Polyploidy: A Biological Force From Cells to Ecosystems

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.

Understanding the Regulation Activities of Transposons in Driving the Variation and Evolution of Polyploid Plant Genome

Transposon is the main component of the eukaryotic genome, and more and more plant genome data show that transposons are diverse in regulating genome structure, variation, function and evolution, with different transposition mechanisms in the genome. Hybridization and polyploidy play an important role in promoting plant speciation and evolution, and recent studies have shown that polyploidy is usually accompanied by the expansion of transposons, which affect the genome size and structure of polyploid plants. Transposons can insert into genes and intergenic regions, resulting in great differences in the overall genome structure of closely related plant species, and it can also capture gene segments in the genome to increase the copy number of genes. In addition, transposons influence the epigenetic modification state of the genome and regulate the expression of the gene, while plant phenotype, biological and abiotic stress response are also regulated by transposons. Overall, transposons play an important role in the plant genome, especially polyploid plant genome, adaptation and evolution.

Haplotype-resolved genome assembly of the tetraploid Youcha tree Camellia meiocarpa Hu

Camellia meiocarpa Hu, a member of Youcha species in the genus Camellia, is an important woody edible Youcha plant with high ecological and economic value. The haplotype-resolved genome assembly of this tetraploid species can shed light on genomic evolution and the functional divergence among subgenomes and haplotypes. In this study, we achieved the first chromosome-level haplotype-resolved genome assembly using PacBio HiFi, Hi-C, and Illumina sequencing. The scaffolds, with an N50 of 44.46 Mb and 41.40 Mb, were mapped to 60 chromosomes and four distinct haplotypes, each with unique transposon features. The haplotypes varied in length (2967.25 Mb to 3041.66 Mb) and contained 51,336 to 52,631 protein-coding genes, 99.4% of which were annotated. Non-coding RNAs and repetitive elements were identified across haplotypes. This comprehensive genomic resource will enhance molecular and genetic studies, aiding in the conservation and utilization of Youcha.

Evolution of Plant Conserved microRNAs After Whole-Genome Duplications

MicroRNAs (miRNAs) are a specialized class of small silencing RNAs that regulate gene expression in numerous biological processes in eukaryotes. While the evolutionary dynamics of protein-coding genes after plant whole-genome duplications (WGDs) has been extensively studied, the patterns of evolution for conserved MIRNAs (miRNA genes) post-WGDs are less understood. In this study, we systematically investigated miRNAs and their targets in 6 plant species with varying WGD histories. Our findings reveal that WGDs significantly contribute to the expansion of conserved miRNA families. Notably, through homologous analyses of conserved miRNA families, we discovered that beyond the loci derived from WGDs and other duplication events, some conserved miRNA families have independently gained new loci and/or lost syntenic loci in specific lineage or species through evolution. Additionally, our analyses of sequence divergence in conserved miRNAs showed that the mature sequences of miRNA duplicates gradually diverge following WGDs, with this sequence divergence being correlated with that of their adjacent protein-coding genes after recent WGDs. Furthermore, expression and functional divergence analyses of duplicated targets in different miRNA-target interaction scenarios suggest that conserved miRNAs may play crucial roles in regulating the expression of duplicated genes and related regulatory networks following WGDs. In summary, our analyses reveal universal evolutionary patterns of plant conserved miRNAs following WGDs and provide evidence that some miRNA copies in conserved families originated independently during evolution.

α-Catenin force-sensitive binding and sequestration of LZTS2 leads to cytokinesis failure

Epithelial cells can become polyploid upon tissue injury, but mechanosensitive cues that trigger this state are poorly understood. Using an Madin Darby Canine Kidney (MDCK) cell knock-out/reconstitution system, we show that α-catenin mutants that alter force-sensitive binding to F-actin or middle (M)-domain promote cytokinesis failure and binucleation, particularly near epithelial wound-fronts. We identified Leucine Zipper Tumor Suppressor 2 (LZTS2), a factor previously implicated in abscission, as a conformation sensitive proximity partner of α-catenin. We show that LZTS2 enriches not only at midbody/intercellular bridges but also at apical adhering junctions. α-Catenin mutants with persistent M-domain opening show elevated junctional enrichment of LZTS2 compared with wild-type cells. LZTS2 knock-down leads to elevated rates of binucleation. These data implicate LZTS2 as a mechanosensitive effector of α-catenin that is critical for cytokinetic fidelity. This model rationalizes how persistent mechanoactivation of α-catenin may drive tension-induced polyploidization of epithelia after injury and suggests an underlying mechanism for how pathogenic α-catenin M-domain mutations drive macular dystrophy.

