Polyploidy: an evolutionary and ecological force in stressful times

Diploidization in a wild rice allopolyploid is both episodic and gradual

Polyploid organisms evolve from their initial doubled genomic condition through a number of processes collectively termed diploidization, whose tempo and mode remain poorly understood mainly due to the difficulty of discriminating de novo evolution subsequent to polyploidy from variation inherited from progenitors. Here, we generated chromosome-scale genome assemblies for the wild rice allopolyploid Oryza minuta and its two diploid progenitors, Oryza punctata and Oryza officinalis, and employed a population genomic approach to investigate the diploidization process in O. minuta at the sequence and transcriptomic level. We show that this wild rice allopolyploid originated around 0.7 Mya, and during subsequent diploidization, its two subgenomes have retained highly conserved synteny with the genomes of its extant diploid progenitors. This populational approach allowed us to distinguish parental legacy of inherited variation from postpolyploidy evolution, and our analyses revealed that whereas gene fractionation occurred in an early burst, accumulation of transposable elements (TEs) and homoeologous exchanges has been gradual. Patterns of homoeolog expression bias are highly variable across tissues, with no consistent subgenome expression bias. Our assessments of the impact of DNA methylation, TE distribution, and parental legacy on expression patterns provide some support for the TE load theory (the theory that the TE densities in flanking regions surrounding genes strongly influence expression levels), while also illustrating the complexity of transcription regulation.

Rapid reprogramming and stabilization of homoeolog expression bias in hexaploid wheat biparental populations

BACKGROUND

Differences in the relative level of expression of homoeologs, known as homoeolog expression bias, are widely observed in allopolyploids. While the evolution of homoeolog expression bias through hybridization has been characterized, on shorter timescales such as those found in crop breeding programs, the extent to which homoeolog expression bias is preserved or altered between generations remains elusive.

RESULTS

Here we use biparental mapping populations of hexaploid wheat (Triticum aestivum) with a common "Paragon" parent to explore the inheritance of homoeolog expression bias in the F5 generation. We found that homoeolog expression bias is inherited for 26-27% of triads in both populations. Most triads conserved a similar homoeolog expression bias pattern as one or both parents. Inherited patterns were largely driven by changes in the expression of one homoeolog, allowing homoeolog expression bias in subsequent generations to match parental expression. Novel patterns of homoeolog expression bias occurred more frequently in the biparental population from a landrace × elite cross, than in the population with two elite parents.

CONCLUSIONS

These results demonstrate that there is significant reprogramming and stabilization of homoeolog expression bias within a small number of generations that differs significantly based on the parental lines used in the crossing.

Haplotype-Resolved Assembly in Polyploid Plants: Methods, Challenges, and Implications for Evolutionary and Breeding Research

Polyploidization has been one of the key drivers of plant evolution, profoundly influencing plant adaptation in nature and crop traits in agriculture. Deciphering polyploid genomes is a crucial step for understanding evolutionary history and advancing agricultural applications. However, the inherent complexity of polyploid genomes has long hindered accurate assembly and annotation. Recent advances in sequencing technologies and improved assembly algorithms have significantly enhanced the resolution of complex polyploid genomes. These innovations have led to the successful assembly and public release of an increasing number of high-quality polyploid plant genomes. This review summarizes the mechanisms of polyploid formation and their evolutionary relevance, with a focus on recent technological progress in sequencing and genome assembly. On this basis, we further discuss the current key challenges of polyploid genome assembly and the ways to address them.

Uncovering the reciprocal effects of plant polyploidy and the microbiome: implications for understanding of polyploid success

Polyploidy plays a major role in diversification and speciation of almost all plants. Separately, the microbiome is recognized for its ubiquitous role in plant functioning. Despite the importance of both processes, we lack a synthetic picture of their reciprocal relationship. I forge this missing linkage by presenting the ways in which plant polyploidy can shape the microbiome and how the microbiome in turn can affect polyploid phenotype and fitness. I illustrate these interactions by drawing on the small, but compelling, set of comparisons of the plant-microbial community interaction with taxa representing different stages of the polyploid continuum and thereby shed light on how the advantages of polyploidy may be influenced by microbes. I use findings from a range of studies to build the case for plant-microbiome reciprocal interactions in both key pathways for polyploid persistence: overcoming their minority cytotype disadvantage and increasing competitive ability and/or niche shifts relative to diploids. I put forward how the microbiome likely plays a role in polyploid stress tolerance, abiotic niche breadth, range limits and coexistence. I conclude by identifying the research needed to test these hypotheses and how doing so could transform our understanding of polyploidy as a driver of plant ecology and evolution.

Origin of Polyploidy, Phylogenetic Relationships, and Biogeography of Botiid Fishes (Teleostei: Cypriniformes)

Botiidae is a small family of freshwater fishes distributed across Southeast Asia, South Asia, and East Asia. It comprises two subfamilies: the diploid Leptobotiinae and the tetraploid Botiinae. Whether species in the Botiinae are autotetraploids or allotetraploids and how many polyploidization events occurred during the evolution of this subfamily remain open questions. The phylogenetic relationships and biogeography of the Botiidae also require further investigation. In the current study, we compared phylogenetic trees constructed using DNA sequences from the mitochondrial genome and five phased nuclear genes. We also performed whole genome sequencing for two tetraploid species: Chromobotia macracanthus and Yasuhikotakia modesta. Genome profiling of five botiine species suggests that they are likely of allotetraploid origin. Nuclear gene tree topologies indicate that the tetraploidization of the Botiinae occurred only once in the common ancestor of this subfamily. Although the possible maternal progenitor and paternal progenitor of the Botiinae cannot be determined, the subfamily Leptobotiinae can be excluded as a progenitor. The gene trees built in this study generally agree on the following sister group relationships: Leptobotiinae/Botiinae, Leptobotia/Parabotia, Chromobotia/Botia, Yasuhikotakia/Syncrossus, and Sinibotia/Ambastaia. Clades formed by the last two generic pairs are also sisters to each other. Timetree analyses and ancestral range reconstruction suggest that the family Botiidae might have originated in East Asia and Mainland Southeast Asia approximately 51 million years ago and later dispersed to South Asia and the islands of Southeast Asia.

Occurrence of aneuploidy across the range of coast redwood (Sequoia sempervirens)

Aneuploidy, a condition characterized by an abnormal number of chromosomes, can have significant consequences for fitness of an organism, often manifesting in reduced fertility and other developmental challenges. In plants, aneuploidy is particularly complex to study, especially in polyploid species such as coast redwood (Sequoia sempervirens (D. Don) Endl.), which is a hexaploid conifer (2n=6×=66). This study leverages a novel Markov Chain Monte Carlo method based on sequence depth to investigate the occurrence of aneuploidy across the range of coast redwood. We show that aneuploidy, defined here as a whole-chromosome gain or loss, is prevalent in second-growth redwoods, predominantly as additional chromosomes, while vegetatively propagated plants frequently experience chromosome loss. Although our study does not directly assess the fitness of aneuploids, the frequency of chromosomal instability observed in vegetatively propagated plants compared to second-growth and old-growth trees raises questions about their long-term developmental viability and potential to become established trees. These findings have significant implications for redwood conservation and restoration strategies, especially as methods such as tissue culture propagation becomes the primary mode of producing nursery stock plants used in reforestation.

Centromere-size reduction and chromatin state dynamics following intergenomic hybridization in cotton

Centromeres are pivotal for accurate chromosome segregation, yet their regulation and evolutionary dynamics remain poorly understood. Here, we investigate centromeres of the diploid species Gossypium anomalum (Ga, B-genome) that were transferred into tetraploid cotton G. hirsutum (Gh, AD-genome) as either an additional or integrated chromosome, as well as in synthetic allohexaploid (AABBDD) lines. We demonstrate consistent size reduction for all Ga centromeres in the Gh background. Histone modification profiling across 10 marks revealed heightened levels of both active and repressive chromatin marks within the Ga centromeres when transferred into the Gh background, particularly for H3K36me2. The centromeric histone modification perturbation extended into pericentromeric regions, with variable CENH3-binding domains consistently exhibiting a more pronounced increase in histone modification levels compared to stable centromere regions, highlighting the role of histone modification elevation in centromere dynamics. In addition, we observed enhanced chromatin accessibility and the presence of non-B-form DNA motifs, such as A-phased DNA repeats within stable centromere domains that are correlated with centromere stability. Hi-C analysis reveals a reorganized 3D chromatin architecture within the introgression line centromeres, including the formation of new topologically associating domains linked to H3K36me2 dynamics, emphasizing the importance of H3K36me2 in centromere organization. Together, these findings elucidate epigenetic mechanisms underlying centromere composition following intergenomic hybridization and allopolyploid formation, offering insights into centromere evolution in plants and its myriad epigenetic and potentially functional dimensions.

