Biology subjects

Mandakova, T.

Publications and source records attributed to Mandakova, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Why woodiness repeatedly evolves--and disappears

Derived woodiness--the evolution of woody growth from herbaceous ancestors--has arisen hundreds of times across flowering plants, yet the environmental conditions associated with its repeated evolution remain poorly understood. Here, we analyse woodiness evolution in the mustard family (Brassicaceae; ~4,150 species) using a time-calibrated phylogeny of 2,927 species, including 374 of the 385 known woody species, together with global growth-form and climatic niche data. We infer 231 independent origins of woodiness alongside 176 reversals to herbaceousness, indicating that woodiness evolves repeatedly but remains evolutionarily unstable. Although woody species are enriched on islands, most occur on the mainland, where woodiness is consistently associated with drought and reduced frost. Correlated-evolution analyses reveal that drought is associated primarily with the persistence of woodiness, whereas reduced frost is associated with gains of woodiness and increased frost with its loss. These findings identify distinct climatic associations with the gain, persistence, and loss of woody growth forms.

evolutionary biology↗

bioRxiv2026

CRISPR-mediated centromere fission generates neo-chromosomes with distorted meiotic inheritance in Arabidopsis

Centromeres are essential for chromosome segregation and are epigenetically defined by CENH3/CENP-A nucleosomes. Centromere position along chromosomes varies within and between species, ranging from telocentric to metacentric architectures. Yet, how centromere position influences chromosome inheritance and karyotype evolution remains poorly understood. To reposition the centromere, we used CRISPR-Cas9 to break the centromeric satellite array of Arabidopsis thaliana chromosome 3. Fission chromosomes rapidly acquired telomeres, converting a metacentric into two stable telocentric neo-chromosomes. Neo-centromere formation involved genetic restructuring and de novo satellite higher-order repeat formation, together with epigenetic remodeling of CENH3 and DNA methylation. Crossing the six-chromosome fission line to five-chromosome wild type produced a meiosis-specific trivalent that mis-segregated and generated aneuploidy. Trivalent recombination doubled through two obligate crossovers, which were shifted towards the telomeres. Inheritance was strongly distorted in favor of the wild type centromere, as telocentrics segregated into inviable monosomic gametes. The reciprocal trisomic gametes were associated with centromere-proximal recombination, demonstrating that crossover position governs trivalent segregation. Distortion further increased when CENH3 was over-expressed, implicating centromere strength in the outcomes of trivalent meiosis. Our results reveal rapid centromere remodeling following karyotype change, and how trivalent centromere architecture distorts inheritance, with implications for hybrid incompatibility and synthetic chromosome design.

genetics↗

bioRxiv2026

Building the meiotic bouquet: A nuclear polarity pathway in Arabidopsis

Meiotic chromosome pairing requires the establishment of a polarized nuclear architecture, but how this polarity emerges from the interplay of telomeres, the nucleolus, and the nuclear envelope remains incompletely understood in plants. Using stage-resolved three-dimensional imaging of intact Arabidopsis thaliana male meiocytes, we reconstruct the early meiotic sequence that links the premeiotic chromosome arrangement to telomere bouquet formation. We show that telomeres enter meiosis positioned around the nucleolus and, at the onset of leptotene, undergo a coordinated and directionally biased departure from the nucleolar surface. This transition establishes asymmetric early contacts with discrete SUN1/2-enriched domains of the nuclear envelope, well before visible clustering occurs, revealing that the envelope is pre-patterned into regions permissive for telomere attachment. As zygotene progresses, these early contacts consolidate into a nucleolus-associated bouquet, whereas the nucleolar organizer regions (NORs) maintain a stable position and remain unsynapsed. Centromeres reorganize in parallel and progressively shift away from the developing telomere domain, giving rise to the classical centromere-telomere opposition. Rare nuclei exhibiting bouquet formation opposite the nucleolus correspond to alternative SUN1/2 microdomain topologies, indicating that nuclear-envelope patterning, rather than telomere behavior, ultimately determines the polarity state. Together, these findings provide a mechanistic framework in which NOR stability, SUN-patterned membrane domains, and telomere migration act sequentially to generate a polarized meiotic nucleus in Arabidopsis.