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.

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.

Transcriptome-Wide Insights: Neonatal Lactose Intolerance Promotes Telomere Damage, Senescence, and Cardiomyopathy in Adult Rat Heart

Cardiovascular diseases (CVD) are the primary cause of mortality globally. A significant aspect of CVD involves their association with aging and susceptibility to neonatal programming. These factors suggest that adverse conditions during neonatal development can disrupt cardiomyocyte differentiation, thereby leading to heart dysfunction. This study focuses on the long-term effects of inflammatory and oxidative stress due to neonatal lactose intolerance (NLI) on cardiomyocyte transcriptome and phenotype. Our recent bioinformatic study focused on toggle genes indicated that NLI correlates with the switch off of some genes in thyroid hormone, calcium, and antioxidant signaling pathways, alongside the switch-on/off genes involved in DNA damage response and inflammation. In the presented study, we evaluated cardiomyocyte ploidy in different regions of the left ventricle (LV), complemented by a transcriptomic analysis of genes with quantitative (gradual) difference in expression. Cytophotometric and morphologic analyses of LV cardiomyocytes identified hyperpolyploidy and bridges between nuclei suggesting telomere fusion. Transcriptomic profiling highlighted telomere damage, aging, and chromatin decompaction, along with the suppression of pathways governing muscle contraction and energy metabolism. Echocardiography revealed statistically significant LV dilation and a decrease in ejection fraction. The estimation of survival rates indicated that NLI shortened the median lifespan by approximately 18% (p < 0.0001) compared with the control. Altogether, these findings suggest that NLI may increase susceptibility to cardiovascular diseases by accelerating aging due to oxidative stress and increased telomere DNA damage, leading to hyperpolyploidization and reduced cardiac contractile function. Collectively, our data emphasize the importance of the early identification and management of neonatal inflammatory and metabolic stressors, such as NLI, to mitigate long-term cardiovascular risks.

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.

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.

Complex but Clear Allopolyploid Pattern of Subtribe Tussilagininae (Asteraceae: Senecioneae) Revealed by Robust Phylogenomic Evidence, with Development of a Novel Homeolog-Sorting Pipeline

Polyploidy is a significant mechanism in eukaryotic evolution and is particularly prevalent in the plant kingdom. However, our knowledge about this phenomenon and its effects on evolution remains limited. A major obstacle to the study of polyploidy is the great difficulty in untangling the origins of allopolyploids. Due to the drastic genome changes and the erosion of allopolyploidy signals caused by the combined effects of hybridization and complex postpolyploid diploidization processes, resolving the origins of allopolyploids has long been a challenging task. Here we revisit this issue with the interesting case of subtribe Tussilagininae (Asteraceae: Senecioneae) and by developing HomeoSorter, a new pipeline for network inferences by phasing homeologs to parental subgenomes. The pipeline is based on the basic idea of a previous study but with major changes to address the scaling problem and implement some new functions. With simulated data, we demonstrate that HomeoSorter works efficiently on genome-scale data and has high accuracy in identifying polyploid patterns and assigning homeologs. Using HomeoSorter, the maximum pseudo-likelihood model of Phylonet, and genome-scale data, we further address the complex origin of Tussilagininae, a speciose group (ca. 45 genera and 710 species) characterized by having high base chromosome numbers (mainly x = 30, 40). In particular, the inferred patterns are strongly supported by the chromosomal evidence. Tussilagininae is revealed to comprise 2 large groups with successive allopolyploid origins: Tussilagininae s.s. (mainly x = 30) and the Gynoxyoid group (x = 40). Two allopolyploidy events first give rise to Tussilagininae s.s., with the first event occurring between the ancestor of subtribe Senecioninae (x = 10) and a lineage (highly probably with x = 10) related to the Brachyglottis alliance, and the resulting hybrid lineage crossing with the ancestor of Chersodoma (x = 10) and leading to Tussilagininae s.s. Then, after early diversification, the Central American group (mainly x = 30) of Tussilagininae s.s., is involved in a third allopolyploidy event with, again, the Chersodoma lineage and produces the Gynoxyoid group. Our study highlights the value of HomeoSorter and the homeolog-sorting approach in polyploid phylogenetics. With rich species diversity and clear evolutionary patterns, Tussilagininae s.s. and the Gynoxyoid group are also excellent models for future investigations of polyploidy.