Epigenetic modification brings new opportunities for gene capture by transposable elements in allopolyploid Brassica napus

Polyploids are widespread in plants and are important drivers for evolution and biodiversity. Allopolyploidy activates transposable elements (TEs) and causes genomic shock. Plant genomes can regulate gene expression by changing the epigenetic modification of TEs, but the mechanism for TEs to capture genes remains to be explored. Helitron TEs used the 'peel-and-paste' mechanism to achieve gene capture. We identified 3156 capture events and 326 donor genes of Helitron TEs in Brassica napus (AnAnCnCn). The donor genes captured by TEs were related to the number, length, and location of their exons. The gene-capturing TEs carrying donor gene fragments were evenly distributed on the genome, and more than half of them were involved in the construction of pseudogenes, becoming the reserve force for polyploid evolution. Gene fragment copies enhanced information storage, providing opportunities for gene mutation and the formation of new genes. Simultaneously, the siRNAs targeting TEs may act on the donor genes due to siRNA crosstalk, and the gene methylation levels increased and the expression levels decreased. The genome sought a balance between sacrificing donor gene expression and silencing TEs, allowing TEs to hide in the genome. In addition, epigenetic modifications may temporarily relax the control of gene capture during allopolyploidization. Our study identified and characterized gene capture events in B. napus, analyzed the effects of DNA methylation and siRNA on gene capture events, and explored the regulation mechanism of gene expression by TE epigenetic modification during allopolyploidization, which will contribute to understanding the formation and evolution mechanism of allopolyploidy.

Comparison of the morphological and physiological characteristics of diploid and tetraploid Luculia pinceana Hook

BACKGROUND

To explore the physiological and biochemical differences between different ploidy Luculia pinceana Hook. varieties and to obtain germplasm resources with excellent horticultural characteristics and strong resistance, we analysed and compared the morphological characteristics, photosynthetic properties, and physiological indices of diploid and tetraploid L. pinceana.

RESULTS

(1) Tetraploid L. pinceana exhibited distinct polyploid characteristics, including a smaller plant, rounder, thicker, and darker green leaves, as well as coarser and longer leaf and stem hairs. Moreover, the flowers of tetraploids are relatively large, and the diameters of the flowers, the lengths of the corolla tubes and the lengths of the pistils are all extremely significantly greater than those of diploids. Compared with those of tetraploids, the leaf width and thickness of the diploid plants increased by 16.38% and 14.71%, respectively, whereas the leaf length, leaf area, and plant height decreased by 21.20%, 3.46%, and 54.86%, respectively. (2) The diurnal variation curve of photosynthesis in L. pinceana was unimodal, reaching a maximum value at approximately 10:00. Compared with diploid plants, tetraploid plants presented a significantly greater maximum net photosynthetic rate (Pmax), light saturation point (LSP), and light compensation point (LCP). (3) Compared with diploids, tetraploid leaves presented significantly greater activities of antioxidant enzymes, including superoxide dismutase (SOD, + 51.61%), peroxidase (POD, + 6226%), and catalase (CAT, + 211.66%). Additionally, the concentrations of osmolytes [soluble sugar (SS, + 80.11%), soluble protein (SP, + 63.49%), and proline (Pro, + 57.40%)] were markedly elevated. Conversely, the malondialdehyde (MDA) content was substantially decreased (-46.16%).

CONCLUSION

These results demonstrate that the tetraploid L. pinceana has greater ornamental value, fertility and resistance. It is an excellent breeding material for the germplasm resources of L. pinceana and provides a material basis for the cultivation of new varieties of L. pinceana.

Polyploidy in potatoes: challenges and possibilities for climate resilience

Solanum section Petota Dumort. consists of tuber-bearing species (i.e., the cultivated potatoes and their wild relatives) that have both asexual and sexual propagation, variation in ploidy, and reproductive isolation. These species have undergone adaptation to a diversity of climates, altitudes, photoperiods, and geographical range. The section defies characterization with the biological species concept due to interspecies hybridization, allo- and auto-polyploidy, and phenotypic plasticity. Genetic studies, and more recently genome sequencing and pangenome analyses, are fostering a greater understanding of genetic processes that shape genome evolution and speciation in the section, shedding light on the phylogeny and providing insights on utilization of potato crop wild relatives in breeding for climate-resilient potato varieties.

A chromosome-level genome assembly of the varied leaved jewelflower, Streptanthus diversifolius, reveals a recent whole genome duplication

The Streptanthoid complex, a clade of primarily Streptanthus and Caulanthus species in the Thelypodieae (Brassicaceae) is an emerging model system for ecological and evolutionary studies. This complex spans the full range of the California Floristic Province including desert, foothill, and mountain environments. The ability of these related species to radiate into dramatically different environments makes them a desirable study subject for exploring how plant species expand their ranges and adapt to new environments over time. Ecological and evolutionary studies for this complex have revealed fascinating variation in serpentine soil adaptation, defense compounds, germination, flowering, and life history strategies. Until now a lack of publicly available genome assemblies has hindered the ability to relate these phenotypic observations to their underlying genetic and molecular mechanisms. To help remedy this situation, we present here a chromosome-level genome assembly and annotation of Streptanthus diversifolius, a member of the Streptanthoid Complex, developed using Illumina, Hi-C, and HiFi sequencing technologies. Construction of this assembly also provides further evidence to support the previously reported recent whole genome duplication unique to the Thelypodieae. This whole genome duplication may have provided individuals in the Streptanthoid Complex the genetic arsenal to rapidly radiate throughout the California Floristic Province and to occupy commonly inhospitable environments including serpentine soils.

Genome-wide identification and unveiling the role of MAP kinase cascade genes involved in sugarcane response to abiotic stressors

BACKGROUND

The MAP Kinase cascade system is a conserved signaling mechanism essential for plant development, growth, and stress tolerance. Thus far, genes from the MAPK cascade have been identified in several plant species but remain uncharacterized in the polyploid Saccharum spp. Hybrid R570 genome.

RESULTS

This study identified 89 ScMAPK, 24 ScMAPKK, and 107 ScMAPKKK genes through genome-wide analysis. Phylogenetic classification revealed that four subgroups were present in each ScMAPK and ScMAPKK family, and three sub-families (ZIK-like, RAF-like, and MEKK-like) presented in the ScMAPKKK family. Conserved motif and gene structure analysis supported the evolutionary relationships of the three families inferred from the phylogenetic analysis. All of the ScMAPK, ScMAPKK and ScMAPKKK genes were mapped on four scaffolds (Scaffold_88/89/91/92) and nine chromosomes (1-8, 10). Collinearity and gene duplication analysis identified 169 pairs of allelic and non-allelic segmentally duplicated MAPK cascade genes, contributing to their expansion. Additionally, 13 putative 'ss-miRNAs' were predicted to target 87 MAPK cascade genes, with 'ssp-miR168a' alone regulating 45 genes. qRT-PCR analysis revealed differential gene expression under abiotic stressors. ScMAPK07, ScMAPK66, and ScRAF43 were down-regulated and acted as negative regulators. Conversely, ScMAPKK13, ScRAF10, and ScZIK18 were up-regulated at specific time points under drought, with ScZIK18 exhibiting strong defense. Under NaCl stress, most genes were down-regulated, except for slight increases in ScZIK18 and ScMAPKK13, suggesting a positive role in salt stress response. Under CaCl2 stress, five genes were significantly down-regulated, while ScRAF43 remained unchanged, reflecting their negative roles in stress adaptation and resource conservation.

CONCLUSION

This study provides insights into MAPK cascade gene evolution and function in sugarcane, highlighting distinct regulatory roles in abiotic stress responses. Interestingly, some genes acted as negative regulators, serving as a mechanism to balance stress responses and prevent overactivation. In contrast, others contributed to defense mechanisms, offering potential targets for stress resilience improvement.

CLINICAL TRAIL NUMBER

This study contains no clinical trials. Not applicable.

