene expression, motivating future experiments: intron positions early in genes may affect the establishment of activating histone marks around transcription start sites, while a greater total number of introns may increase the number of intronic motifs and gene length in general, allowing for the increased accumulation of gene-body-associated chromatin features. Short summaryHere we investigate the association between intron architecture and chromatin features in Arabidopsis thaliana. We found that the position of the first intron is negatively correlated with marks found near the transcription start site and associated with active expression. We also found that the number of introns within genes is correlated with marks found in gene bodies and are associated with actively transcribed genes.

genomics↗

bioRxiv2025

Extreme somatic mutation variation through time and space in walnut clones

Many plants, unlike most animals, can reproduce as clones1. Cloning plants is critical for agriculture2,3 and biotechnology4, but the extent of somatic mutation arising during different propagation methods remains an important question for both fundamental research and agriculture. Here, we discover a surprisingly complex mutational history in a multi-decade natural experiment of isogenic walnut clones derived and maintained through three alternative methods: budwood propagation of field-grown trees, in vitro shoot culturing, and in vitro somatic embryogenesis. We generated a haplotype-phased reference genome assembly and revealed a >3500% increase in somatic embryo mutation rates compared to field-grown trees, along with a distinct mutation spectrum. The assembly also helped reveal extreme genomic instability in the somatic embryos, including multiple chromosomal duplications, megabase-scale deletions, telomere expansions, somatic recombination events, and ongoing transposable element activation. Our survey of somatic mutation also provides high-resolution insight into clonal stem cell dynamics, confirming the canonical meristem layers of flowering plants in the tree and shoot clones, while uncovering clear evidence of frequent single-cell bottlenecks in the somatic embryos. These discoveries inform practical questions about mutagenesis through plant tissue culture and serve as a benchmark to complement emerging paradigms of somatic mutation research in humans and other organisms.

genomics↗

bioRxiv2025

Unlocking Genetic Diversity in Colombian Cassava Landraces for Accelerated Breeding

Cassava (Manihot esculenta Crantz) is a staple food for hundreds of millions across the global south. In this study, we investigated genomic diversity among over 1000 cassava genotypes, with a particular focus on the addition of 387 newly sequenced landrace varieties originating from diverse climates across Colombia. As cassava was domesticated in or near the Amazon basin, these landraces represent untapped genetic diversity that could be used to help improve modern varieties. As theory predicts, we found that landraces retain high genetic diversity, observing variation lacking in breeding lines from Asia and Africa, where introductions likely caused population bottlenecks. Genetic differentiation in landraces reflects both space and climate of origin, suggesting the combined effects of demography and selection. To identify alleles with the potential to inform targets for gene editing, we assessed the diversity of loss-of-function (LoF) mutations across these landraces. We found evidence that deleterious LoF alleles were purged by inbreeding. Notably, genes retaining LoF alleles despite inbreeding were significantly enriched for functions related to the biosynthesis of coumarins and the regulation of plant immunity, suggesting selection on postharvest quality and disease resistance. We further identified specific loci associated with climates of origin, motivating future experiments using targeted knockouts to test hypotheses about the adaptive value of specific LoF alleles. This work supports longstanding hypotheses about landraces as a reservoir of genetic diversity and establishes the foundation to leverage this variation in cassava to discover alleles for accelerated breeding via gene editing. Short summaryThis study explores the genetic diversity of cassava by sequencing 387 landrace varieties and wild relatives from diverse climates in Colombia, aiming to identify potential gene targets for gene editing to enhance climate resilience. The research focuses on loss-of-function mutations, which are expected to have large effects and provide testable targets. Genome-wide association analysis reveals multiple potential targets associated with climate adaptation in cassava.