plant biology↗

bioRxiv2025

Post-transcriptional regulation of meiotic transcripts by the RNA binding protein CDM1 is associated with cytoplasmic condensate assemblies

The transition from diploid to haploid life phases requires extensive reprogramming of gene expression that drive meiotic cell division and the differentiation of haploid forms. A hallmark of meiosis is widespread post-transcriptional regulation, including delayed translation that ensures timely protein production at specific stages. Here, we identify a mechanism controlling the translation of meiotic transcripts in Arabidopsis pollen mother cells, mediated by CALLOSE DEFECTIVE MICROSPORES1 (CDM1). We show that CDM1 affects several meiotic processes, including chromosome pairing, condensation, and cytokinesis. CDM1 forms dynamic, meiosis specific cytoplasmic foci that associate with components of processing bodies and stress granules, giving rise to three-phase condensate assemblies. Biochemical and cellular analyses reveal that CDM1 is an RNA-binding protein with an intrinsic ability to form ribonucleoprotein condensates. Furthermore, we demonstrate that CDM1 binds mRNAs expressed in prophase I and represses their translation until later meiotic stages, coinciding with the disassembly of CDM1 condensates. These findings establish CDM1 as a key post-transcriptional regulator that fine-tunes the expression of meiotic genes to ensure proper progression of microsporogenesis.

plant biology↗

bioRxiv2025

Genome structure and molecular phylogeny of the only Eurasian Boechera species, Boechera falcata (Brassicaceae)

Boechera falcata (Turcz.) Al-Shehbaz (earlier known as Arabis turczaninowii Ledeb.) is a herbaceous perennial belonging to the East Siberian, boreal-steppe ecotype. It is the only species of the diverse genus Boechera that grows on the Eurasian continent, all others being endemic to North America and Greenland. In all likelihood, Boechera falcata or its ancestral lineage migrated from North America to Eastern Siberia across the Bering Land Bridge when it was exposed during the height of Pleistocene glaciation. Boechera is interesting in that many species in this genus are allodiploid and triploid apomicts that arose through complex hybridization of sexual species and ecotypes. To date, the genomes of only two American Boechera species, B. stricta and B. retrofracta, have been sequenced, analyzed, and published. In the present study, we sequenced, assembled to the chromosome level, and analyzed the B. falcata genome, which was highly homozygous with a size of 189.36 Mb. Molecular phylogenetic analysis of the nuclear and organelle genomes revealed a high degree of relatedness of B. falcata to North American relatives. Investigation of the structure of pachytene, mitotic, and diakinesis chromosome spreads (n = 14) using cytogenetic analysis and comparative chromosome painting (CCP) allowed us to identify all 22 genomic blocks of crucifers and found that five of the seven B. falcata chromosomes were collinear with their corresponding chromosomes in the ancestral Boechereae genome, and two chromosomes had undergone pericentric and paracentric inversions. Allelic analysis of the apomixis marker APOLLO gene revealed that B. falcata contains only sex alleles of this gene. The availability of the genome of the only Asian Boechera species will facilitate studies of the evolution and phylogeny of Brassicaceae species and apomixis.

genomics↗

bioRxiv2025

Boechera or not? Genomic insights and taxonomic reassessment of the misclassified Asian species B. calcarea (Brassicaceae)

The genus Boechera (Brassicaceae) serves as a model system for studying apomictic reproduction and ecological adaptations, with most species concentrated in North America. Rare occurrences of Boechera species beyond their typical range offers unique opportunities to investigate genome evolution in extralimital environments. One such species, B. calcarea, was described from the Chandalaz Range in northeastern Asia (Russia). This study aimed to investigate the genome structure and evolutionary history of B. calcarea. However, our analyses reveal that the species does not belong to Boechera. Instead, an integrative approach combining cytogenetic, phylogenetic and repeatome analyses identified the species as a member of an ancestral clades within the tribe Arabideae. The diploid Parryodes calcarea (Dudkin) D.A.German & Lysak (2n = 16) exhibits Arabideae-specific chromosomal signatures, including multiple centromere repositionings. These findings clarify the misattribution of P. calcarea to Boechera, leaving Boechera falcata and Borodinia macrophylla as the only Old World representatives of the Boechereae. This study highlights the importance of integrative methodologies in resolving taxonomic ambiguities and provides new insights into the diversification of the largest cruciferous tribe, Arabideae.