Nanoparticles alter the nature and strength of intraploidy and interploidy interactions in plants

Engineered nanoparticles have profound impacts on organisms, yet there is limited understanding of how nanoparticle exposure shapes species interactions that are key to natural community dynamics. By growing plants of the same (intraploidy) and different ploidy levels (interploidy) of Fragaria in axenic microcosms, we examined the influence of nanoparticles on species interactions in polyploid and diploid plants. Under copper oxide (CuO) nanoparticle exposure, polyploids experienced reduced competition and a shift towards facilitation, when growing with both polyploids (the effect of polyploids on polyploids measured by the relative interaction index, RII8x,8x) and diploids (the effect of diploids on polyploids, RII8x,2x). This reduction in competitive interactions in polyploids, in line with the stress gradient hypothesis, was primarily driven by nanoscale effects. In contrast, the strength of competitive interactions (RII8x,8× and RII8x,2x) increased under CuO bulk particles compared to control conditions. Different from polyploids, diploids experienced neutral interactions (RII2x,2x and RII2x,8x) under both nanoparticles and bulk particles. These findings highlight ploidy-specific interaction dynamics and the need to consider species interactions when predicting organismal responses to nanoparticle pollution in ecological communities, providing critical insights for conservation strategies and sustainable nanotechnology applications.

Dynamics of Mixed-Ploidy Populations under Demographic and Environmental Stochasticities

AbstractThe population dynamics of autopolyploids-organisms with more than two genome copies of a single species-and their diploid progenitors have been extensively studied. The acquisition of multiple genome copies is heavily influenced by stochasticity, which strongly suggests the efficacy of a probabilistic approach to examine the long-term dynamics of a population with multiple cytotypes. Yet our current understanding of the dynamics of autopolyploid populations has not incorporated stochastic population dynamics and coexistence theory. To investigate the factors contributing to the probability and stability of coexisting cytotypes, we designed a new population dynamics model that incorporates demographic and environmental stochasticities to simulate the formation, establishment, and persistence of diploids, triploids, and autotetraploids in the face of gene flow among cytotypes. We found that increased selfing rates and pronounced reproductive isolation promote coexistence of multiple cytotypes. In stressful environments and with strong competitive effects among cytotypes, these dynamics are more complex; our stochastic modeling approach reveals the resulting intricacies that give autotetraploids competitive advantage over their diploid progenitors. Our work is foundational for a better understanding of the dynamics of coexistence of multiple cytotypes.

The ecology of polyploid establishment and exclusion, with implications for polyploid biogeography

The relationship between polyploid formation, triploid fitness and plant reproduction has been studied for over a century, and uniparental reproduction has long been recognized to play a crucial role in polyploid establishment. Yet, we lack a synthesized framework of how polyploid establishment is expected to be influenced by different reproductive modes among angiosperms. Here, we provide new perspectives on how uniparental reproduction, pollination ecology, triploid fitness and assortative mating can impact minority cytotype exclusion (MCE) and, thereby, the likelihood of polyploid establishment. We review the current state of knowledge of the reproductive mechanisms that impact polyploid establishment and discuss often overlooked aspects of these processes, such as the influence of pollinator communities on rates of self-pollination. We propose a framework for considering how variation in reproductive strategies and pollinator communities can impact the ability of a polyploid to overcome MCE. Finally, we propose links between patterns of variation in uniparental reproduction across plant communities and observed patterns in the distribution and abundance of polyploids.

Polyploidization leads to salt stress resilience via ethylene signaling in citrus plants

Polyploidization is a common occurrence in the evolutionary history of flowering plants, significantly contributing to their adaptability and diversity. However, the molecular mechanisms behind these adaptive advantages are not well understood. Through comprehensive phenotyping of diploid and tetraploid clones from Citrus and Poncirus genera, we discovered that genome doubling significantly enhances salt stress resilience. Epigenetic and transcriptomic analyses revealed that increased ethylene production in the roots of tetraploid plants was associated with hypomethylation and enhanced chromatin accessibility of the ACO1 gene. This increased ethylene production activates the transcription of reactive oxygen species scavenging genes and stress-related hormone biosynthesis genes. Consequently, tetraploid plants exhibited superior root functionality under salt stress, maintaining improved cytosolic K+/Na+ homeostasis. To genetically validate the link between salt stress resilience and ACO1 expression, we generated overexpression and knockout lines, confirming the central role of ACO1 expression regulation following genome doubling in salt stress resilience. Our work elucidates the molecular mechanisms underlying the role of genome doubling in stress resilience. We also highlight the importance of chromatin dynamics in fine-tuning ethylene gene expression and activating salt stress resilience pathways, offering valuable insights into plant adaptation and crop genome evolution.

The C24-methyl/ethyl sterol ratio is increased by Rhizophagus irregularis colonization

Plant-microorganism interactions underlie many ecosystem roles, in particular the enhancement of plant nutrition through mutualistic relationships, such as the arbuscular mycorrhizal symbiosis that affects a large proportion of land plants. The establishment of this interaction induces a wide range of signaling pathways in which lipids, and particularly sterols, may play a central role. However, their supported functions are poorly known. We performed a study on eleven model plants (banana, barrelclover, flax, grapevine, maize, pea, poplar, potato, rice, sorghum and tomato) to measure the sterol content and characterize the sterol composition of roots that were either non-colonized or colonized by the arbuscular mycorrhizal fungal model Rhizophagus irregularis DAOM197198. Our results reveal a systematic increase in the content of C24-methyl sterols in crude extracts of colonized roots as compared to non-colonized roots. In addition, the transcripts of SMT1 and SMT2 (which encode enzymes that produce C24-methyl and C24-ethyl sterols, respectively) were differentially accumulated in colonized plant roots. No common regulation pattern was observed among plants. The phylogenetic relationship of members of the SMT1 and SMT2 families in more than 100 fully sequenced genomes of plants, ferns, mosses, algae and fungi has allowed the identification of unambiguous clades. Our results therefore highlight a conserved arbuscular mycorrhizal symbiosis-dependent regulation of the root sterol composition in angiosperms, with some plant specificities.

Morphological and metabolic changes in Changshan Huyou (Citrus changshan-huyou) following natural tetraploidization

BACKGROUND

Polyploids in citrus are generally used to improve crop varieties. Changshan Huyou (Citrus changshan-huyou) is a native citrus species in China that is highly adaptable and has pharmaceutical value. However, the influence in Changshan Huyou following polyploidization remains unclear. Here we evaluated the adult tetraploid scions of Changshan Huyou with contemporary diploid scions as the control in the phenotypic variations, metabolic alterations of fruits and associated transcriptomic changes.

RESULT

The tetraploid scions had rounder and thicker leaves, larger floral organs and fruits, and satisfactory viability of pollen grains and ovules. The tetraploid fruits accumulated lower levels of soluble solids but similar levels of organic acids. Metabolic profiling of three tissues of fruits revealed that most of 2064 differentially accumulated metabolites (DAMs), including flavonoids, lignans, and coumarins, were downregulated. In contrast, the upregulated DAMs mainly included alkaloids (clausine K and 2-(1-pentenyl)quinoline), amino acids (L-asparagine and L-ornithine), and terpenoids (deacetylnomilin and evodol) in tetraploid peels, as well as, flavonoids (neohesperidin and quercetin-5-O-β-D-glucoside) and organic acids (2-methylsuccinic acid and dimethylmalonic acid) in juice sacs. The upregulated genes were associated with phenylpropanoid biosynthesis, secondary metabolite biosynthesis, and the biosynthesis of various alkaloid pathways. Pearson Correlation Analysis showed that the upregulated genes encoding PEROXIDASE and CYTOCHROME P450 (CYP450) were closely related to the higher accumulation of amino acids and alkaloids in tetraploid peels, and up-regulated neohesperidin and quercetin glucoside were positively associated with FERULATE-5-HYDROXYLASE (F5H), CYP450 81Q32, FLAVONOID 3'-MONOOXYGENASE (F3'H), 4-COUMARATE-CoA LIGASE 1 (4CL1), and UDP-GLUCOSE FLAVONOID 3-O-GLUCOSYLTRANSFERASE (UFOG), as well as, some transcription factors in tetraploid juice sacs.

CONCLUSION

The tetraploid Changshan Huyou investigated here may be used in triploids breeding to produce seedless citrus, and for fruit processing on pharmaceutical purpose due to the alteration of metabolites following polyploidization.