Single-cell detection of copy number changes reveals dynamic mechanisms of adaptation to antifungals in Candida albicans

Genomic copy number changes are associated with antifungal drug resistance and virulence across diverse fungal pathogens, but the rate and dynamics of these genomic changes in the presence of antifungal drugs are unknown. Here we optimized a dual-fluorescent reporter system in the diploid pathogen Candida albicans to quantify haplotype-specific copy number variation (CNV) and loss of heterozygosity (LOH) at the single-cell level with flow cytometry. We followed the frequency and dynamics of CNV and LOH at two distinct genomic locations in the presence and absence of antifungal drugs in vitro and in a murine model of candidiasis. Copy number changes were rapid and dynamic during adaptation to fluconazole and frequently involved competing subpopulations with distinct genotypes. This study provides quantitative evidence for the rapid speed at which diverse genotypes arise and undergo dynamic population-level fluctuations during adaptation to antifungal drugs in vitro and in vivo.

Recent and Recurrent Autopolyploidization Fueled Diversification of Snow Carp on the Tibetan Plateau

Whole-genome duplication (WGD), or polyploidization, is a major contributor to biodiversity. However, the establishment and survival of WGDs are often considered to be stochastic, since elucidating the processes of WGD establishment remains challenging. In the current study, we explored the processes leading to polyploidy establishment in snow carp (Cyprinidae: Schizothoracinae), a predominant component of the ichthyofauna of the Tibetan Plateau and its surrounding areas. Using large-scale genomic data from isoform sequencing, we analyzed ohnolog genealogies and divergence in hundreds to thousands of gene families across major snow carp lineages. Our findings demonstrated that independent autopolyploidization subsequent to speciation was prevalent, while autopolyploidization followed by speciation also occurred in the diversification of snow carp. This was further supported by matrilineal divergence and drainage evolution evidence. Contrary to the long-standing hypothesis that ancient polyploidization preceded the diversification of snow carp, we determined that polyploidy in extant snow carp was established by recurrent autopolyploidization events during the Pleistocene. These findings indicate that the diversification of extant snow carp resembles a coordinated duet: first, the uplift of the Tibetan Plateau orchestrated the biogeography and diversification of their diploid progenitors; then, the extensive Pliocene-Pleistocene climate changes acted as relay runners, further fueling diversification through recurrent autopolyploidization. Overall, this study not only reveals a hitherto unrecognized recent WGD lineage in vertebrates but also advances current understanding of WGD processes, emphasizing that WGD establishment is a nonstochastic event, emerging from numerous adaptations to environmental challenges and recurring throughout evolutionary history rather than merely in plants.

Ploidy as a leaky reproductive barrier: mechanisms, rates and evolutionary significance of interploidy gene flow

BACKGROUND

Whole-genome duplication (polyploidization) is a dominant force in sympatric speciation, particularly in plants. Genome doubling instantly poses a barrier to gene flow owing to the strong crossing incompatibilities between individuals differing in ploidy. The strength of the barrier, however, varies from species to species and recent genetic investigations revealed cases of rampant interploidy introgression in multiple ploidy-variable species.

SCOPE

Here, we review novel insights into the frequency of interploidy gene flow in natural systems and summarize the underlying mechanisms promoting interploidy gene flow. Field surveys, occasionally complemented by crossing experiments, suggest frequent opportunities for interploidy gene flow, particularly in the direction from diploid to tetraploid, and between (higher) polyploids. However, a scarcity of accompanying population genetic evidence and a virtual lack of integration of these approaches leave the underlying mechanisms and levels of realized interploidy gene flow in nature largely unknown. Finally, we discuss potential consequences of interploidy genome permeability on polyploid speciation and adaptation and highlight novel avenues that have just recently been opened by the very first genomic studies of ploidy-variable species. Standing in stark contrast with rapidly accumulating evidence for evolutionary importance of homoploid introgression, similar cases in ploidy-variable systems are yet to be documented.

CONCLUSIONS

The genomics era provides novel opportunity to re-evaluate the role of interploidy introgression in speciation and adaptation. To achieve this goal, interdisciplinary studies bordering ecology and population genetics and genomics are needed.