plant biology↗

bioRxiv2025

The genus Boechera as a model for apomixis research

The genus Boechera, a prominent member of the tribe Boechereae within the family Brassicaceae, has emerged as an exceptional model for apomixis research, owing to its unique evolutionary, reproductive, and genomic characteristics. With over 480 genetically distinct taxa and a distribution spanning North America, Greenland, and parts of Asia, Boechera exemplifies remarkable ecological and genetic diversity. A hallmark of the genus is its high frequency of gametophytic apomixis, including diplospory and apospory, which, combined with hybridization, drive genetic innovation and environmental adaptability. Moreover, Boechera is notable for its diploid expression of apomixis, independent of polyploidy, providing an unparalleled system for dissecting asexual reproduction. Genomic adaptations, such as heterochromatic supernumerary chromosomes, further highlight its evolutionary complexity. Recent advances, including the discovery of critical regulatory genes like APOLLO and UPGRADE2, have deepened our understanding of the genetic basis of apomixis. These insights position Boechera as a cornerstone for elucidating apomictic pathways and leveraging these mechanisms for crop improvement. The genus not only enhances our understanding of apomixis but also offers transformative potential for agriculture.

plant biology↗

bioRxiv2024

Overcoming ploidy barriers: the role of triploid bridges in the genetic introgression of Cardamine amara

O_LIPolyploidisation is a significant reproductive barrier, yet genetic evidence indicates that interploidy admixture is more common than previously thought. Theoretical models and controlled crosses support the triploid bridge hypothesis supposing that hybrids of intermediate ploidy facilitate gene flow. However, comprehensive evidence combining experimental and genetic data is missing. C_LIO_LIIn this study, we investigated the rates and directions of gene flow within a diploid- autotetraploid contact zone of Cardamine amara, a species with abundant natural triploids. We cytotyped over 400 wild individuals, conducted reciprocal interploidy crosses and inferred gene flow based on genome-wide sequencing of 84 individuals. C_LIO_LITriploids represent a conspicuous entity in mixed-ploidy populations (5%), yet only part of them arose through interploidy hybridisation. Despite being rarely formed, triploid hybrids can backcross with their parental cytotypes, producing viable offspring that are often euploid (in 42% of cases). In correspondence, we found a significant genome-wide signal of gene flow for sympatric, but not allopatric, diploids and tetraploids. Coalescent simulations demonstrated significant bidirectional introgression which is stronger in the direction towards the tetraploid cytotype. C_LIO_LITriploids, though rare, play a key role in overcoming polyploidy-related reproductive barriers. We present integrative evidence for bidirectional interploidy gene flow mediated by a triploid bridge in natural populations. C_LI

evolutionary biology↗

bioRxiv2023

Kinetochore and ionomic adaptation to whole genome duplication

Transforming genomic and cellular landscapes in a single generation, whole genome duplication (WGD) brings fundamental challenges, but is also associated with diversification. How is WGD tolerated, and what processes commonly evolve to stabilize the resulting polyploid? Here we study this in Cochlearia spp., which have experienced multiple WGDs in the last 300,000 years. We first generate a chromosome-scale genome and sequence 113 individuals from 33 diploid, tetraploid, hexaploid, and outgroup populations. We detect the clearest post-WGD selection signatures in functionally interacting kinetochore components and ion transporters. We structurally model these derived selected alleles, identifying striking WGD-relevant functional variation, and then compare these results to independent recent post-WGD selection in Arabidopsis arenosa and Cardamine amara. Most prominent in these results is genetic evidence of at least four functionally interacting kinetochore complex subunits in adaptation to WGD at the centromere among our very top selective sweep outliers. In addition, some of the same biological processes evolve in all three WGDs, but specific genes recruited are flexible. This points to a polygenic basis for modifying systems that control the kinetochore, meiotic crossover number, DNA repair, ion homeostasis, and cell cycle. Given that DNA management (especially repair) is the most salient category with the strongest selection signal, we speculate that the generation rate of structural genomic variants may be altered by WGD in young polyploids, contributing to their occasionally spectacular adaptability observed across kingdoms. Significance StatementWhole-genome duplication (WGD) occurs in all kingdoms and is linked to adaptation, speciation, domestication, and even cancer outcome. But WGD is a shock to the system, and commonly disrupts cell division due to increased DNA management burden and transformed cell physiology. Nevertheless, the hopeful monster that survives WGD is special, occasionally experiencing runaway success. Why do some thrive but others die? Here we introduce a powerful new model, Cochlearia, which has benefitted from multiple WGDs, and we provide the first genetic evidence of rapid adaptation of functionally interacting components of the cell division machinery, the kinetochore. We also compare which processes and genes evolve to stabilize the new polyploid in three independent cases and highlight common mechanisms.