Ancient large-scale gene duplications and diversification in bryophytes illuminate the plant terrestrialization

Large-scale gene duplications (LSGDs) are crucial for evolutionary adaptation and recurrent in vascular plants. However, the role of ancient LSGDs in the terrestrialization and diversification of bryophytes, the second most species-rich group of land plants, remains largely elusive due to limited sampling in bryophytes. Employing the most extensive nuclear gene dataset in bryophytes to date, we reconstructed a time-calibrated phylogenetic tree from 209 species, covering virtually all key bryophyte lineages, for phylogenomic analyses of LSGDs and diversification. We newly identified two ancient LSGDs: one in the most recent common ancestor (MRCA) of extant bryophytes and another in the MRCA of the majority of Jungermanniales s. lato. Duplicated genes from these two LSGDs show significant enrichment in photosynthesis-related processes and structures. Rhizoid-responsive ROOTHAIR DEFECTIVE SIX-LIKE (RSL) genes from ancient LSGDs are present in rhizoidless bryophytes, challenging assumptions about rhizoid absence mechanisms. We highlighted four major diversification rate upshifts, two of which slightly postdated LSGDs, potentially linked to the flourishing of gymnosperms and angiosperms and explaining over 80% of bryophyte diversity. Our findings, supported by extensive bryophyte sampling, highlight the significance of LSGDs in the early terrestrialization and diversification of bryophytes, offering new insights into land plant evolution.

Genome duplication in a long-term multicellularity evolution experiment

Whole-genome duplication (WGD) is widespread across eukaryotes and can promote adaptive evolution1-4. However, given the instability of newly formed polyploid genomes5-7, understanding how WGDs arise in a population, persist, and underpin adaptations remains a challenge. Here, using our ongoing Multicellularity Long Term Evolution Experiment (MuLTEE)8, we show that diploid snowflake yeast (Saccharomyces cerevisiae) under selection for larger multicellular size rapidly evolve to be tetraploid. From their origin within the first 50 days of the experiment, tetraploids persisted for the next 950 days (nearly 5,000 generations, the current leading edge of our experiment) in 10 replicate populations, despite being genomically unstable. Using synthetic reconstruction, biophysical modelling and counter-selection, we found that tetraploidy evolved because it confers immediate fitness benefits under this selection, by producing larger, longer cells that yield larger clusters. The same selective benefit also maintained tetraploidy over long evolutionary timescales, inhibiting the reversion to diploidy that is typically seen in laboratory evolution experiments. Once established, tetraploidy facilitated novel genetic routes for adaptation, having a key role in the evolution of macroscopic multicellular size via the origin of evolutionarily conserved aneuploidy. These results provide unique empirical insights into the evolutionary dynamics and impacts of WGD, showing how it can initially arise due to its immediate adaptive benefits, be maintained by selection and fuel long-term innovations by creating additional dimensions of heritable genetic variation.

Mobility of four structural regions drives isoform-specific properties of photoenzyme LPOR in plants

Light-dependent protochlorophyllide oxidoreductase (LPOR) is a photocatalytic enzyme in the chlorophyll biosynthetic pathway that underwent duplications in angiosperms, resulting in the emergence of multiple isoforms across various plant species. The physiological roles of these LPOR homologs remained unclear, so we selected six plant species with different number of isoforms of the enzyme, having diverse phylogenetic backgrounds, and characterized their properties in vitro. Our findings revealed that these isoforms vary in their affinity for the reaction product, chlorophyllide (Chlide), as well as for NADPH under lipid-free conditions and in reaction mixtures supplemented with plant lipids. Additionally, we observed differences in their oligomerization behavior. Our experimental approach generated a dataset comprising several hundred pairs of spectra, recorded before and after reaction-triggering illumination. This data was used to analyze the correlation between fluorescence emission maxima before and after photoconversion. The analysis showed that some isoforms rapidly release Chlide after the reaction, while others retain the pigment in the binding pocket, especially at high NADPH concentrations. These results suggest that LPOR isoforms differ in their rates of Chlide release and complex disassembly, potentially influencing the overall rate of the chlorophyll biosynthetic pathway, even in mature leaves. We further analyzed the flexibility of these isoforms using AlphaFold2 predictions, identifying four regions of the enzyme that are particularly mobile. Two of these regions are involved in pigment binding, while the other two play a role in oligomerization. Based on these findings, we propose a model of conformational changes that drive the formation of LPOR oligomers.

Polyploidy drives changes in tissue allocation modifying whole-plant water relations

Polyploid plants often display functional trait values distinct from those of diploids, influencing their stress tolerance and adaptive capacity. These differences shape how polyploids interact with their environment, a factor that is crucial to their evolutionary success. Here, we investigated the species complex Dianthus broteri, where ploidy level is known to correlate with water availability, as a model system to understand the possible link between ploidy and whole-plant water relations. We quantified allocation between leaves, xylem, and roots in 4 different ploidies of D. broteri (2×, 4×, 6×, 12×), and examined its relationship with hydraulic efficiency (Kr-s), water potential regulation, and stomatal conductance (gc) in response to varying leaf-to-air vapor pressure deficits (VPDL). A gradient in tissue allocation with increasing ploidy led to contrasting water-use strategies within D. broteri. Higher ploidy was associated with greater allocation to roots and xylem, resulting in higher Kr-s and gc and lower water potential gradients. Despite these differences, gc responses to VPDL were largely consistent across ploidies. In D. broteri 12×, the significant investment in water uptake and transport without a proportional increase in leaf area appeared suboptimal, incurring high xylem costs per unit water transport. However, this trade-off also led to increased water uptake and transport efficiency, potentially advantageous under water-limited conditions. Overall, our results indicate that multiple rounds of genome duplication cause substantial changes in whole-plant water relations, likely impacting water stress exposure in the field.

On the way to diploidization and unexpected ploidy in the grass Sporobolus section Spartina mesopolyploids

Plant history is characterized by cyclical whole genome duplication and diploidization with important biological and ecological consequences. Here, we explore the genome history of two related iconic polyploid grasses (Sporobolus alterniflorus and S. maritimus), involved in a well-known example of neopolyploid speciation. We report particular genome dynamics where an ancestral Sporobolus genome (n = 2x = 20) duplicated 9.6-24.4 million years ago (MYA), which was followed by descending dysploidy resulting in a genome with an unexpected base chromosome number (n = 15). This diploidized genome duplicated again 2.1-6.2 MYA to form a tetraploid lineage (2n = 4x = 60), thus reshuffling the ploidy of these species previously thought hexaploids. We also elucidate the mechanism accompanying the speciation between S. maritimus (2n = 60) and S. alterniflorus (2n = 62), resulting from chromosome restructuring, and identify key adaptive genes in the corresponding regions. This represents critical findings to decipher molecular mechanisms underlying species expansion, adaptation to environmental challenge and invasiveness.

Polyploidy linked with species richness but not diversification rates or niche breadth in Australian Pomaderreae (Rhamnaceae)

BACKGROUND AND AIMS

Polyploidy is an important evolutionary driver for plants and has been linked with higher species richness and increases in diversification rate. These correlations between ploidy and plant radiations could be the result of polyploid lineages exploiting broader niche space and novel niches due to their enhanced adaptability. The evolution of ploidy and its link to plant diversification across the Australian continent is not well understood. Here, we focus on the ploidy evolution of the Australasian Rhamnaceae tribe Pomaderreae.

METHODS

We generated a densely sampled phylogeny (90 %, 215/240 species) of the tribe and used it to test for the evolution of ploidy. We obtained 30 orthologous nuclear loci per sample and dated the phylogeny using treePL. Ploidy estimates for each sequenced species were obtained using nQuire, based on phased sequence data. We used MiSSE to obtain tip diversification rates and tested for significant relationships between diversification rates and ploidy. We also assessed for relationships between ploidy level and niche breadth, using distributional records, species distributional modelling and WorldClim data.

KEY RESULTS

Polyploidy is extensive across the tribe, with almost half (45 %) of species and the majority of genera exhibiting this trait. We found a significant positive relationship between polyploidy and genus size (i.e. species richness), but a non-significant positive relationship between polyploidy and diversification rates. Polyploidy did not result in significantly wider niche space occupancy for Pomaderreae; however, polyploidy did allow transitions into novel wetter niches. Spatially, eastern Australia is the diversification hotspot for Pomaderreae in contrast to the species hotspot of south-west Western Australia.

CONCLUSIONS

The relationship between polyploidy and diversification is complex. Ancient polyploidization events likely played an important role in the diversification of species-rich genera. A lag time effect may explain the uncoupling of tip diversification rates and polyploidy of extant lineages. Further studies on other groups are required to validate these hypotheses.