Dosage sensitivity shapes balanced expression and gene longevity of homoeologs after whole-genome duplications in angiosperms

Following whole-genome duplication (WGD), duplicate gene pairs (homoeologs) can evolve varying degrees of expression divergence. However, the determinants influencing these relative expression level differences (RFPKM) between homoeologs remain elusive. In this study, we analyzed the RFPKM between homoeologs in 3 angiosperms, Nymphaea colorata, Nelumbo nucifera, and Acorus tatarinowii, all having undergone a single WGD since the origin of angiosperms. Our results show significant positive correlations in RFPKM of homoeologs among tissues within the same species, and among orthologs across these 3 species, indicating convergent expression balance/bias between homoeologous gene copies following independent WGDs. We linked RFPKM between homoeologs to gene attributes associated with dosage-balance constraints, such as protein-protein interactions, lethal-phenotype scores in Arabidopsis (Arabidopsis thaliana) orthologs, domain numbers, and expression breadth. Notably, homoeologs with lower RFPKM often had more interactions and higher lethal-phenotype scores, indicating selective pressures favoring balanced expression. Also, homoeologs with lower RFPKM were more likely to be retained after WGDs in angiosperms. Within Nelumbo, greater RFPKM between homoeologs correlated with increased cis- and trans-regulatory differentiation between species, highlighting the ongoing escalation of gene expression divergence. We further found that expression degeneration in 1 copy of homoeologs is inclined toward nonfunctionalization. Our research highlights the importance of balanced expression, shaped by dosage-balance constraints, in the evolutionary retention of homoeologs in plants.

Influence of polyploidy on morphology and distribution of the Cypress Spurge (Euphorbia cyparissias, Euphorbiaceae)

Polyploidy can cause differences in phenotypic and physiological traits among different cytotypes of the same species. Polyploids may have larger organs or occupy different ecological niches than their diploid counterparts, therefore they are hypothesized to have larger distributions or prosper in stressful environments, such as higher elevations. The Cypress spurge (Euphorbia cyparissias L.; Euphorbiaceae) is a widespread European heteroploid species including di- (2x), tetra- (4x) and hexaploid (6x) cytotypes. We tested the hypotheses that polyploids are more widespread and more abundant at higher elevations and have larger organs than their diploid ancestors in the case of E. cyparissias. We also analysed whether genome downsizing had occurred after polyploidisation. We conducted a comprehensive geographic sampling of 617 populations of E. cyparissias throughout Europe. We estimated their relative genome size using flow cytometry and inferred ploidy level of each population. We scored 13 morphological traits of vegetative and seed characters and performed statistical analyses. The study indicates that polyploidisation facilitated colonisation of new areas in E. cyparissias, where the tetraploids are most widespread, whereas the diploids are limited to putative Pleistocene refugia, mostly in southern Europe. On the other hand, the three ploidies do not differ in their elevational distribution. Although some quantitative morphological traits exhibited an increasing trend with increasing ploidy, most traits did not differ significantly among the three ploidies, and there was no overall phenotypic differentiation among them. Given that individuals of different ploidies thrive in similar habitats across the same elevations, we suggest that ecological segregation following polyploidisation is a more important trigger for morphological differentiation than polyploidisation itself in autopolyploid plants. The study demonstrates that polyploidisation can be crucial for the colonisation of new areas and for range expansion, but it does not necessarily influence elevational distribution nor confer a different phenotype.

Multi-Omics Analyses Uncover the Mechanism Underlying Polyploidization-Enhanced Steviol Glycosides Biosynthesis in Stevia rebaudiana

Stevia rebaudiana (Bertoni) is a valuable sweetener plant whose sweetness primarily derives from steviol glycosides (SGs), especially rebaudioside A (RA). Polyploidization has the potential to enhance the content of active ingredients in medicinal plants, making this strategy a promising avenue for genetic improvement. However, the underlying regulatory mechanisms that contribute to the fluctuating SGs content between autotetraploid and diploid stevia remain unclear. In this study, we employed metabolic analysis to identify 916 differentially accumulated metabolites (DAMs), with the majority, specifically terpenoids, flavonoids, and lipids, exhibiting upregulation due to polyploidization. Notably, the content of stevia's signature metabolite SGs (including RA, steviolbioside, and rebaudioside C), along with their precursor steviol, increased significantly after polyploidization. Furthermore, a comprehensive analysis of the transcriptome and metabolome revealed that the majority of differentially expressed genes (DEGs) involved in the SG-synthesis pathway (ent-KAH, ent-KS1, UGT73E1, UGT74G1, UGT76G1, UGT85C2, and UGT91D2) were upregulated in autotetraploid stevia, and these DEGs exhibited a positive correlation with the polyploidization-enhanced SGs. Additionally, multi-omics network analysis indicated that several transcription factor families (such as five NACs, four WRKYs, three MYBs, eight bHLHs, and three AP2/ERFs), various transporter genes (four ABC transporters, three triose-phosphate transporters, and two sugar efflux transporters for intercellular exchange), as well as microorganisms (including Ceratobasidium and Flavobacterium) were positively correlated with the accumulation of RA and steviol. Overall, our results indicate the presence of a regulatory circuit orchestrated by polyploidization, which recruits beneficial rhizosphere microbes and modulates the expression of genes associated with SG biosynthesis, ultimately enhancing the SG content in stevia. This finding will provide new insights for promoting the propagation and industrial development of stevia.

