Biology subjects

Lowry, D.

Publications and source records attributed to Lowry, D..

13 recordsLinked to original sources

bioRxiv2026

Chromosome-level Atlantic switchgrass assemblies reveal a supernumerary B-Chromosome with transcriptional and evolutionary impacts

Supernumerary B-Chromosomes are extra genetic elements that frequently deviate from Mendelian inheritance to ensure their own survival. Their evolutionary origins and biological impacts within natural plant populations remain largely unexplored. Switchgrass (Panicum virgatum) is a model for studies of local adaptation, but reliance on a single reference genome has limited the detection of lineage-specific genomic content. We generated chromosome-level genome assemblies from the diverged Atlantic switchgrass subpopulation and discovered a previously undetected genomic element: a ~34 Mb supernumerary B-Chromosome, validated by Hi-C contact mapping and long-read depth, which indicates two to four B copies per nucleus. The B-Chromosome has a bipartite architecture including a gene-rich, single-copy proximal region (~8 Mb) and a repeat-rich, gene-poor distal region (~27 Mb) dominated by LTR/Ty3 (Gypsy) elements and punctuated by Mutator TIR peaks. High-resolution mapping reveals a highly rearranged chimera of fragments from multiple autosomes, biased toward the N-subgenome. Intact LTR retrotransposons on the B-Chromosome are younger than those on the A-Chromosomes, especially in its distal region, consistent with a B-Chromosome that arose and expanded within the Atlantic lineage. Population screening and phylogenetic analysis indicate that the B-Chromosome is largely restricted to the Atlantic subpopulation and likely has a single origin. In a typical family, 70% of open-pollinated progeny of B-positive maternal plants were B-positive, with substantial variation among families. Finally, B-Chromosome presence is associated with expression differences in A-Chromosome genes that differ between genetic backgrounds. Together, our results show how accessory chromosomes contribute to the evolutionary and genomic diversity of natural plant populations.

genomics↗

bioRxiv2026

Extreme cooling enables survival in extreme heat

Complex, multicellular extremophiles face intense challenges in coordinating their cells, tissues, and organs to function in harsh environments. Tidestromia oblongifolia is a desert plant that thrives in Death Valley, where air temperatures exceed 49 {degrees}C. Using natural collections of T. oblongifolia seed, we identified individuals that survive in daily air temperature regimens at the eukaryotic upper thermal limit of 60 {degrees}C. Genome-wide association testing detected genetic variation for survival in extreme heat, and transcriptomics implicated pathways regulating leaf cooling. High-throughput infrared imaging revealed that survival was enabled by leaf cooling far below air temperature, identifying a physiological mechanism of thermophily in a multicellular organism. These discoveries provide insights into mechanisms of extreme heat adaptation that could be leveraged to engineer heat-resilient crops.

plant biology↗

bioRxiv2026

Uncovering genetic mechanisms underlying trait variation in switchgrass using explainable artificial intelligence

Uncovering the genetic architecture of quantitative traits is challenging because polygenic control yields small individual gene effects and because gene-gene and genotype-by-environment interactions add further complexity. To understand the genetic basis of polygenic traits and their plasticity across environments, we integrated genome-wide SNPs and RNA-seq transcript data with interpretable statistical and machine learning models in a switchgrass (Panicum virgatum) diversity panel grown at contrasting field sites in Michigan and Texas. Notably, in addition to single environments, our trait prediction models were able to predict phenotypic differences, across environments i.e., plasticity. By interpreting trait prediction models with explainable machine learning methods, we identified genes that are the most predictive of flowering time and annual biomass production across environments, based on their associated gene expression levels and nearby SNPs. This approach recovered canonical flowering regulators and revealed novel, environment-specific candidate flowering genes. Further, transcriptome models consistently recovered more switchgrass genes homologous to experimentally validated genes in Arabidopsis and rice than SNP-based models. Feature interaction scores from the models also allow the identification of trait and environment-dependent gene-gene interactions, where flowering time showed stronger and more abundant interactions than biomass. While some of the interactions identified are consistent with the link between flowering time and yield, most are novel predictors that need to be further evaluated. These findings provide insight into the genetic basis of trait variation and plasticity across environments and help prioritize candidate genes for functional validation and cultivar improvement.

genetics↗

bioRxiv2025

Seasonal variation in wind speed and oceanic salt spray favors delayed reproduction in coastal yellow monkeyflowers