Chromosome number variation and phylogenetic divergence of East Asian Cirsium sect. Onotrophe subsect. Nipponocirsium (Compositae), with a new species from Taiwan

BACKGROUND

This study explored chromosome number variation, phylogenetic divergence, and mechanisms underlying speciation in East Asian thistle Cirsium Mill. sect. Onotrophe (Cass.) DC. subsect. Nipponocirsium Kitam. (Compositae). The study focused on the newly identified species from Taiwan: Cirsium pengii Y.H. Tseng, P.C. Liao & Chih Y. Chang. Utilizing phylotranscriptomic data to reconstruct evolutionary relationships between the Taiwanese and Japanese taxa of Cirsium subsect. Nipponocirsium as well as their divergence times and chromosomal characteristics. Additionally, the chromosome number, morphology, and pollen morphology of the unknown Cirsium taxon are compared with other known subsect. Nipponocirsium taxa from Taiwan.

RESULTS

Phylotranscriptomic analysis reveals a division within subsect. Nipponocirsium into Japanese and Taiwanese clades. In the Taiwanese clade, C. pengii is basal, while C. tatakaense remains monophyletic with other Taiwanese species despite higher genetic diversity. The prevalent chromosome number in this subsection is tetraploid (2n = 4x = 68), common in Japanese taxa, while Taiwanese members have 2n = 4x = 64. Notably, C. pengii has a diploid number (2n = 32), indicating descending dysploidy followed by polyploidization in Taiwan. This polyploidization, driven by glaciations, likely shaped the evolution of Nipponocirsium. Divergence time estimates suggest the separation of Japanese and Taiwanese clades around 0.74 million years ago (Myr) during glacial periods. Cirsium pengii diverged around 0.47 Myr, while tetraploid species C. kawakamii and C. tatakaense diverged around 0.35 Myr. These species likely evolved in separate refugia, with distinct species boundaries confirmed through species delimitation analysis, karyotype, morphology, and pollen morphology comparisons.

CONCLUSIONS

These findings enhance our understanding of chromosomal evolution and speciation within subsect. Nipponocirsium and underscore the importance of integrating transcriptomic data in phylogenetic studies. This study provides a comprehensive framework for further investigations into the genetic diversity and adaptive mechanisms of this ecologically vital group.

Convergent evolution in angiosperms adapted to cold climates

Convergent and parallel evolution occur more frequently than previously thought. Here, we focus on the evolutionary adaptations of angiosperms at sub-zero temperatures. We begin by introducing the history of research on convergent and parallel evolution, defining all independent similarities as convergent evolution. Our analysis reveals that frost zones (periodic or constant), which cover 49.1% of Earth's land surface, host 137 angiosperm families, with over 90% of their species thriving in these regions. In this context, we revisit the global biogeography and evolutionary trajectories of plant traits, such as herbaceous form and deciduous leaves, that are thought to be evasion strategies for frost adaptation. At the physiological and molecular levels, many angiosperms have independently evolved cold acclimation mechanisms through multiple pathways in addition to the well-characterized C-repeat binding factor/dehydration-responsive element binding protein 1 (CBF/DREB1) regulatory pathway. These convergent adaptations have occurred across various molecular levels, including amino acid substitutions and changes in gene duplication and expression within the same or similar functional pathways; however, identical amino acid changes are rare. Our results also highlight the prevalence of polyploidy in frost zones and the occurrence of paleopolyploidization events during global cooling. These patterns suggest repeated evolution in cold climates. Finally, we discuss plant domestication and predict climate zone shifts due to global warming and their effects on plant migration and in situ adaptation. Overall, the integration of ecological and molecular perspectives is essential for understanding and forecasting plant responses to climate change.

Tetraploidization Altered Phenotypic Traits and Metabolite Profile of Java Ginseng (Talinum paniculatum (Jacq.) Gaertn.)

Polyploidization is a beneficial technique for enhancing the biomass of and secondary metabolite concentrations in plants. Java ginseng (Talinum paniculatum (Jacq.) Gaertn.) can be used as an alternative source of nutrition and has both ornamental and medicinal value. To improve the biomass and content of medicinal ingredients, this study established an in vitro system that was used to induce polyploidy of java ginseng. Tetraploids were successfully produced by exposing the axillary buds to colchicine. The most favorable medium for inducing polyploidy was Murashige and Skoog medium devoid of hormonal substances, while immersing stem segments in a solution of 1-3 mg/mL colchicine for 48 h could achieve tetraploidy induction with a maximum rate of 18.03%. Tetraploids were distinguished from diploids by flow cytometry, with the tetraploids exhibiting darker and thicker leaves, bigger fruit and pollen, and larger stomata but lower stomatal density, while the aboveground biomass yield was reduced significantly compared with that of the diploids. Tetraploidization also altered the metabolite profile, with 22 metabolite concentrations being significantly increased (p < 0.05) and 74 metabolite concentrations being significantly decreased (p < 0.05) in the leaves of the tetraploids. The autotetraploid produced in this study could provide novel insights into artificial polyploid breeding and could be utilized as a germplasm to generate new polyploids.

Genotyping-by-sequencing derived SNP markers reveal genetic diversity and population structure of Dactylis glomerata germplasm

Orchardgrass (Dactylis glomerata L.), a widely cultivated cool-season perennial, is an important forage crop due to its adaptability, high nutritional value, and substantial biomass. Understanding its genetic diversity and population structure is crucial for developing resilient cultivars that can withstand climate change, diseases, and resource limitations. Despite its global significance in fodder production, the genetic potential of many regional accessions remains unexplored, limiting breeding efforts. This study investigates the genetic diversity (GD) and population structure of 91 accessions of D. glomerata from Turkey and Iran using genotyping-by-sequencing based single nucleotide polymorphism (SNP) markers. A total of 2913 high-quality SNP markers revealed substantial genetic variability across provinces. Notably, accessions from Erzurum exhibited the highest GD (mean GD: 0.26; He: 0.5328), while provinces such as Bursa and Muğla demonstrated lower GD (mean GD: 0.15; He < 0.22), suggesting potential genetic bottlenecks. Population structure analysis using Bayesian clustering, PCoA and UPGMA dendrograms divided the accessions into three distinct clusters, with cluster membership largely reflecting geographical origins, and dry biomass content. Cluster II revealed higher GD, associated with enhanced biomass production (128 g/plant), the most important agronomic trait in forage species, supporting the notion of heterosis in breeding programs. The majority of the genetic variation (85.8%) was observed within clusters, with minimal differentiation among clusters (FST = 0.007). Genome-wide association studies (GWAS) identified significant marker-trait associations for dry biomass weight, a critical agronomic trait, with markers DArT-100715788, DArT-101043591, and DArT-101171265 and DArT-101090822 located on Chromosomes 1, 6, and 7 respectively. These findings highlight the importance of regional diversity for maintaining adaptive potential in future breeding programs.

Local endoreduplication of the host is a conserved process during Phytomyxea-host interaction

Background

Endoreduplication, a modified cell cycle, involves cells duplicating DNA without undergoing mitosis. This phenomenon is frequently observed in plants, algae, and animals. Biotrophic pathogens have been demonstrated to induce endoreduplication in plants to secure more space or nutrients.

Methods

In this study, we investigated the endoreduplication process triggered by two phylogenetically distant Rhizaria organisms-Maullinia spp. (in brown algae) and Plasmodiophora brassicae (in plants)-by combining fluorescent in situ hybridization (FISH) with nuclear area measurements.

Results

We could confirm that Plasmodiophora brassicae (Plasmodiophorida) triggers endoreduplication in infected plants. For the first time, we also demonstrated pathogen-induced endoreduplication in brown algae infected with Maullinia ectocarpii and Maullinia braseltonii (Phagomyxida). We identified molecular signatures of endoreduplication in RNA-seq datasets of P. brassicae-infected Brassica oleracea and M. ectocarpii-infected Ectocarpus siliculosus.

Discussion

Cell cycle switch proteins such as CCS52A1 and B in plants, CCS52 in algae, and the protein kinase WEE1 in plants were upregulated in RNA-seq datasets hinting at a potential role in the phytomyxean-induced transition from mitotic cell cycle to endocycle. By demonstrating the consistent induction of endoreduplication in hosts during phytomyxid infections, our study expands our understanding of Phytomyxea-host interaction. The induction of this cellular mechanism by phytomyxid parasites in phylogenetically distant hosts further emphasizes the importance of endoreduplication in these biotrophic interactions.