An unscheduled switch to endocycles induces a reversible senescent arrest that impairs growth of the Drosophila wing disc

A programmed developmental switch to G / S endocycles results in tissue growth through an increase in cell size. Unscheduled, induced endocycling cells (iECs) promote wound healing but also contribute to cancer. Much remains unknown, however, about how these iECs affect tissue growth. Using the D. melanogaster wing disc as model, we find that populations of iECs initially increase in size but then subsequently undergo a heterogenous arrest that causes severe tissue undergrowth. iECs acquired DNA damage and activated a Jun N-terminal kinase (JNK) pathway, but, unlike other stressed cells, were apoptosis-resistant and not eliminated from the epithelium. Instead, iECs entered a JNK-dependent and reversible senescent-like arrest. Senescent iECs promoted division of diploid neighbors, but this compensatory proliferation did not rescue tissue growth. Our study has uncovered unique attributes of iECs and their effects on tissue growth that have important implications for understanding their roles in wound healing and cancer.

Can ploidy levels explain the variation of Herbertia lahue (Iridaceae)?

Polyploidy is often related with phenotypic variation, as observed in Herbertia lahue, a geophyte species. This study examined the H. lahue polyploid series and departure in cytogenetic, morphometric, and pollen data. Diploids (2n=2x=14) present bimodal karyotype with two long and five short chromosome pairs, while hexaploids (2n=6x=42) and octoploids (2n=8x=56) present a gradual decrease in chromosome size. All cytotypes have CMA+/DAPI- bands co-localized with 18S rDNA sites in the satellite region (no DAPI+ bands in any cytotype). Unlike diploids and octoploids, 5S rDNA interstitial sites in hexaploids are not in a syntenic position with 18S rDNA sites. Genome size is effective as an indirect predictor of the cytotypes since 2C-values increased according to ploidy level. The reduction in the number of the rDNA sites in polyploids associated with their lower 1Cx-values compared to diploids may suggest a genome downsizing process. Morphometric analysis revealed significant differences among cytotypes, and discriminant analysis identified three morphometric groupings corresponding to the cytotypes. The phenotypic variation observed in pollen grains, bulbs, and ovary characters suggested the gigas effect. Concluding, remarkable differentiation was observed at both genomic and phenotypic characters in all the cytotypes analyzed, suggesting a possible ongoing speciation process in H. lahue.

Neopolyploidy-induced changes in giant duckweed (Spirodela polyrhiza) alter herbivore preference and performance and plant population performance

PREMISE

Polyploidy is a widespread mutational process in angiosperms that may alter population performance of not only plants but also their interacting species. Yet, knowledge of whether polyploidy affects plant-herbivore dynamics is scarce. Here, we tested whether aphid herbivores exhibit preference for diploid or neopolyploid plants, whether polyploidy impacts plant and herbivore performance, and whether these interactions depend on the plant genetic background.

METHODS

Using independently synthesized neotetraploid strains paired with their diploid progenitors of greater duckweed (Spirodela polyrhiza), we evaluated the effect of neopolyploidy on duckweed's interaction with the water-lily aphid (Rhopalosiphum nymphaeae). Using paired-choice experiments, we evaluated feeding preference of the herbivore. We then evaluated the consequences of polyploidy on aphid and plant performance by measuring population growth over multiple generations.

RESULTS

Aphids preferred neopolyploids when plants were provided at equal abundances but not at equal surface areas, suggesting the role of plant population surface area in driving this preference. Additionally, neopolyploidy increased aphid population performance, but this result was dependent on the plant's genetic lineage. Lastly, the impact of herbivory on neopolyploid vs. diploid duckweed varied greatly with genetic lineage, where neopolyploids appeared to be variably tolerant compared to diploids, sometimes mirroring the effect on herbivore performance.