PremiseThe optimal timing of reproduction depends on the relative risk and benefit of continued growth. These risks and benefits depend on the local environment, which varies seasonally. While temperature and water availability are well studied selective agents on reproductive timing, less is known about other seasonally variable factors. MethodsTo test whether seasonal variation in wind and salt spray influences selection on reproductive timing, we performed an experimental manipulation of flowering time and ocean exposure in a coastal environment. Flowering plants from twelve yellow monkeyflower populations spanning a coastal-to-inland gradient were placed on a coastal bluff in spring and summer, which differ in average wind speed. A subset of plants were protected from wind and salt spray, and the remaining plants were exposed to these factors. ResultsIn the windier spring cohort, ocean-exposed individuals had severe necrosis and produced few flowers and seeds, while protected plants had little-to-no necrosis, producing more flowers and seeds than exposed plants. In the calmer summer cohort, ocean-exposed individuals had less severe necrosis and produced comparable numbers of flowers as protected plants. However, only coastal populations produced appreciable numbers of seeds when exposed to the ocean, consistent with prior evidence that coastal ecotypes are locally adapted. ConclusionsOverall, these results suggest that seasonal variation in wind and salt spray is a key selective factor contributing to population differences in flowering time.

ecology↗

bioRxiv2025

Foliar salt spray exclusion and tissue tolerance underlie local adaptation to oceanic salt spray

PremiseSurviving under oceanic salt spray is critical for plants in coastal ecosystems, yet the mechanisms of coastal plant resilience to salt spray are not well understood. We investigated mechanisms of salt spray adaptation by comparing five latitudinal pairs of yellow monkeyflower accessions locally adapted to coastal and inland habitats. MethodsWe measured sodium levels in coastal and inland leaves exposed to experimental salt spray in the lab, and compared leaf surface traits that may contribute to differences in sodium uptake between ecotypes. We assayed tissue tolerance by allowing sodium to enter leaves through wounding and recording time to necrosis for coastal and inland accessions. Key ResultsCoastal monkeyflowers take up less sodium through the leaf surface under experimental salt spray, which may contribute to local adaptation under oceanic salt spray in coastal habitats. Higher water content per unit leaf area and less water loss under salt spray further reduce sodium concentrations in salt-sprayed coastal leaves compared to inland counterparts. The coastal ecotype also shows greater tissue tolerance to sodium than the inland ecotype. ConclusionsCoastal monkeyflowers employ salt spray exclusion and tissue tolerance mechanisms for salt spray resilience. Our results suggest that plant adaptation to coastal habitats may often involve the evolution of multiple mechanisms to survive stress imposed by oceanic salt spray.

evolutionary biology↗

bioRxiv2024

Just add water: A simple floral bud injection method for stable Agrobacterium-mediated transformation in two ecotypes of Mimulus guttatus

Stable transformation is the biggest challenge for studying gene function in plants. In most plant species, stable transformation requires the development of arduous tissue culture and regeneration methods that often fail and can cause undesirable genetic changes. Floral transformation methods bypass these challenges by infiltrating Agrobacterium directly into the ovules of developing flowers. However, this method has had limited success outside of a handful of plant species and genotypes within those species. Here, we demonstrate that the floral infiltration method is effective for some, but not all genotypes of the yellow monkeyflower, Mimulus guttatus, a model system for studies of ecology and evolution. To conduct transformation in genotypes where infiltration failed, we developed a novel floral injection method. Beyond expanding the number of genotypes that can be transformed, the floral injection method has other advantages, such as allowing plants to be infiltrated multiple times and a reduction in floral abscission and male sterility. Through a combination of floral infiltration and injection methods, we were able to transform both coastal perennial and inland annual genotypes of M. guttatus, which sets the stage for understanding the molecular genetic underpinnings of local adaptation to the divergent habitats occupied by these distinctive ecotypes. Overall, the development of these efficient transformation methods will open up a wide range of new research avenues in the M. guttatus species complex.

plant biology↗

bioRxiv2024

Plant hormone manipulation impacts salt spray tolerance, which preempts herbivory as a driver of local adaptation in the yellow monkeyflower, Mimulus guttatus