plant biology↗

bioRxiv2025

Evolutionary trajectories of cohesin gatekeepers across the Tree of Life

Eukaryotic genomes are physically organized into chromatin, which regulates virtually every dimension of genome biology, including replication, recombination, transcription, and DNA repair. Precocious Dissociation of Sisters 5 (PDS5) protein is a key regulator of the cohesin complex, responsible for generating higher-order chromatin structures within and between chromosomes. In yeast and vertebrates, PDS5 can lead to cohesin establishment or disassembly, depending on its interaction with other proteins. In this study, we explored the diversity of PDS5 proteins across eukaryotes; HEAT-repeats forming a hook-like structure (PDS5 domain), followed by a predicted disordered region of variable lengths, are observed across the Tree of Life. Interestingly, two homolog types (A and B) with signs of varying chromatin localization emerged independently in later branches of animal and plant kingdoms, in vertebrates and vascular plants, respectively ([~]400-500 MYA). We also investigated the emergence of two plant-specific features in the PDS5 proteins: 1.) An ancestral acquisition of a Tudor domain with conserved H3K4me1-binding amino acids in land plants 2.) A truncated version of PDS5 proteins that lacks essential features of PDS5 domain and is involved in the RNA-directed DNA methylation (RdDM) plant-specific pathway which emerged in seed plants. This work provides the most comprehensive study of PDS5 diversity, and suggests the emergence of specialized cohesin regulatory mechanisms that could shape distinct strategies for genome organization across eukaryotes. Short summaryHere, we analyzed the diversification of PDS5 proteins; sequence, domain content, and structure, providing new observations that evidence different evolutionary trajectories of this protein across the Tree of Life. These results suggest neofunctional evolution in cohesin regulatory proteins that could shape distinct strategies for genome organization across eukaryotes.

evolutionary biology↗

bioRxiv2025

Functional Insights into Dispensable Genes using Genome-Wide Loss-of-Function Burden Tests in Arabidopsis

Not all genes are essential for plant survival. With the rise of pan-genomics, it is evident that certain genes can be lost without negatively affecting fitness. Naturally occurring loss-of-function (LoF) mutations provide a valuable perspective on gene dispensability, offering insights into deleterious and adaptive gene loss. In this study, we identified 91,751 naturally occurring LoF variants from publicly available Arabidopsis genome data. Our findings demonstrate that LoF-intolerant genes are enriched in essential biological functions and associated with specific histone marks linked to active transcription. In contrast, LoF-tolerant genes exhibit relaxed selective pressure and are enriched in functions related to pollen rejection and defense responses, and can be used as a proxy for dispensable genes in the pan-genome. Using a random forest model trained on histone marks, we achieved moderate success in predicting gene LoF tolerance, with an AUC of 0.717 in Arabidopsis and 0.768 in rice, and even across species. We also pioneered genome-wide LoF burden tests in Arabidopsis, collapsing independent LoF alleles into a single state to reduce allelic heterogeneity. By integrating LoF burden tests with transcriptomic data, we identified thousands of LoF-expression associations. Notably, this analysis accurately recapitulated the flowering time networks and identified FRIGIDA as a key regulator of flowering time genes. Furthermore, we found that collapsing alleles based on functional outcomes enhances association sensitivity. These results provide insight into gene dispensability and a framework for leveraging LoF mutations to study gene functions with improved association studies.

plant biology↗

bioRxiv2024

Climate adaptation in P. trichocarpa: key adaptive loci identified for stomata and leaf traits

Identifying the genetic basis of traits underlying climate adaptation remains a key goal for predicting species responses to climate change, enabling the elucidation of gene targets for future climate-resilient crops. Here, we measured 14 leaf and stomatal traits under control (well-watered) and drought conditions, subsampling a diversity collection of over 1,300 Populus trichocarpa genotypes, a potential biofuel feedstock crop. Stomatal traits were correlated with the climate of origin for genotypes, such that those originating from environments subject to water deficit tended to have smaller stomata, but with higher density. Stomatal traits were also correlated with leaf morphology, with larger leaves having larger stomata and lower stomatal density mirrored in correlations to climate of origin. The direction of plastic responses - reduced stomatal size under drought - mirrors the correlations seen among genotypes with respect to the aridity of environmental origin. Genome-Wide Association Studies (GWAS) identified loci underlying trait diversity, including candidates contributing to stomatal size. We used climate of origin to predict stomatal size in genotypes with unknown trait values and found that these predicted phenotypes confirmed empirically measured allele effects. Finally, we found evidence that future climates may select for alleles contributing to decreased stomatal size, with the strength of selection depending on the availability of moisture. These findings reveal adaptive variation in stomatal and physiological traits along with underlying genetic loci, with implications for future selection and breeding - providing insights into the responses to future climate change. HighlightResearch on Populus trichocarpa reveals adaptation of physiological and stomatal traits linked to drought tolerance, with genotypes from arid regions exhibiting smaller stomata, offering insights for climate change adaptation and sustainable biofuel production.

