Biology subjects

Novikova, P. Y.

Publications and source records attributed to Novikova, P. Y..

13 recordsLinked to original sources

bioRxiv2026

The Nature of Centromeric Repeat Turnovers in the genus Arabidopsis

Centromeres are critical for accurate segregation of chromosomes and are often composed of megabases of tandemly arranged satellite repeats. Yet, despite their conserved function, the DNA sequence of centromeres is, paradoxically, rapidly evolving. To understand the nature of centromeric sequence turnover, we assembled 417 centromeres from nine species representing the entire Arabidopsis genus. In the genus, centromeres are formed by four main satellite repeats with homologous sequences forming central arrays and minor repeat types. We identify the ancestral centromeric repeat type for the Arabidopsis genus and three independent turnovers to different repeats: (1) a complete turnover in A. thaliana, (2) a turnover of seven out of the eight centromeres in the ancestor of A. cebennensis and A. pedemontana, (3) turnovers of three to five centromeres in the genomes of A. halleri and A. lyrata. Most centromeric repeats are also present throughout the genome with shared syntenic locations between Arabidopsis species, and some being similar to parts of transposable elements and genes, suggesting that centromeric repeats originate outside of the centromeres. In allotetraploid A. suecica we find that the repeats from centromeric arrays on one subgenome can transpose and invade the other, likely via transposable element activity. All four main centromeric repeats can recruit the CENH3 (CENP-A) histone variant, however, when a new repeat successfully proliferates in an old array, CENH3 is primarily recruited to the new array marking functional take over. Complete centromeric turnovers occurred in species that experienced severe bottlenecks in their evolutionary history, where new centromeric alleles may have been fixed by genetic drift. Yet, we also observe segregation distortion between two different centromeric repeat types in A. lyrata, suggestive of centromere drive and we propose that both drift and drive contribute to centromeric repeat turnover. Together, our findings reveal the origin of centromeric repeats, mechanisms of repeat proliferation and spread, and the evolutionary dynamics of centromeric repeat turnovers in the Arabidopsis genus.

evolutionary biology↗

bioRxiv2026

A Global Genomic Resource for Outcrossing Arabidopsis lyrata and Arabidopsis arenosa

Genetic studies leveraging natural variation in Arabidopsis species have improved our understanding of evolutionary genetic processes underlying ecologically important and adaptive traits. Integrating the thorough functional knowledge accumulated in A. thaliana with the extensive natural variation in outcrossing Arabidopsis species is a powerful approach to study the basis of adaptation in natural evolutionary and ecological contexts. Here we present an integrated genomics database of sequenced genomes from several studies in A. lyrata (1018 genomes in total) and A. arenosa (736 genomes in total), spanning the geographic ranges of these two ploidy-variable, outcrossing taxa. We provide a searchable genome browser with population data mapped to respective reference genomes, an interactive geographic map of population structure clusters, and an efficient way to subsample the full dataset of genetic variation, available at arabidopsislyrata.org. To demonstrate its utility, we perform a genome-wide association study on a latitudinal cline of A. lyrata and find strong associations of several loci with latitude, including variants in key regulators of photoperiodic growth. This resource provides access to genetic diversity data in a single repository, enabling further studies of comparative genetics and local adaptation, as well as of individual genes of interest.

evolutionary biology↗

bioRxiv2025

Copy Number Variation: A Substrate for Plant Adaptation and Stress Response in Arabidopsis

Copy number variation (CNV) is a major source of genomic diversity that shapes gene family evolution and may contribute to ecological differentiation, yet its genome-wide ecological relevance remains poorly understood. Here, we analyzed CNV across four Brassicaceae species (Arabidopsis thaliana, A. lyrata, A. halleri, and Arabis alpina) to identify gene families undergoing rapid expansion or contraction. Using a birth-death model, we identified 231 rapidly evolving gene families spanning diverse functional categories. We then characterized CNV within populations of A. thaliana and A. lyrata using population-scale long-read assemblies. CNV exhibited strong heterogeneity across gene families and species, with contrasting evolutionary outcomes: A. thaliana showed greater retention of duplicated copies, whereas A. lyrata exhibited higher pseudogenization and turnover. CNV profiles were strongly structured geographically, reflecting known demographic and phylogeographic patterns in both species. Environmental association analyses revealed species-specific architectures: CNV in A. thaliana showed a diffuse, polygenic association with climate, whereas in A. lyrata associations were more strongly coupled to population structure. Despite the functional diversity of rapidly evolving families, environmentally associated CNVs were significantly enriched in defense- and stress-related functions. These results demonstrate that CNV-environment relationships emerge at the level of gene family networks and are shaped by genomic architecture and lineage history, highlighting CNV as a context-dependent driver of genome evolution and ecological differentiation. SummaryGene copy number variation--where individuals carry different numbers of copies of the same gene--is a potentially important but poorly understood source of genetic diversity. The authors studied how copy numbers evolve across four mustard family plant species and whether this variation helps plants adapt to different environments. They found that gene families involved in disease resistance and stress responses were especially prone to rapid copy number changes. These changes tracked geography and local climate, but in ways that differed between species depending on their evolutionary history. The findings highlight gene copy number variation as a key, underappreciated contributor to how plants adapt to their environments.