A major challenge in evolutionary biology is identifying the selective agents and phenotypes underlying local adaptation. Local adaptation along environmental gradients may be driven by trade-offs in allocation to reproduction, growth, and herbivore resistance. To identify environmental agents of selection and their phenotypic targets, we performed a manipulative field reciprocal transplant experiment with coastal perennial and inland annual ecotypes of the common yellow monkeyflower (Mimulus guttatus). We manipulated herbivory with exclosures built in the field and exogenously manipulated gibberellin and jasmonic acid to shift allocation of plant resources among growth, reproduction, and herbivore resistance. Our hormone treatments influenced the timing of allocation to reproduction and allocation to phytochemical defense, but this shift was small relative to ecotype differences in allocation. Herbivore exclosures reduced herbivory and increased fitness of plants at the coastal site. However, this reduction in herbivory did not decrease the homesite advantage of coastal perennials. Unexpectedly, we found that the application of exogenous gibberellin increased mortality due to salt spray at the coastal site for both ecotypes. Our results suggest that divergence in salt spray tolerance, potentially mediated by ecotype differences in gibberellin synthesis or bioactivity, is a strong driver of local adaptation and preempts any impacts of herbivory in coastal habitats that experience salt spray.

evolutionary biology↗

bioRxiv2023

The role of breakpoint mutations, supergene effects, and ancient nested rearrangements in the evolution of adaptive chromosome inversions in the yellow monkey flower, Mimulus guttatus

Chromosomal inversion polymorphisms are ubiquitous across the diversity of diploid organisms and play a significant role in the evolution of adaptations in those species. Inversions are thought to operate as supergenes by trapping adaptive alleles at multiple linked loci through the suppression of recombination. While there is now considerable support for the supergene mechanism of inversion evolution, the extent to which inversions trap pre-existing adaptive genetic variation versus accumulate new adaptive variants over time remains unclear. In this study, we report new insights into the evolutionary dynamics of a locally adaptive chromosomal inversion polymorphism (inv_chr8A), which contributes to the evolutionary divergence between coastal perennial and inland annual ecotypes of the yellow monkeyflower, Mimulus guttatus. This research was enabled by the sequencing, assembly, and annotation of new annual and perennial genomes of M. guttatus using Oxford Nanopore long-read sequencing technology. In addition to the adaptive inv_chr8A inversion, we identified three other large inversion polymorphisms, including a previously unknown large inversion (inv_chr8B) nested within the inv_chr8A. Through population genomic analyses and comparative genomics, we determined that the nested inv_chr8B inversion is significantly older than the larger chromosomal inversion in which it resides. We also evaluated key candidate genes involved in gibberellin biosynthesis and anthocyanin regulation, which we hypothesize to underlie the adaptive phenotypic effects of the inv_chr8A inversion. Although little evidence was found to suggest that inversion breakpoint mutations drive adaptive phenotypic effects, our findings support the supergene mechanism of adaptive evolution as a dynamic and continuous process.

genomics↗

bioRxiv2021

Frequency-dependent hybridization contributes to habitat segregation in monkeyflowers

Spatial segregation of closely related species is usually attributed to differences in stress tolerance and competitive ability. For both animals and plants, reproductive interactions between close relatives can impose a fitness cost that is more detrimental to the rarer species. Frequencydependent mating interactions may thus prevent the establishment of immigrants within heterospecific populations, maintaining spatial segregation of species. Despite strong spatial segregation in natural populations, two sympatric California monkeyflowers (Mimulus nudatus and M. guttatus) survive and reproduce in the others habitat when transplanted reciprocally. We hypothesized that a frequency-dependent mating disadvantage maintains spatial segregation of these monkeyflowers during natural immigration. To evaluate this hypothesis, we performed two field experiments. First, we experimentally added immigrants in varying numbers to sites dominated by heterospecifics. Second, we reciprocally transplanted arrays of varying resident and immigrant frequencies. Immigrant seed viability decreased with conspecific rarity for M. guttatus, but not M. nudatus. We observed immigrant minority disadvantage for both species, but driven by different factors- frequency-dependent hybridization for M. guttatus, and competition for resources and/or pollinators for M. nudatus. Overall, our results suggest a major role for reproductive interference in spatial segregation that should be evaluated along with stress tolerance and competitive ability.

ecology↗

bioRxiv2021

Host genetic control of succession in the switchgrass leaf fungal microbiome

Leaf fungal microbiomes can be fundamental drivers of host plant success, as they contain pathogens that devastate crop plants and taxa that enhance nutrient uptake, discourage herbivory, and antagonize pathogens. We measured leaf fungal diversity with amplicon sequencing across an entire growing season in a diversity panel of switchgrass (Panicum virgatum). We also sampled a replicated subset of genotypes across three additional sites to compare the importance of time, space, ecology, and genetics. We found a strong successional pattern in the microbiome shaped both by host genetics and environmental factors. Further, we used genome-wide association mapping and RNA-sequencing to show that three cysteine-rich receptor-like kinases were linked to a genetic locus associated with microbiome structure. These genes were more highly expressed in genotypes susceptible to fungal pathogens, which were central to microbial covariance networks, suggesting that host immune genes are a principal means of controlling the entire leaf microbiome.