Every Gain Comes With Loss: Ecological and Physiological Shifts Associated With Polyploidization in a Pygmy Frog

Polyploidization plays a pivotal role in vertebrate evolution and diversification. However, the effects of polyploidization on animals across various biological levels, and how these differences drive ecological shifts, remain unclear. Through karyotype analysis and whole-genome sequencing, we identified an autotetraploid Microhyla fissipes from Hainan Island, which shows reproductive isolation and geographic differentiation from its diploid counterpart. Tetraploids exhibited larger cell size, improved tadpole growth rates, and greater whole-body size, along with reduced cell cycle activity. Rather than being simple scaled-up diploids, tetraploids showed shifts in physiological performance, organ allometry, gene expression profiles, and metabolic patterns. Tetraploid adults demonstrated superior jumping ability and increased reproductive investment (e.g. larger gonads and steeper slopes in the relationship between gonadal weight and body weight), suggesting a potential competitive advantage over diploids. However, tetraploids exhibited higher energy expenditure at elevated temperatures, reduced hepatic energy storage, and altered pulmonary regulatory metabolites at 25 °C. Males had smaller relative heart sizes, and females showed flatter slopes in the relationship between heart and lung weight and body weight, indicating reduced investment in cardiopulmonary system. These variations suggest an increased risk of metabolic constraints under heat stress, putting tetraploids at a disadvantage in warmer regions. Importantly, the physiological tradeoffs associated with polyploidization help explain the geographical differentiation between diploids and tetraploids, which reflects a climatic boundary, with tetraploids occupying cooler northeastern areas. Our findings identify an autotetraploid frog, report the first autotetraploid genome in amphibians, and demonstrate how vertebrate polyploids physiologically and ecologically diverge from their diploid counterparts.

The Genetic Consequences of Range Expansion and Its Influence on Diploidization in Polyploids

AbstractDespite newly formed polyploids being subjected to myriad fitness consequences, the relative prevalence of polyploidy, both contemporarily and in ancestral branches of the tree of life, suggests alternative advantages that outweigh these consequences. One proposed advantage is that polyploids may more easily colonize novel habitats, such as deglaciated areas. However, previous research conducted in diploids suggests that range expansion comes with a fitness cost, as deleterious mutations may fix rapidly on the expansion front. Here, we interrogate the potential consequences of expansion in polyploids by conducting spatially explicit forward-in-time simulations to investigate how ploidy and inheritance patterns impact the relative ability of polyploids to expand their range. We show that under realistic dominance models, autopolyploids suffer greater fitness reductions than diploids as a result of range expansion due to the fixation of increased mutational load that is masked in the range core. Alternatively, the disomic inheritance of allopolyploids provides a shield to this fixation, resulting in minimal fitness consequences. In light of this advantage provided by disomy, we investigate how range expansion may influence cytogenetic diploidization through the reversion to disomy in autotetraploids. We show that under a wide range of parameters investigated for two models of diploidization, disomy frequently evolves more rapidly on the expansion front than in the range core, and that this dynamic inheritance model has additional effects on fitness. Together our results point to a complex interaction among dominance, ploidy, inheritance, and recombination on fitness as a population spreads across a geographic range.

ChromEvol v.3: modeling rate heterogeneity in chromosome number evolution

Changes in chromosome numbers are a prominent driver of plant evolution, impacting ecological diversification, stress tolerance, and phenotypes. ChromEvol is a widely used software tool for deciphering patterns of chromosome-number change along a phylogeny of interest. It evaluates the fit of alternative models to the data, estimates transition rates of different types of events, and infers the expected number of events along each branch of the phylogeny. We introduce ChromEvol v.3, featuring multiple novel methodological advancements that capture variation in the transition rates along a phylogeny. This version better allows researchers to identify how dysploidy and polyploidy rates change based on the number of chromosomes in the genome, with respect to a discrete trait, or at certain subclades of the phylogeny. We demonstrate the applicability of the new models on the Solanaceae phylogeny. Our analyses identify four chromosome-number transition regimes that characterize distinct Solanaceae clades and demonstrate an association between self-compatibility and altered dynamics of chromosome-number evolution. ChromEvol v.3, available at https://github.com/anatshafir1/chromevol, offers researchers a more flexible, comprehensive, and accurate tool to investigate the evolution of chromosome numbers and the various processes affecting it.

Polyploidization-driven transcriptomic dynamics in Medicago sativa neotetraploids: mRNA, smRNA and allele-specific gene expression

Whole genome duplication (WGD) is a powerful evolutionary mechanism in plants. Autopolyploids have been comparatively less studied than allopolyploids, with sexual autopolyploidization receiving even less attention. In this work, we studied the transcriptomes of neotetraploids (2n = 4x = 32) obtained by crossing two diploid (2n = 2x = 16) plants of Medicago sativa that produce a significant percentage of either 2n eggs or pollen. Diploid progeny from the same cross allowed us to separate the transcriptional outcomes of hybridization from those of WGD. This material can help to elucidate events at the base of the domestication of cultivated 4x alfalfa, the world's most important leguminous forage. Three 2x and three 4x progeny plants and 2x parental plants were used for this study. The RNA-seq data revealed that WGD did not dramatically affect the transcription of leaf protein-coding genes. The two parental genotypes did not contribute equally to the progeny transcriptomes, and genome-wide expression level dominance of the male parent was observed. A large majority of the genes whose expression level changed due to WGD presented increased expression, indicating that the 4x state requires the upregulation of approximately 2.66% of the protein-coding genes. Overall, we estimated that 3.63% of the protein-coding genes were transcriptionally affected by WGD and may contribute to the phenotypic novelty of the neotetraploid plants. Pathway analysis suggested that WGD could affect secondary metabolite biosynthesis, which in turn may influence forage quality. We found four times as many transcription factor genes among the polyploidization-affected genes than among those affected only by hybridization. Several of these belong to classes involved in stress response. Small RNA-seq revealed that very few miRNAs were significantly associated with WGD, but they target several hundred genes, and their role in the WGD response may be relevant. Integrated network analysis led to the identification of putative miRNA: mRNA interactions potentially involved in transcriptome reprogramming. Allele-specific expression analysis indicated that parent-of-origin bias was not a significant outcome of WGD, but we found that parentally biased RNA editing may be a significant source of variation in neopolyploids.

Phylogeny-based comparative analysis of gene expression modulation upon drought stress across three cotton diploids

BACKGROUND

Drought stress is a significant global challenge that negatively impacts cotton fiber yield and quality. Although many drought-stress responsive genes have been identified in cotton species (Gossypium spp.), the diversity of drought response mechanisms across cotton species remains largely unexplored. This study compared gene expression modulation in response to drought stress across three diploid cotton species: G. arboreum, G. stocksii, and G. bickii.

RESULTS

We observed significant variation in the content and biological roles of differentially expressed genes among the studied species, along with enhanced divergence in ortholog expression patterns under drought stress. These findings suggest a remodeling of drought response mechanisms during the independent evolution of cotton species. Additionally, we identified 287 genes exhibiting similar regulatory responses to drought across species, highlighting pathways including starch and sucrose metabolism, chlorophyll catabolite degradation and synthesis, and hormone-mediated signal transduction. Notably, 16 transcription factors were identified as potential central regulators of the conserved stress response mechanisms.

CONCLUSIONS

This study reveals the diversity of drought response mechanisms among individual cotton species, identifies valuable targets for genetically enhancing drought tolerance, and provides a strategic framework for identifying candidate genes for breeding programs.

Allopolyploidy expanded gene content but not pangenomic variation in the hexaploid oilseed Camelina sativa

Ancient whole-genome duplications are believed to facilitate novelty and adaptation by providing the raw fuel for new genes. However, it is unclear how recent whole-genome duplications may contribute to evolvability within recent polyploids. Hybridization accompanying some whole-genome duplications may combine divergent gene content among diploid species. Some theory and evidence suggest that polyploids have a greater accumulation and tolerance of gene presence-absence and genomic structural variation, but it is unclear to what extent either is true. To test how recent polyploidy may influence pangenomic variation, we sequenced, assembled, and annotated 12 complete, chromosome-scale genomes of Camelina sativa, an allohexaploid biofuel crop with 3 distinct subgenomes. Using pangenomic comparative analyses, we characterized gene presence-absence and genomic structural variation both within and between the subgenomes. We found over 75% of ortholog gene clusters are core in C. sativa and <10% of sequence space was affected by genomic structural rearrangements. In contrast, 19% of gene clusters were unique to one subgenome, and the majority of these were Camelina specific (no ortholog in Arabidopsis). We identified an inversion that may contribute to vernalization requirements in winter-type Camelina and an enrichment of Camelina-specific genes with enzymatic processes related to seed oil quality and Camelina's unique glucosinolate profile. Genes related to these traits exhibited little presence-absence variation. Our results reveal minimal pangenomic variation in this species and instead show how hybridization accompanied by whole-genome duplication may benefit polyploids by merging diverged gene content of different species.

