Biology subjects

Bomblies, K.

Publications and source records attributed to Bomblies, K..

7 recordsLinked to original sources

bioRxiv2026

Chromosomal breakage in Arabidopsis thaliana neo-polyploids occurs preferentially at candidate fragile sites colocalized with ancient genome rearrangements

Newly formed polyploids often suffer extensive aneuploidy and chromosome rearrangement. We explored whether these are predictable and conserved across genotypes. We quantified whole-chromosome and segmental aneuploidy in progeny arrays of neo-polyploid Arabidopsis thaliana from two accessions (Col-0 and Ler). 29% of progeny had whole-chromosome and/or segmental aneuploidies. Strikingly, segmental aneuploidy arose exclusively from Ler, preferentially maternally, showing that genotype and sex of origin matter. Breakpoints of segmental aneuploidies were non-random, with over 2/3 mapping to five potentially fragile regions (PFRs). Two PFRs overlap with junctions of ancient chromosomal fusions that differentiate the A. thaliana genome from that of its relatives and also overlap more broadly with hotspots of recurrent chromosomal rearrangements differentiating species in the Brassicaceae family. Several PFRs overlap with large tandemly repeated disease resistance gene clusters. Our results support the hypothesis of a link between ancestral genome rearrangements and present-day chromosome fragility. Polyploidy serving as a context that makes aneuploidies more likely to arise and survive, with fragile sites lending a degree of predictability.

genomics↗

bioRxiv2025

Adaptation of protein stability to thermally heterogeneous environments

Proper protein folding is essential for biological function, and its disruption can lead to disease, reduced fitness, or death. The ability of a protein to maintain its folded conformation is thus critical for life, making it a key target of adaptive evolution. However, protein stability is sensitive to environmental factors, particularly temperature, which can threaten phenotypic integrity and organismal survival under thermal changes. Despite its importance, the influence of complex thermal environments - characterized here by mean temperature, thermal fluctuations, and environmental heterogeneity - on the evolution of protein stability remains poorly understood. To address this, we developed a mathematical framework that combines two well-established models: a population genetic model describing species distributed across habitats with distinct thermal environments, and a thermodynamic model of protein stability incorporating temperature-dependent enthalpy and entropy contributions. We focus on two-state proteins that alternate between folded and unfolded states and assume that allelic fitness is maximized in proteins that achieve an optimal balance between flexibility and rigidity. Using this framework, we performed an invasion analysis of mutations (sensu adaptive dynamics framework) affecting three thermodynamic parameters that fully determine protein stability profiles. Where possible, we derived analytical expressions for evolutionarily optimal thermodynamic parameters and complemented these with numerical solutions. Our results show that mean temperature and thermal fluctuations have orthogonal effects on thermodynamic parameters, underscoring the need to consider both when studying protein stability adaptation. We further examined thermally heterogeneous environments, where subpopulations connected by migration experience different mean temperatures, identifying conditions that favor either local (specialist) or global (generalist) adaptation. Our results may explain why one thermodynamic parameter shows little association with thermal adaptation and suggest that local adaptation is more likely for proteins with stability profiles limited to narrow temperature ranges. Additionally, our analysis reveals whether a locally adapted protein originated in a colder or warmer habitat. Finally, we identified trade-offs in thermodynamic parameters that influence local or global adaptation. This study offers key predictions about protein evolution in complex thermal environments and lays the groundwork for developing practical tools to understand how temperature shapes adaptation and biodiversity.

evolutionary biology↗

bioRxiv2025

Improved synapsis dynamics accompany meiotic stability in Arabidopsis arenosa autotetraploids

During meiosis, the correct pairing, synapsis, and recombination of homologous chromosome pairs is critical for fertility of sexual eukaryotes. These processes are challenged in polyploids, which possess additional copies of each chromosome. Polyploidy thus provides a unique context to study how evolution can modify meiotic programs in response to challenges. We previously observed that in Arabidopsis arenosa newly formed (neo-)polyploids, synapsis defects precede chromosomes associating in aberrant multivalent and univalent configurations. Here we study synapsis dynamics in genotypes with varying levels of meiotic stability to ask whether efficient synaptic progression is a key component of evolving stable tetraploid meiosis. We develop a method to quantify synapsis dynamics using the progression of foci of the pro-crossover factor HEI10 as a reference. HEI10 initially appears at many small loci before accumulating only at crossover sites. In diploids, this transition begins while there is still significant asynapsis, which quickly declines as HEI10 accumulation to fewer foci progresses. In neo-tetraploids, suboptimal elongation of synaptic initiation sites, and perhaps defective pairing, precedes synapsis stalling before the onset of HEI10 accumulation. In established tetraploids, HEI10 accumulation begins only when asynapsis is minimal, suggesting an enhanced HEI10/synapsis co-dynamic (even compared to diploids). Hybrids generated by crossing neo- and established tetraploids exhibit intermediate phenotypes. We find the extent of asynapsis correlates positively with crossover numbers, as well as a higher frequency of multivalents and univalent, which can disturb chromosome segregation. Our work supports the hypothesis that improving the efficiency of synapsis is important for evolving polyploid meiotic stability. Significance StatementDuring meiosis, homologous chromosomes pair and subsequently form the synaptonemal complex, which provides a context for maturation of DNA recombination events. How synapsis and crossover formation are coordinated in polyploids, where multiple chromosome sets complicate pair-wise interactions, remains unclear. Leveraging the dynamics of the pro-crossover factor HEI10 as a developmental clock, we quantified synapsis progression in new and established tetraploids of Arabidopsis arenosa. Synapsis is severely compromised in neo-tetraploids, while in established ones it is more efficient even than diploids. Notably, the extent of synaptic defects correlated with excess crossovers, which compromises meiotic stability in tetraploids by connecting connect multiple homologs in multivalents. These findings highlight that improving synapsis dynamics are important for the evolution of meiotic stability in polyploids.