ecology↗

bioRxiv2021

FIBRIN POLYMER ON THE SURFACE OF BIOMATERIAL IMPLANTS DRIVES THE FOREIGN BODY REACTION

ABSTRACTImplantation of biomaterials and medical devices in the body triggers the foreign body reaction (FBR) which is characterized by macrophage fusion at the implant surface leading to the formation of foreign body giant cells and the development of the fibrous capsule enveloping the implant. While adhesion of macrophages to the surface is an essential step in macrophage fusion and implanted biomaterials are known to rapidly acquire a layer of host proteins, a biological substrate that is responsible for this process in vivo is unknown. Here we show that mice with genetically-imposed fibrinogen deficiency display a dramatic reduction of macrophage fusion on implanted biomaterials and are protected from the formation of fibrin-containing granulation tissue, a precursor of the fibrous capsule. Furthermore, macrophage fusion on biomaterials implanted in FibAEK mice that express a mutated form of fibrinogen incapable of thrombin-mediated polymerization was strongly reduced. Surprisingly, despite the lack of fibrin, the capsule was formed in FibAEK mice, although it had a different composition and distinct mechanical properties than that in wild-type mice. Specifically, while mononuclear -SMA-expressing macrophages embedded in the capsule of both strains of mice secreted collagen, the amount of collagen and its density in the tissue of FibAEK mice was reduced. These data identify fibrin polymer as a key biological substrate driving the development of the FBR.

immunology↗

bioRxiv2020

TRANSITION OF PODOSOMES INTO ZIPPER-LIKE STRUCTURES INMACROPHAGE-DERIVED MULTINUCLEATED GIANT CELLS

Macrophage fusion resulting in the formation of multinucleated giant cells (MGCs) is a multistage process that requires many adhesion-dependent steps and involves the rearrangement of the actin cytoskeleton. The diversity of actin-based structures and their role in macrophage fusion is poorly understood. In this study, we revealed hitherto unrecognized actin-based zipper-like structures (ZLSs) that arise between MGCs formed on the surface of implanted biomaterials. We established an in vitro model for the induction of these structures in mouse macrophages undergoing IL-4- mediated fusion. Using this model, we show that over time MGCs develop cell-cell contacts containing ZLSs. Live-cell imaging using macrophages isolated from mRFP- or GFP-Lifeact mice demonstrated that ZLSs are dynamic formations undergoing continuous assembly and disassembly and that podosomes are precursors of these structures. Immunostaining experiments showed that vinculin, talin, integrin M{beta}2, and other components of podosomes are present in ZLSs. Macrophages deficient in WASp or Cdc42, two key molecules involved in actin core organization in podosomes, as well as cells treated with the inhibitors of the Arp2/3 complex failed to form ZLSs. Furthermore, E-cadherin and nectin-2 were found between adjoining membranes, suggesting that the transition of podosomes into ZLSs is induced by bridging plasma membranes by junctional proteins.

cell biology↗

bioRxiv2018

Mechanisms of a locally adaptive shift in allocation among growth, reproduction, and herbivore resistance in Mimulus guttatus

Environmental gradients can drive adaptive evolutionary shifts in plant resource allocation among growth, reproduction, and herbivore resistance. However, few studies have attempted to connect these adaptations to underlying physiological and genetic mechanisms. Here, we evaluate potential mechanisms responsible for a coordinated locally adaptive shift between growth, reproduction, and herbivore defense in the yellow monkeyflower, Mimulus guttatus. Through manipulative laboratory experiments we found that gibberellin (GA) growth hormones may play a role in the developmental divergence between perennial and annual ecotypes of M. guttatus. Further, we detected an interaction between a locally adaptive chromosomal inversion, DIV1, and GA addition. This finding is consistent with the inversion contributing to the evolutionary divergence between inland annual and coastal perennial ecotypes by reducing GA biosynthesis/activity in perennials. Finally, we found evidence that the DIV1 inversion is partially responsible for a coordinated shift in the divergence of growth, reproduction, and herbivore resistance traits between coastal perennial and inland annual M. guttatus. The inversion has already been established to have a substantial impact on the life-history shift between long-term growth and rapid reproduction. Here, we demonstrate that the DIV1 inversion also has sizable impacts on both the total abundance and composition of phytochemical compounds involved in herbivore resistance.

evolutionary biology↗