RNA-seq analysis and lipid profiling reveal the competitive regulation of starch and triacylglycerol synthesis during grain-filling stage in tetraploid rice

Autotetraploid rice is a useful germplasm for polyploid rice breeding in improving nutritional values. Nevertheless, underlying mechanism of starch and lipid accumulation in tetraploid rice caryopsis remains largely unknown. Here, regulatory mode of starch and triacylglycerol (TAG) synthesis during grain-filling stage in diploid and tetraploid indica rice varieties 9311 was investigated. As a result, tetraploid rice exhibited the reduced starch (-13.22 %) and apparent amylose (-24.76 %) contents, increased the in vitro starch digestion percentage. Meanwhile, lipid detection and thin layer chromatography revealed an increase in fatty acids (+15.26 %) and TAG (+28.82 %) contents characterized by a significant increase in the mole ratio of C18:1 and the decrease of C16:0 and C18:2. Moreover, RNA-seq and functional analyses identified that OsAGPL1, encoding a rate-limiting enzyme involved in starch synthesis, was consistently down-regulated. Additionally, two TAG synthesis-associated genes OsSAD1 and OsFATB2 were up-regulated and down-regulated, respectively, which contributed to higher mole ratio of C18:1 and lower ratio of C16:0 in tetraploid rice caryopses. This study proposes a regulatory model of increased lipid and reduced starch synthesis during grain-filling stage and provides three candidate genes for genetic engineering in nutritional quality improvement of autotetraploid rice.

Asymmetric genome merging leads to gene expression novelty through nucleo-cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids

Genome merging is a common phenomenon causing a wide range of consequences on phenotype, adaptation, and gene expression, yet its broader implications are not well-understood. Two consequences of genome merging on gene expression remain particularly poorly understood: dosage effects and evolution of expression. We employed Chlamydomonas reinhardtii as a model to investigate the effects of asymmetric genome merging by crossing a diploid with a haploid strain to create a novel triploid line. Five independent clonal lineages derived from this triploid line were evolved for 425 asexual generations in a laboratory natural selection experiment. Utilizing fitness assays, flow cytometry, and RNA-Seq, we assessed the immediate consequences of genome merging and subsequent evolution. Our findings reveal substantial alterations in genome size, gene expression, protein homeostasis, and cytonuclear stoichiometry. Gene expression exhibited expression-level dominance and transgressivity (i.e. expression level higher or lower than either parent). Ongoing expression-level dominance and a pattern of 'functional dominance' from the haploid parent was observed. Despite major genomic and nucleo-cytoplasmic disruptions, enhanced fitness was detected in the triploid strain. By comparing gene expression across generations, our results indicate that proteostasis restoration is a critical component of rapid adaptation following genome merging in Chlamydomonas reinhardtii and possibly other systems.

Herbarium specimens reveal a cryptic invasion of polyploid Centaurea stoebe in Europe

Numerous plant species are expanding their native ranges due to anthropogenic environmental change. Because cytotypes of polyploid complexes often show similar morphologies, there may be unnoticed range expansions (i.e. cryptic invasions) of one cytotype into regions where only the other cytotype is native. We critically revised herbarium specimens of diploid and tetraploid Centaurea stoebe, collected across Europe between 1790 and 2023. Based on their distribution in natural and relict habitats and phylogeographic data, we estimated the native ranges of both cytotypes. Diploids are native across their entire European range, whereas tetraploids are native only to South-Eastern Europe and have recently expanded their range toward Central Europe. The proportion of tetraploids has exponentially increased over time in their expanded but not in their native range. This cryptic invasion predominantly occurred in ruderal habitats and enlarged the climatic niche of tetraploids toward a more oceanic climate. We conclude that spatio-temporally explicit assessments of range shifts, habitat preferences and niche evolution can improve our understanding of cryptic invasions. We also emphasize the value of herbarium specimens for accurate estimation of species´ native ranges, with fundamental implications for the design of research studies and the assessment of biodiversity trends.

The power of independent generations in plants

This article is a Commentary on Blake‐Mahmud et al. (2025), 245: 885–898.

Polyploidy and environmental stress response: a comparative study of fern gametophytes

Climate change is rapidly altering natural habitats and generating complex patterns of environmental stress. Ferns are major components of many forest understories and, given their independent gametophyte generation, may experience unique pressures in emerging temperature and drought regimes. Polyploidy is widespread in ferns and may provide a selective advantage in these rapidly changing environments. This work aimed to understand whether the gametophytes of allopolyploid ferns respond differently to climate-related physiological stress than their diploid parents. The experimental approach involved a multifactorial design with 27 treatment combinations including exposure to multiple levels of drought and temperature over three treatment durations, with recovery measured at multiple timepoints. We measured Chl fluorescence from over 2000 gametophytes to evaluate stress avoidance and tolerance in diploid and polyploid species. Polyploids generally showed a greater ability to avoid and/or tolerate a range of stress conditions compared with their diploid counterparts, suggesting that polyploidy may confer enhanced flexibility and resilience under climate stress. Overall, these results suggest that polyploidy may provide some resilience to climate change in mixed ploidy populations. However, all species remain susceptible to the impacts of extreme drought and heat stress.

Epigenomic and 3D genomic mapping reveals developmental dynamics and subgenomic asymmetry of transcriptional regulatory architecture in allotetraploid cotton

Although epigenetic modification has long been recognized as a vital force influencing gene regulation in plants, the dynamics of chromatin structure implicated in the intertwined transcriptional regulation of duplicated genes in polyploids have yet to be understood. Here, we document the dynamic organization of chromatin structure in two subgenomes of allotetraploid cotton (Gossypium hirsutum) by generating 3D genomic, epigenomic and transcriptomic datasets from 12 major tissues/developmental stages covering the life cycle. We systematically identify a subset of genes that are closely associated with specific tissue functions. Interestingly, these genes exhibit not only higher tissue specificity but also a more pronounced homoeologous bias. We comprehensively elucidate the intricate process of subgenomic collaboration and divergence across various tissues. A comparison among subgenomes in the 12 tissues reveals widespread differences in the reorganization of 3D genome structures, with the Dt subgenome exhibiting a higher extent of dynamic chromatin status than the At subgenome. Moreover, we construct a comprehensive atlas of putative functional genome elements and discover that 37 cis-regulatory elements (CREs) have selection signals acquired during domestication and improvement. These data and analyses are publicly available to the research community through a web portal. In summary, this study provides abundant resources and depicts the regulatory architecture of the genome, which thereby facilitates the understanding of biological processes and guides cotton breeding.

Polyploid genome assembly of Cardamine chenopodiifolia

Cardamine chenopodiifolia is an amphicarpic plant in the Brassicaceae family. Plants develop two fruit types, one above and another below ground. This rare trait is associated with octoploidy in C. chenopodiifolia. The absence of genomic data for C. chenopodiifolia currently limits our understanding of the development and evolution of amphicarpy. Here, we produced a chromosome-scale assembly of the C. chenopodiifolia genome using high-fidelity long read sequencing with the Pacific Biosciences platform. We assembled 32 chromosomes and two organelle genomes with a total length of 597.2 Mb and an N50 of 18.8 Mb. Genome completeness was estimated at 99.8%. We observed structural variation among homeologous chromosomes, suggesting that C. chenopodiifolia originated via allopolyploidy, and phased the octoploid genome into four sub-genomes using orthogroup trees. This fully phased, chromosome-level genome assembly is an important resource to help investigate amphicarpy in C. chenopodiifolia and the origin of trait novelties by allopolyploidy.

Phylogeny and Polyploidy Evolution of the Suckers (Teleostei: Catostomidae)

Fishes in the cypriniform family Catostomidae (suckers) are evolutionary tetraploids. The use of nuclear markers in the phylogenetic study of this important group has been greatly hindered by the challenge of identifying paralogous copies of genes. In the present study, we used two different methods to separate the gene copies of five single-copy nuclear genes (i.e., RAG1, EGR2B, EGR3, IRBP2, and RAG2). For each gene, all sequences of Copy I formed a clade that was sister to the clade formed by all sequences of Copy II in the phylogenetic trees. The maternal and paternal progenitor of the tetraploid ancestor of the Catostomidae could not be determined. We also constructed a mitochondrial tree to reflect the maternal relationships among major catostomid lineages. Our data appear to support a sister relationship between Catostominae and a monophyletic group composed of Myxocyprininae, Cycleptinae, and Ictiobinae. However, within Catostominae, there is significant conflict between mitochondrial and nuclear data regarding the relationships among Erimyzonini, Catostomini, and Moxostomatini/Thoburnini. Many indels, unexpected stop codons, and possible gene loss were identified in one gene copy of RAG1, RAG2, and IRBP2. We believe that additional nuclear genome data are needed to better resolve the phylogenetic relationships within the family Catostomidae.