evolutionary biology↗

bioRxiv2025

Autopolyploidy exacerbates dominance masking under negative frequency-dependent selection: evidence from sporophytic self-incompatibility in Arabidopsis arenosa and A. lyrata

Polyploidy is a widespread phenomenon in flowering plants, with up to 30% of extant species being recent polyploids. Whether and how polyploidy modulates the action of natural selection remains debated, and the particular case of balancing selection has been poorly explored. This study investigates the impact of autopolyploidy on sporophytic self-incompatibility in plants, a striking example of a genetic system evolving under a special form of balancing selection (strong negative frequency-dependent selection). Numerical simulations reveal that under strict codominance, the number of S-alleles maintained in tetraploid populations is expected to double as compared to diploid populations. However, under a model with strict hierarchical dominance among alleles, the number of S-alleles increases only slightly, but gene diversity and observed heterozygosity are substantially lower in tetraploids as compared to diploids, due to enhanced dominance masking effects. Empirical data on Arabidopsis arenosa and A. lyrata confirm the latter predictions, showing similar levels of allelic diversity but dramatically lower observed and expected heterozygosity at the self-incompatibility locus in tetraploids compared to diploids. The study highlights the significant impact of autopolyploidy on patterns of diversity at the self-incompatibility locus, emphasizing the increased dominance effect in tetraploids. The results also allow us to reject a scenario of strong founder effects associated with evolution of the polyploid lineages.

evolutionary biology↗

bioRxiv2025

Life-history trade-offs explain local adaptation in Arabidopsis thaliana

Local adaptation has been demonstrated in many organisms, but the traits involved, and the temporal and spatial scales at which selection acts are generally unknown. We carried out a multi-year study of 200 accessions (natural inbred lines) of Swedish Arabidopsis thaliana using local field sites and a combination of common-garden experiments that measured adult survival and fecundity, and selection experiments that measured fitness over the full life cycle. We found evidence of strong and variable selection, with particular genotypes favored more than five-fold in certain years and locations. Fecundity showed evidence of classical local adaptation, with accessions generally performing better closer to their home. However, relative to other accessions, southern ones usually had the highest fecundity---but were far more sensitive to harsh winters and slug herbivory, which strongly decreased both survival and fecundity. Furthermore, accessions originally sampled on beaches had low fecundity in all common-garden experiments, but massively outperformed all other accessions in the selection experiments, presumably due to an advantage during seedling establishment associated with their very large seeds. We conclude that local adaptation in A. thaliana reflects strong temporally and spatially varying selection on multiple traits, generally involving trade-offs and different life-history strategies, making fitness difficult to predict and measure.

genetics↗

bioRxiv2024

Diploid origins, adaptation to polyploidy, and the beginning of rediploidization in allotetraploid Arabidopsis suecica

Polyploidization, followed by genome downsizing, is a recurrent evolutionary cycle that dramatically reshapes genome structure. Newly formed polyploids must quickly adjust their cell division machinery to maintain stable chromosome inheritance, while long-term stabilization involves rediploidization, returning the genome to a diploid-like state. Here, we investigate the origin and early genome evolution of Arabidopsis suecica, a hybrid polyploid derived from A. thaliana and A. arenosa Leveraging a recent genome assembly for A. suecica along with population level whole-genome resequencing of all three species, we identify the closest progenitors to A. suecica and use this knowledge to examine genes under positive selection and to assess compensatory dynamics between homeologs carrying loss-of-function mutations. Our findings show that both parental species were diploid, including the paternal A. arenosa progenitor. We identify evidence for de novo adaptation to allopolyploidy within the A. arenosa sub-genome of A. suecica, including genes involved in homolog pairing and recombination. Although relaxed purifying selection is evident, likely due to the genome-wide redundancy, we observe functional compensation between homeologous gene pairs in A. suecica: when one copy loses function, the other maintains it Together, these findings revise the origin of A. suecica and identify early genome stabilization mechanisms, including evidence for meiotic adaptation and mutational buffering through homeologous gene compensation.