genetics↗

bioRxiv2024

The plant specific cohesin subunit SYN4 contributes to 3D genome organization and activity

O_LIChromatin architecture in the cells of animals and fungi influences gene expression. The molecular factors that influence higher genome architecture in plants and their effects on gene expression remain unknown. Cohesin complexes, conserved in eukaryotes, are essential factors in genome structuring. Here, we investigated the relevance of the plant-specific somatic cohesin subunit SYN4 for chromatin organisation in Arabidopsis thaliana. C_LIO_LIPlants mutated in SYN4 were studied using HRM, Hi-C, RNA sequencing, untargeted and targeted metabolomics and physiological assays to understand the role of this plant-specific cohesin. C_LIO_LIWe show that syn4 mutants exhibit altered intra- and interchromosomal interactions, expressed as sharply reduced contacts between telomeres and chromosome arms but not between centromeres, and differences in the placement and number of topologically associated domains (TADs)-like structures. By transcriptome sequencing, we also show that syn4 mutants have altered gene expression, including numerous genes that control abiotic stress responses. C_LIO_LIThe response to drought stress in Arabidopsis is strongly influenced by the genome structure in syn4 mutants, potentially due to altered expression of CYP707A3, an ABA 8-hydroxylase. C_LI In briefThe 3D architecture of the genome extensively influences gene expression in animals and fungi. We show that the plant-specific cohesin subunit SYN4 affects intra- and interchromosomal interactions including telomere clustering, with consequences for the expression of genes of transient and induced biological pathways and the biosynthesis of bioactive compounds. Highly condensed genome structures at the CYP707A3 locus positively affects the stress response to water deprivation regulated by abscisic acid.

genetics↗

bioRxiv2019

Transposable element over-accumulation in autopolyploids results from relaxed purifying selection and provides variants for rapid local adaptation

Polyploidization is frequently associated with increased transposable element (TE) content. However, what drives TE dynamics following whole genome duplication (WGD) and the evolutionary implications remain unclear. Here, we leveraged whole-genome resequencing data of [~]300 individual Arabidopsis arenosa plants, a well characterized natural diploid-autotetraploid species, to address these questions. Based on 43,176 polymorphic TE insertions we detected in these genomes, we demonstrate that relaxed purifying selection rather than transposition bursts is the main driver of TE over-accumulation after WGD. Furthermore, the increased pool of TE insertions in tetraploids is especially enriched within or near abiotic and biotic stress response genes. Notably, we uncovered one such insertion in a major flowering-time repressor gene and found that the resulting allele is specific to the rapid-cycling tetraploid lineage that colonized mainland railways. Together, our findings indicate that tetrasomy by itself leads to an enhanced tolerance to accumulating genic TE variants, some of which can potentially contribute to local adaptation.

genomics↗

bioRxiv2018

Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa

Ploidy-variable species allow direct inference of the effects of chromosome copy number on fundamental evolutionary processes. While an abundance of theoretical work suggests polyploidy should leave distinct population genomic signatures, empirical data remains sparse. We sequenced [~]300 individuals from 39 populations of Arabidopsis arenosa, a naturally diploid-autotetraploid species. We find the impacts of polyploidy on population genomic processes are subtle yet pervasive, including reduced efficiency on linked and purifying selection as well as rampant gene flow from diploids. Initial masking of deleterious mutations, faster rates of nucleotide substitution, and interploidy introgression all conspire to shape the evolutionary potential of polyploids.

evolutionary biology↗

bioRxiv2017

A ticket to ride - Allele delivery by rail in secondary ruderal colonization by Arabidopsis arenosa

Human-generated ruderal habitats are abundant, but challenging for plants. Some ruderal habitats, however, provide networked corridors (e.g. roadsides and railways) that can facilitate rapid long-distance spread of successfully adapted variants. Here we use transcriptomic and genomic analyses, coupled with genetic mapping and transgenics to understand adaptation to railways in Arabidopsis arenosa. We show normally perennial A. arenosa switched to rapid cycling, a common adaptation for ruderal plants, at least twice upon railway colonization. We further show substantial gene flow from a widely distributed railway colonist likely contributed to secondary colonization by a non-ruderal type, highlighting how connectivity can affect adaptability. We find loss of expression of the reproductive repressor FLOWERING LOCUS C (FLC) is likely primarily responsible for rapid cycling in the widely distributed railway variant. However, a second railway colonist in the Alps also cycles rapidly, but retains high FLC. Some alleles in this population encode non-functional proteins, suggesting FLC has started to decay, but most are functional. Instead, this population likely circumvents FLC via a derived allele of CONSTANS (CO), which shows strong evidence of selection in this population. Importantly, we find this CO allele arrived via gene flow from the widespread ruderal, where it was also previously under selection. This suggests ruderal adaptation may have been progressive, perhaps in both cases, with FLC-circumvention arising first, and FLC loss arising later but ultimately obscuring its earlier circumvention. These snapshots of railway adaptation highlight that gene flow from widespread ruderals can provide opportunities for subsequent adaptation by local genotypes.

evolutionary biology↗