evolutionary biology↗

bioRxiv2022

Global Phylogeny of the Brassicaceae Provides Important Insights into Gene Discordance

The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most published family phylogenies are incompletely sampled, generally contain massive polytomies, and/or show incongruent topologies between datasets. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life, or BrassiToL) based on nuclear (>1,000 genes, almost all 349 genera and 53 tribes) and plastome (60 genes, 79% of the genera, all tribes) data. We found cytonuclear discordance between nuclear and plastome-derived phylogenies, which is likely a result of rampant hybridisation among closely and more distantly related species, and highlight rogue taxa. To evaluate the impact of this rampant hybridisation on the nuclear phylogeny reconstruction, we performed four different sampling routines that increasingly removed variable data and likely paralogs. Our resulting cleaned subset of 297 nuclear genes revealed high support for the tribes, while support for the main lineages remained relatively low. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene icehouse origin of the family. Finally, we propose five new or re-established tribes, including the recognition of Arabidopsideae, a monotypic tribe to accommodate Arabidopsis. With a worldwide community of thousands of researchers working on this family, our new, densely sampled family phylogeny will be an indispensable tool to further highlight Brassicaceae as an excellent model family for studies on biodiversity and plant biology.

evolutionary biology↗

bioRxiv2022

Chromosome-level genome assembly of Rorippa aquatica revealed its allotetraploid origin and mechanisms of heterophylly upon submergence

The ability to respond to environmental variability is essential for living systems, especially to sessile organisms such as plants. The amphibious plant Rorippa aquatica exhibits a drastic type of phenotypic plasticity known as heterophylly, a phenomenon where leaf form is altered in response to the surrounding environment. Although heterophylly has been studied in various plant species, its molecular mechanism has not been fully elucidated. To establish the genetic basis and analyze the evolutionary processes responsible for heterophylly, we assembled the chromosome-level genome of R. aquatica by combining data from Illumina short-read sequencing, PacBio long-read sequencing, and High-throughput Chromosome Conformation Capture (Hi-C) sequencing technologies. Fine-scale comparative chromosome painting and chromosomal genomics revealed that allopolyploidization and subsequent post-polyploid descending dysploidy occurred during R. aquatica speciation. The genomic information above was the basis for the transcriptome analyses to examine the mechanisms involved in heterophylly, especially in response to the submerged condition, which uncovered that the ethylene and blue light signaling pathways participate in regulating heterophylly under submerged conditions. The assembled R. aquatica reference genome provides novel insights into the molecular mechanisms and evolution of heterophylly.

plant biology↗

bioRxiv2021

Intact rDNA arrays of Potentilla-origin detected in Erythronium nucleus suggest recent eudicot-to-monocot horizontal transfer