plant biology↗

bioRxiv2024

In a nutshell: pistachio genome and kernel development

Pistachio is a sustainable nut crop with exceptional climate resilience and nutritional value. To advance pistachios as a future food source and a model system for hard-shelled fruits, we generated a chromosome-scale reference genome of the most widely grown pistachio cultivar (Pistacia vera Kerman) and a spatiotemporal developmental study of the hull, shell, and kernel. Our study defined four distinct stages of pistachio growth and maturation by integrating tissue-level physiological and molecular data from thousands of nuts across twenty-four time points over three growing seasons. Transcriptional and metabolic changes in the kernel elucidate molecular pathways governing nutritional quality, such as the accumulation of unsaturated fatty acids, which are vital for shelf-life and dietary value. This work yields new knowledge and resources that will inform other woody crops and facilitate further improvement of pistachio as a globally significant, sustainable, and nutritious crop.

plant biology↗

bioRxiv2023

High intraspecies allelic diversity in Arabidopsis NLR immune receptors is associated with higher transcription, gene body hypomethylation, and proximity to transposable elements

Plants rely on Nucleotide-binding, Leucine-rich repeat Receptors (NLRs) for pathogen recognition. Highly variable NLRs (hvNLRs) show remarkable intraspecies diversity, while their low variability paralogs (non-hvNLRs) are conserved between ecotypes. At a population level, hvNLRs provide new pathogen recognition specificities, but the association between allelic diversity and genomic and epigenomic features has not been established. Our investigation of NLRs in Arabidopsis Col-0 has revealed that hvNLRs show higher expression, less gene body cytosine methylation, and closer proximity to transposable elements than non-hvNLRs. hvNLRs show elevated synonymous and nonsynonymous nucleotide diversity and are in chromatin states associated with an increased probability of mutation. Diversifying selection maintains variability at a subset of codons of hvNLRs, while purifying selection maintains conservation at non-hvNLRs. How these features are established and maintained, and whether they contribute to the observed diversity of hvNLRs is key to understanding the evolution of plant innate immune receptors.

plant biology↗

bioRxiv2022

Report of mutation biases mirroring selection in Arabidopsis thaliana unlikely to be entirely due to variant calling errors

It has recently been proposed that the uneven distribution of epigenomic features might facilitate reduced mutation rate in constrained regions of the Arabidopsis thaliana genome, even though previous work had shown that it would be difficult for reduced mutation rates to evolve on a gene-by-gene basis. A solution to Lynchs equations for the barrier imposed by genetic drift on the evolution of targeted hypomutation can, however, come from epigenomic features that are enriched in certain portions of the genome, for example, coding regions of essential genes, and which simultaneously affect mutation rate. Such theoretical considerations draw on what is known about DNA repair guided by epigenomic features. A recent publication challenged these conclusions, because several mutation data sets that support a lower mutation rate in constrained regions suffered from variant calling errors. Here we show that neither homopolymer errors nor elevated mutation rates at transposable elements are likely to entirely explain reported mutation rate biases. Observed mutation biases are also supported by a meta-analysis of several independent germline mutation data sets, with complementary experimental data providing a mechanistic basis for reduced mutation rate in genes and specifically in essential genes. Finally, models derived from the drift-barrier hypothesis demonstrate that mechanisms linking DNA repair to chromatin marks and other epigenomic features can evolve in response to second-order selection on emergent mutation biases.

evolutionary biology↗

bioRxiv2022

N1-Methylpseudouridine and pseudouridine modifications modulate mRNA decoding during translation

The ribosome relies on hydrogen bonding interactions between mRNA codons and incoming aminoacyl-tRNAs to ensure rapid and accurate protein production. The inclusion of chemically modified bases into mRNAs has the potential to alter the strength and pattern of hydrogen bonding between mRNAs and aminoacyl-tRNAs to alter protein synthesis. We investigated how the Nl-methylpseudouridine (m1{Psi}) modification, commonly incorporated into therapeutic and vaccine mRNA sequences, influences the ability of codons to react with cognate and near-cognate tRNAs and release factors. We find that the presence of a single m1{Psi} does not substantially change the rate constants for amino acid addition by cognate tRNAs or termination by release factors. However, insertion of m1{Psi} can affect the selection of near-cognate tRNAs both in vitro and in human cells. Our observations demonstrate that m1{Psi}, and the related naturally occurring pseudouridine ({Psi}) modification, exhibit the ability to both increase and decrease the extent of amino acid misincorporation in a codon-position and tRNA dependent manner. To ascertain the chemical logic for our biochemical and cellular observations, we computationally modeled tRNAIle(GAU) bound to unmodified and m1{Psi}- or {Psi}-modified phenylalanine codons (UUU). Our modeling suggests that changes in the energetics of mRNA:tRNA interactions largely correlate with the context specificity of Ile-miscoding events we observe on {Psi} and m1{Psi} containing Phe codons. These studies reveal that the sequence context of a given modification within an mRNA plays a large role in determining how (and if) the modification impacts the number and distribution of proteoforms synthesized by the ribosome.