genomics↗

bioRxiv2024

Multiple polyploidizations in Arabidopsis lyrata stabilized by long-range adaptive introgression across Eurasia

Abundance of polyploidy varies across lineages, evolutionary time and geography, suggesting both genetics and environment play a role in polyploid persistence. Arabidopsis lyrata appears to be the most polyploidy-rich species-complex in the Arabidopsis genus, with multiple origins of autotetraploidy. This is revealed by genomic data from over 400 samples across Eurasia. We found over 30 previously undescribed autotetraploid populations in Siberia with a minimum of two separate origins, independent of those previously reported in Central Europe. The establishment of Siberian tetraploids is mediated by meiotic adaptation at the same genes as in European tetraploid A. lyrata and Arabidopsis arenosa, despite high divergence and geographical separation. Haplotype analysis based on synthetic long-read assemblies supports the long-range introgression of adaptive alleles from the tetraploid interspecific pool of European A. lyrata and A. arenosa to tetraploid Siberian A. lyrata. Once evolved, adaptation to polyploidy promotes the establishment of new polyploid lineages through adaptive inter- and intraspecific introgression.

genomics↗

bioRxiv2024

Polyploid genome assembly of Cardamine chenopodiifolia

BackgroundCardamine chenopodiifolia is an amphicarpic plant that develops two fruit morphs, one above and the other below ground. Above-ground fruit disperse their seeds by explosive coiling of the fruit valves, while below-ground fruit are non-explosive. Amphicarpy is a rare trait that is associated with polyploidy in C. chenopodiifolia. Studies into the development and evolution of this trait are currently limited by the absence of genomic data for C. chenopodiifolia. ResultsWe produced a chromosome-scale assembly of the octoploid C. chenopodiifolia genome using high-fidelity long read sequencing with the Pacific Biosciences platform. We successfully assembled 32 chromosomes and two organelle genomes with a total length of 597.2 Mbp and an N50 of 18.8 kbp (estimated genome size from flow cytometry: 626 Mbp). We assessed the quality of this assembly using genome-wide chromosome conformation capture (Omni-C) and BUSCO analysis (97.1% genome completeness). Additionally, we conducted synteny analysis to infer that C. chenopodiifolia likely originated via allo-rather than auto-polyploidy and phased one of the four sub-genomes. ConclusionsThis study provides a draft genome assembly for C. chenopodiifolia, which is a polyploid, amphicarpic species within the Brassicaceae family. This genome offers a valuable resource to investigate the under-studied trait of amphicarpy and the origin of new traits by allopolyploidy.

plant biology↗

bioRxiv2022

Genome of selfing Siberian Arabidopsis lyrata explains establishment of allopolyploid Arabidopsis kamchatica

A transition to selfing can be beneficial when mating partners are scarce, for example, due to ploidy changes or at species range edges. Here we explain how self-compatibility evolved in diploid Siberian Arabidopsis lyrata, and how it contributed to the establishment of allotetraploid A. kamchatica. First, we provide chromosome-level genome assemblies for two self-fertilizing diploid A. lyrata accessions, one from North America and one from Siberia, including a fully assembled S-locus for the latter. We then propose a sequence of events leading to the loss of self-incompatibility in Siberian A. lyrata, date this independent transition to [~]90 Kya, and infer evolutionary relationships between Siberian and North American A. lyrata, showing an independent transition to selfing in Siberia. Finally, we provide evidence that this selfing Siberian A. lyrata lineage contributed to the formation of the allotetraploid A. kamchatica and propose that the selfing of the latter is mediated by the loss-of-function mutation in a dominant S-allele inherited from A. lyrata.