The occurrence of horizontal gene transfer (HGT) in Eukarya is increasingly gaining recognition. Nuclear-to-nuclear jump of DNA between plant species at high phylogenetic distance and devoid of intimate association (e.g., parasitism) is still scarcely reported. Within eukaryotes, components of ribosomal DNA (rDNA) multigene family have been found to be horizontally transferred in protists, fungi and grasses. However, in neither case HGT occurred between phylogenetic families, nor the transferred rDNA remained tandemly arrayed and transcriptionally active in the recipient organism. This study aimed to characterize an alien eudicot-type of 45S nuclear rDNA, assumingly transferred horizontally to the genome of monocot European Erythronium (Liliaceae). Genome skimming coupled by PacBio HiFi sequencing of a BAC clone were applied to determine DNA sequence of the alien rDNA. A clear phylogenetic signal traced the origin of the alien rDNA of Erythronium back to the Argentea clade of Potentilla (Rosaceae) and deemed the transfer to have occurred in the common ancestor of E. dens-canis and E. caucasicum. Though being discontinuous, transferred rDNA preserved its general tandemly arrayed feature in the host organism. Southern blotting, molecular cytogenetics, and sequencing of a BAC clone derived from flow-sorted nuclei indicated integration of the alien rDNA into the recipients nuclear genome. Unprecedently, dicot-type alien rDNA was found to be transcribed in the monocot Erythronium albeit much less efficiently than the native counterpart. This study adds a new example to the growing list of naturally transgenic plants while holding the scientific community continually in suspense about the mode of DNA transfer. Significance StatementRibosomal DNA is an essential component of all cellular genomes. In plants, accidental movement of rDNA via horizontal gene transfer has only been reported in sexually incompatible grasses (monocots) where it involved non-functional rDNA units. In this study, we propose that evolutionary trajectories of eudicots and monocots were bypassed by the jump of rDNA from a Potentilla species (Rosaceae) to a common ancestor of Erythronium dens-canis and E. caucasicum (Liliaceae). The alien eudicot-type rDNA appeared relatively well conserved in the examined host Erythronium genome, being able to be expressed while preserving its general tandemly repeated feature, evidences that have no match in earlier literature.

plant biology↗

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↗

bioRxiv2020

Human-like telomeres in Zostera marina reveal a mode of transition from the plant to the human telomeric sequences

A previous study describing the genome of Zostera marina, the most widespread seagrass in the Northern hemisphere, revealed some genomic signatures of adaptation to the aquatic environment. Important features related to the back-to-the-sea reverse evolutionary pathway were found, such as the loss of stomatal genes, while other functions like an algal-like cell wall composition were acquired. Beyond these, the genome structure and organization were comparable to the majority of plant genomes sequenced, except for one striking feature that went unnoticed at that time: the presence of human-like instead of the expected plant-type telomeric sequences. By using different experimental approaches including FISH, NGS and Ba131 analysis, we have confirmed its telomeric location in the chromosomes of Z. marina. We have also identified its telomerase RNA subunit (TR), confirming the presence of the human-type telomeric sequence in the template region. Remarkably, this region was found to be very variable even in clades with a highly conserved telomeric sequence across their species. Based on this observation, we propose that alternative annealing preferences in the template borders can explain the transition between the plant and human telomeric sequences. The further identification of paralogues of TR in several plant genomes brought us to the hypothesis that plants may keep an increased ability to change their telomeric sequence. We discuss the implications of this occurrence in the evolution of telomeres while introducing a mechanistic model for the transition from the plant to the human telomeric sequences.

evolutionary biology↗

bioRxiv2020

Parallelism in gene expression between foothill and alpine ecotypes in Arabidopsis arenosa

Parallel adaptation results from independent evolution of similar traits between closely related lineages and allows testing to which extent evolution is repeatable. Parallel adaptation often involves similar gene expression changes but the identity of genes shaped by parallel selection and the causes of expression parallelism remains largely unknown. By comparing genomes and transcriptomes of four independent foothill-alpine population pairs across four treatments, we addressed genetic basis, plasticity and functional consequences of gene expression parallelism in alpine adaptation. Seeds of four population pairs of Arabidopsis arenosa from distinct mountain regions were raised under four treatments that differed in temperature and irradiance, factors varying strongly with elevation. Parallelism in gene expression was quantified by RNA-seq in leaves of young plants. By manipulating temperature and irradiance, we also tested for parallelism in plasticity (gene-by-environment interaction [GEI]). We found significant parallelism in differential gene expression across four independently recruited alpine ecotypes with an overrepresentation of genes involved in biotic stress response. In addition, we demonstrated significant parallelism in GEI indicating shared response to environmental variation in our foothill and alpine populations. Fraction of genes showing expression parallelism also encompassed genomic variants showing outlying differentiation, with greater enrichment of such variants in cis-regulatory elements. In summary, our results suggest frequent evolutionary repeatability in shaping expression difference associated with colonization of an alpine environment and support the hypothesis of an important role of genetic variation in cis-regulatory elements in gene expression parallelism.