biochemistry↗

bioRxiv2020

Mutation bias shapes gene evolution in Arabidopsis thaliana

Classical evolutionary theory maintains that mutation rate variation between genes should be random with respect to fitness 1-4 and evolutionary optimization of genic mutation rates remains controversial 3,5. However, it has now become known that cytogenetic (DNA sequence + epigenomic) features influence local mutation probabilities 6, which is predicted by more recent theory to be a prerequisite for beneficial mutation rates between different classes of genes to readily evolve 7. To test this possibility, we used de novo mutations in Arabidopsis thaliana to create a high resolution predictive model of mutation rates as a function of cytogenetic features across the genome. As expected, mutation rates are significantly predicted by features such as GC content, histone modifications, and chromatin accessibility. Deeper analyses of predicted mutation rates reveal effects of introns and untranslated exon regions in distancing coding sequences from mutational hotspots at the start and end of transcribed regions in A. thaliana. Finally, predicted coding region mutation rates are significantly lower in genes where mutations are more likely to be deleterious, supported by numerous estimates of evolutionary and functional constraint. These findings contradict neutral expectations that mutation probabilities are independent of fitness consequences. Instead they are consistent with the evolution of lower mutation rates in functionally constrained loci due to cytogenetic features, with important implications for evolutionary biology8.

evolutionary biology↗

bioRxiv2020

Trait plasticity and covariance along a continuous soil moisture gradient

Water availability is perhaps the greatest environmental determinant of plant yield and fitness. However, our understanding of plant-water relations is limited because it is primarily informed by experiments considering soil moisture variability at two discrete levels - wet and dry - rather than as a continuously varying environmental gradient. Here we used experimental and statistical methods based on function-valued traits to explore responses to a continuous soil moisture gradient in physiological and morphological traits in two species and five genotypes each of the model grass Brachypodium. We find that most traits exhibit non-linear responses to soil moisture variability. We also observe differences in the shape of these non-linear responses between traits, species, and genotypes. Emergent phenomena arise from this variation including changes in trait correlations and evolutionary constraints as a function of soil moisture. These results point to the importance of considering non-linearity in plant-water relations to understand plastic and evolutionary responses to changing climates.

plant biology↗

bioRxiv2018

Drought frequency predicts life history strategies in Heliophila

Explaining variation in life history strategies is a long-standing goal of evolutionary biology. For plants, annual and perennial life histories are thought to reflect adaptation to environments that differ in the frequency of stress events such as drought. Here we test this hypothesis in Heliophila (Brassicaceae), a diverse genus of flowering plants native to Africa, by integrating 34 years of satellite-based drought measurements with 2192 herbaria occurrence records. Consistent with predictions from classic life history theory, we find that perennial Heliophila species occur in environments where droughts are significantly less frequent compared to annuals. These associations are predictive while controlling for phylogeny, lending support to the hypothesis that drought related natural selection has influenced the distributions of these strategies. Additionally, the collection dates of annual and perennial species indicate that annuals escape drought prone seasons during the seed phase of their life cycle. Together, these findings provide empirical support for classic hypotheses about the drivers of life history strategy in plants - that perennials out compete annuals in environments with less frequent drought and that annuals are adapted to environments with more frequent drought by escaping drought prone seasons as seeds.

evolutionary biology↗

bioRxiv2018

Drought adaptation in nature by extensive genetic loss-of-function

Visions of a second green revolution empowered by emerging technologies have called for interdisciplinary syntheses to scale up the discovery of functionally definitive gene variants responsible for climate adaptation in plants. We integrated novel approaches using whole genome sequences and satellite remote sensing to identify natural knockout alleles associated with drought histories in wild Arabidopsis thaliana. Genes identified exhibit signatures of parallel molecular evolution, selection for loss-of-function alleles, and shared associations with flowering time phenotypes in directions consistent with longstanding adaptive hypotheses 7 times more often than expected by chance. Artificial knockout lines then confirmed predicted phenotypes experimentally. These findings further challenge popular assumptions about the adaptive value of genetic loss-of-function in nature and inspire new opportunities for engineering climate resilience in crops.\n\nOne sentence summaryWhole genome sequences and satellite-detected droughts point to gene knockouts as valuable genetic fuel for climate adaptation.

evolutionary biology↗