Plant growth Enhancement in Colchicine-Treated Tomato Seeds without Polyploidy Induction

Plant breeding plays a pivotal role in the development of improved tomato cultivars, addressing various challenges faced by this crop worldwide. Tomato crop yield is affected by biotic and abiotic stress, including diverse pathogens and pests, extreme temperatures, drought, and soil salinity, thus affecting fruit quality, and overall crop productivity. Through strategic plant breeding approaches, it is possible to increase the genetic diversity of tomato cultivars, leading to the development of varieties with increased resistance to prevalent diseases and pests, improved tolerance to environmental stress, and enhanced adaptability to changing agroclimatic conditions. The induction of genetic variability using antimitotic agents, such as colchicine, has been widely employed in plant breeding precisely to this end. In this study, we analyzed the transcriptome of colchicine-treated tomato plants exhibiting larger size, characterized by larger leaves, while seedlings of the T2 generation harbored three cotyledons. A total of 382 differentially expressed genes encoding proteins associated with anatomical structure development, hormone synthesis and transport, flavonoid biosynthesis, and responses to various stimuli, stresses, and defense mechanisms were identified. Gene enrichment analysis suggests a role for auxin and flavonoid biosynthesis in cotyledon formation. Furthermore, single-nucleotide polymorphisms were mapped in colchicine-treated plants and determined which corresponded to differentially- expressed genes. Interestingly, most were associated to only a few genes in a similar location. This study provides significant insights into the genes and metabolic pathways affected in colchicine-treated tomatoes that exhibit improved agronomic traits, such as plant vigor and improved photosynthesis rate.

Accurate Inference of the Polyploid Continuum Using Forward-Time Simulations

Multiple rounds of whole-genome duplication (WGD) followed by diploidization have occurred throughout the evolutionary history of angiosperms. Much work has been done to model the genomic consequences and evolutionary significance of WGD. While researchers have historically modeled polyploids as either allopolyploids or autopolyploids, the variety of natural polyploids span a continuum of differentiation across multiple parameters, such as the extent of polysomic versus disomic inheritance, and the degree of genetic differentiation between the ancestral lineages. Here we present a forward-time polyploid genome evolution simulator called SpecKS. SpecKS models polyploid speciation as originating from a 2D continuum, whose dimensions account for both the level of genetic differentiation between the ancestral parental genomes, as well the time lag between ancestral speciation and their subsequent reunion in the derived polyploid. Using extensive simulations, we demonstrate that changes in initial conditions along either dimension of the 2D continuum deterministically affect the shape of the Ks histogram. Our findings indicate that the error in the common method of estimating WGD time from the Ks histogram peak scales with the degree of allopolyploidy, and we present an alternative, accurate estimation method that is independent of the degree of allopolyploidy. Lastly, we use SpecKS to derive tests that infer both the lag time between parental divergence and WGD time, and the diversity of the ancestral species, from an input Ks histogram. We apply the latter test to transcriptomic data from over 200 species across the plant kingdom, the results of which are concordant with the prevailing theory that the majority of angiosperm lineages are derived from diverse parental genomes and may be of allopolyploid origin.

Evolution of Plant Genome Size and Composition

The rapid development of sequencing technology has led to an explosion of plant genome data, opening up more opportunities for research in the field of comparative evolutionary analysis of plant genomes. In this review, we focus on changes in plant genome size and composition, examining the effects of polyploidy, whole-genome duplication, and alternations in transposable elements on plant genome architecture and evolution, respectively. In addition, to address gaps in the available information, we also collected and analyzed 234 representative plant genome data as a supplement. We aim to provide a comprehensive, up-to-date summary of information on plant genome architecture and evolution in this review.

Repeated shifts out of tropical climates preceded by whole genome duplication

While flowering plants have diversified in virtually every terrestrial clime, climate constrains the distribution of individual lineages. Overcoming climatic constraints may be associated with diverse evolutionary phenomena including whole genome duplication (WGD), gene-tree conflict, and life-history changes. Climatic shifts may also have facilitated increases in flowering plant diversification rates. We investigate climatic shifts in the flowering plant order Ericales, which consists of c. 14 000 species with diverse climatic tolerances. We estimate phylogenetic trees from transcriptomic data, 64 chloroplast loci, and Angiosperms353 nuclear loci that, respectively, incorporate 147, 4508, and 2870 Ericales species. We use these phylogenetic trees to analyse how climatic shifts are associated with WGD, gene-tree conflict, life-history, and diversification rates. Early branches in the phylogenetic trees are extremely short, and have high levels of gene-tree conflict and at least one WGD. On lineages descended from these early branches, there is a significant association between climatic shifts (primarily out of tropical climates), further WGDs, and life-history. Extremely short early branches, and their associated gene-tree conflict and WGDs, appear to underpin the explosive origin of numerous species rich Ericales clades. The evolution of diverse climatic tolerances in these species rich clades is tightly associated with WGD and life-history.

Heat shock responsive genes in Brassicaceae: genome-wide identification, phylogeny, and evolutionary associations within and between genera

Heat stress affects the growth and development of Brassicaceae crops. Plant breeders aim to mitigate the effects of heat stress by selecting for heat stress tolerance, but the genes responsible for heat stress in Brassicaceae remain largely unknown. During heat stress, heat shock proteins (HSPs) function as molecular chaperones to aid in protein folding, and heat shock transcription factors (HSFs) serve as transcriptional regulators of HSP expression. We identified 5002 heat shock related genes, including HSPs and HSFs, across 32 genomes in Brassicaceae. Among these, 3347 genes were duplicated, with segmented duplication primarily contributing to their expansion. We identified 466 physical gene clusters, including 240 homogenous clusters and 226 heterogeneous clusters, shedding light on the organization of heat shock related genes. Notably, 37 genes were co-located with published thermotolerance quantitative trait loci, which supports their functional role in conferring heat stress tolerance. This study provides a comprehensive resource for the identification of functional Brassicaceae heat shock related genes, elucidates their clustering and duplication patterns and establishes the genomic foundation for future heat tolerance research. We hypothesise that genetic variants in HSP and HSF genes in certain species have potential for improving heat stress tolerance in Brassicaceae crops.

Bona Fide Plant Steroid Receptors are Innovated in Seed Plants and Angiosperms through Successive Whole-Genome Duplication Events

Whole-genome duplication (WGD) events are widespread in plants and animals, thus their long-term evolutionary contribution has long been speculated, yet a specific contribution is difficult to verify. Here, we show that ɛ-WGD and ζ-WGD contribute to the origin and evolution of bona fide brassinosteroid (BR) signaling through the innovation of active BR biosynthetic enzymes and active BR receptors from their respective ancestors. We found that BR receptors BRI1 (BR INSENSITIVE 1) and BRL1/3 (BRI1-LIKES 1/3) derived by ɛ-WGD and ζ-WGD, which occurred in the common ancestor of angiosperms and seed plants, respectively, while orphan BR receptor BRL2 first appeared in stomatophytes. Additionally, CYP85A enzymes synthesizing the bioactive BRs derived from a common ancestor of seed plants, while its sister enzymes CYP90 synthesizing BR precursors presented in all land plants, implying possible ligand-receptor coevolution. Consistently, the island domains (IDs) responsible for BR perception in BR receptors were most divergent among different receptor branches, supporting ligand-driven evolution. As a result, BRI1 was the most diversified BR receptor in angiosperms. Importantly, relative to the BR biosynthetic DET2 gene presented in all land plants, BRL2, BRL1/3 and BRI1 had high expression in vascular plants ferns, gymnosperms and angiosperms, respectively. Notably, BRI1 is the most diversified BR receptor with the most abundant expression in angiosperms, suggesting potential positive selection. Therefore, WGDs initiate a neofunctionalization process diverged by ligand-perception and transcriptional expression, which might optimize both BR biosynthetic enzymes and BR receptors, likely contributing to the evolution of land plants, especially seed plants and angiosperms.