molecular biology↗

bioRxiv2019

A hypomorphic allele of telomerase reverse transcriptase uncovers the minimal functional length of telomeres in Arabidopsis.

Despite the essential requirement of telomeric DNA for genome stability, the length of telomere tracts between species differs by up to four orders of magnitude, raising the question of the minimal length of telomeric DNA necessary for proper function. Here we address this question using a hypomorphic allele of the telomerase catalytic subunit, TERT. We show that although this construct partially restored telomerase activity to a tert mutant, telomeres continued to shorten over several generations, ultimately stabilizing at a bimodal size distribution. Telomeres on two chromosome arms were maintained at a length of 1kb, while the remaining telomeres were maintained at 400 bp. The longest telomeres identified in this background were also significantly longer in wild type populations, suggesting cis-acting elements on these arms either promote telomerase processivity or recruitment. Genetically disrupting telomerase processivity in this background resulted in immediate lethality. Thus, telomeres of 400 bp are both necessary and sufficient for Arabidopsis viability. As this length is the estimated minimal length for t-loop formation, our data suggest that telomeres long enough to form a t-loop constitute the minimal functional length.

genetics↗

bioRxiv2018

The Aquilegia genome: adaptive radiation and an extraordinarily polymorphic chromosome with a unique history

The columbine genus Aquilegia is a classic example of an adaptive radiation, involving a wide variety of pollinators and habitats. Here we present the genome assembly of A. coerulea Goldsmith, complemented by high-coverage sequencing data from 10 wild species covering the world-wide distribution. Our analyses reveal extensive allele sharing among species and demonstrate that introgression and selection played a role in the Aquilegia radiation. We also present the remarkable discovery that the evolutionary history of an entire chromosome differs from that of the rest of the genome - a phenomenon which we do not fully understand, but which highlights the need to consider chromosomes in an evolutionary context.

evolutionary biology↗

bioRxiv2017

Diverse genome organization following 13 independent mesopolyploid events in Brassicaceae contrasts with convergent patterns of gene retention

Hybridization and polyploidy followed by genome-wide diploidization significantly impacted the diversification of land plants. The ancient At- whole-genome duplication (WGD) preceded the diversification of crucifers (Brassicaceae). Some genera and tribes also experienced younger, mesopolyploid WGDs concealed by subsequent genome diploidization. Here we tested if multiple base chromosome numbers originated due to genome diploidization after independent mesopolyploid WGDs and how diploidization impacted post-polyploid gene retention. Sixteen species representing ten Brassicaceae tribes were analyzed by comparative chromosome painting and/or whole-transcriptome analysis of gene age distributions and phylogenetic analyses of gene duplications. Overall, we found evidence for at least 13 independent mesopolyploidies followed by different degrees of diploidization across the Brassicaceae. New mesotetraploid events were uncovered for tribes Anastaticeae, Iberideae and Schizopetaleae, and mesohexaploid WGDs for Cochlearieae and Physarieae. In contrast, we found convergent patterns of gene retention and loss among these independent WGDs. Our combined analyses of Brassicaceae genomic data indicate that the extant chromosome number variation in many plant groups, and especially polybasic but monophyletic taxa, can result from clade-specific genome duplications followed by diploidization. Our observation of parallel gene retention and loss across multiple independent WGDs provides one of the first multi-species tests that post-polyploid genome evolution is predictable.\n\nSignificance statementOur data show that multiple base chromosome numbers in some Brassicaceae clades originated due to genome diploidization following multiple independent whole-genome duplications (WGD). The parallel gene retention/loss across independent WGDs and diploidizations provides one of the first tests that post-polyploid genome evolution is predictable.

evolutionary biology↗