plant biology↗

bioRxiv2021

Inference of polyploid origin and inheritance mode from population genomic data

Summary/AbstractWhole-genome duplications yield varied chromosomal pairing patterns, ranging from strictly bivalent to multivalent, resulting in disomic and polysomic inheritance modes. In the bivalent case, homeologous chromosomes form pairs, where in a multivalent pattern all copies are homologous and are therefore free to pair and recombine. As sufficient sequencing data is more readily available than high-quality cytological assessments of meiotic behavior or population genetic assessment of allelic segregation, especially for non-model organisms, here we describe two bioinformatics approaches to infer origins and inheritance modes of polyploids using short-read sequencing data. The first approach is based on distributions of allelic read depth at the heterozygous sites within an individual, as the expectations of such distributions are different for disomic and polysomic inheritance modes. The second approach is more laborious and based on a phylogenetic assessment of partially phased haplotypes of a polyploid in comparison to the closest diploid relatives. We discuss the sources of deviations from expected inheritance patterns, advantages and pitfalls of both methods, effects of mating types on the performance of the methods, and possible future developments.

genomics↗

bioRxiv2020

Gradual evolution of allopolyploidy in Arabidopsis suecica

The majority of diploid organisms have polyploid ancestors. The evolutionary process of polyploidization (and subsequent re-diploidization) is poorly understood, but has frequently been conjectured to involve some form of "genome shock" -- partly inspired by studies in crops, where polyploidy has been linked to major genomic changes such as genome reorganization and subgenome expression dominance. It is unclear, however, whether such dramatic changes would be characteristic of natural polyploidization, or whether they are a product of domestication. Here, we study polyploidization in Arabidopsis suecica (n = 13), a post-glacial allopolyploid species formed via hybridization of A. thaliana (n = 5) and A. arenosa (n = 8). We generated a chromosome-level genome assembly of A. suecica and complemented it with polymorphism and transcriptome data from multiple individuals of all species. Despite a divergence of [~]6 Mya between the two ancestral species and appreciable differences in their genome composition, we see no evidence of a genome shock: the A. suecica genome is highly colinear with the ancestral genomes, there is no subgenome dominance in expression, and transposable element dynamics appear to be stable. We do, however, find strong evidence for changes suggesting gradual adaptation to polyploidy. In particular, the A. thaliana subgenome shows upregulation of meiosis-related genes, possibly in order to prevent aneuploidy and undesirable homeologous exchanges that are frequently observed in experimentally generated A. suecica, and the A. arenosa subgenome shows upregulation of cyto-nuclear related processes, possibly in response to the new cytoplasmic environment of A. suecica, with plastids maternally inherited from A. thaliana.

evolutionary biology↗

bioRxiv2019

Whole genome duplication potentiates inter-specific hybridisation and niche shifts in Australian burrowing frogs Neobatrachus

Polyploidy has played an important role in evolution across the tree of life but it is still unclear how polyploid lineages may persist after their initial formation. While both common and well-studied in plants, polyploidy is rare in animals and generally less well-understood. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful animal polyploid model system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin and inheritance mode of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We resolve the phylogenetic relationships among Neobatrachus species and provide further support that the three polyploid species have independent autotetraploid origins. We document higher genetic diversity in tetraploids, resulting from widespread gene flow specifically between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and current isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate variation on frogs with differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which in turn corresponds to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow into tetraploid lineages specifically. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on the evolution of adaptation in animals.

evolutionary biology↗

bioRxiv2016

Unstable inheritance of 45S rRNA genes in Arabidopsis thaliana

The considerable genome size variation in Arabidopsis thaliana has been shown largely to be due to copy number variation (CNV) in 45S ribosomal RNA (rRNA) genes. Surprisingly, attempts to map this variation by means of genome-wide association studies (GWAS) failed to identify either of the two likely sources, namely the nucleolar organizer regions (NORs). Instead, GWAS implicated a trans-acting locus, as if rRNA CNV was a phenotype rather than a genotype. To explain these results, we investigated the inheritance and stability of rRNA gene copy number using the variety of genetic resources available in A. thaliana -- F2 crosses, recombinant inbred lines, the multiparent advanced generation inter-cross population, and mutation accumulation lines. Our results clearly show that rRNA gene CNV can be mapped to the NORs themselves, with both loci contributing equally to the variation. However, NOR size is unstably inherited, and dramatic copy number changes are visible already within tens of generations, which explains why it is not possible to map the NORs using GWAS. We did not find any evidence of trans-acting loci in crosses, which is also expected since changes due to such loci would take very many generations to manifest themselves. rRNA gene copy number is thus an interesting example of \"missing heritability\" -- a trait that is heritable in pedigrees, but not in the general population.

genetics↗