CONCLUSIONS

By experimentally testing the impacts of polyploidy on trophic species interactions, we showed that polyploidization can impact the preference and performance of herbivores on their plant hosts. These results have significant implications for the establishment and persistence of plants and herbivores in the face of plant polyploidy.

The immediate metabolomic effects of whole-genome duplication in the greater duckweed, Spirodela polyrhiza

PREMISE

In plants, whole-genome duplication (WGD) is a common mutation with profound evolutionary potential. Given the costs associated with a superfluous genome copy, polyploid establishment is enigmatic. However, in the right environment, immediate phenotypic changes following WGD can facilitate establishment. Metabolite abundances are the direct output of the cell's regulatory network and determine much of the impact of environmental and genetic change on the phenotype. While it is well known that an increase in the bulk amount of genetic material can increase cell size, the impact of gene dosage multiplication on the metabolome remains largely unknown.

METHODS

We used untargeted metabolomics on four genetically distinct diploid-neoautotetraploid pairs of the greater duckweed, Spirodela polyrhiza, to investigate how WGD affects metabolite abundances per cell and per biomass.

RESULTS

Autopolyploidy increased metabolite levels per cell, but the response of individual metabolites varied considerably. However, the impact on metabolite level per biomass was restricted because the increased cell size reduced the metabolite concentration per cell. Nevertheless, we detected both quantitative and qualitative effects of WGD on the metabolome. Many effects were strain-specific, but some were shared by all four strains.

CONCLUSIONS

The nature and impact of metabolic changes after WGD depended strongly on the genotype. Dosage effects have the potential to alter the plant metabolome qualitatively and quantitatively, but were largely balanced out by the reduction in metabolite concentration due to an increase in cell size in this species.

Doubling down on polyploid discoveries: Global advances in genomics and ecological impacts of polyploidy

All flowering plants are now recognized as diploidized paleopolyploids (Jiao et al., 2011; One Thousand Plant Transcriptomes Initiative, 2019), and polyploid species comprise approximately 30% of contemporary plant species (Wood et al., 2009; Barker et al., 2016a). A major implication of these discoveries is that, to appreciate the evolution of plant diversity, we need to understand the fundamental biology of polyploids and diploidization. This need is broadly recognized by our community as there is a continued, growing interest in polyploidy as a research topic. Over the past 25 years, the sequencing and analysis of plant genomes has revolutionized our understanding of the importance of polyploid speciation to the evolution of land plants.

Why are triploid quaking aspen (Populus tremuloides) common?

PREMISE

Quaking aspen is a clonal tree species that has mixed ploidy, often with high relative abundance of both diploids and triploids but no haploids or tetraploids. Triploids typically have low fertility, leaving their occurrence apparently unlikely from an evolutionary perspective, unless they provide a "triploid bridge" to generating higher-fitness tetraploids-which are not observed in this species. This study focused on how triploidy can be maintained in quaking aspen.

METHODS

A computational model was used to simulate gamete production, sexual reproduction, asexual reproduction, parent survival, and offspring survival in a population. All parameters were assumed to be cytotype-dependent and environment-independent. Sampling methods were used to identify parameter combinations consistent with observed cytotype frequencies.

RESULTS

Many processes and parameter values were sufficient to yield a moderate frequency of triploids, and very few were necessary. The most plausible route involved higher triploid survival at the parent or offspring stage and limited unreduced gamete production by either diploid or triploid parents. Triploid fertility was helpful but not necessary.

CONCLUSIONS

The coexistence of diploids and triploids in quaking aspen is statistically likely and promoted by the existence of commonly observed, long-lived triploid clones. However, other mechanisms not captured by the model related to environmental variation could also occur. Further empirical data or more complex but difficult-to-parameterize models are needed to gain further insight.

Polyploid giant cancer cells: origin, possible pathways of formation, characteristics, and mechanisms of regulation

Polyploid giant cancer cells (PGCCs) are characterized by the presence of either a single enlarged nucleus or multiple nuclei and are closely associated with tumor progression and treatment resistance. These cells contribute significantly to cellular heterogeneity and can arise from various stressors, including radiation, chemotherapy, hypoxia, and environmental factors. The formation of PGCCs can occur through mechanisms such as endoreplication, cell fusion, cytokinesis failure, mitotic slippage, or cell cannibalism. Notably, PGCCs exhibit traits similar to cancer stem cells (CSCs) and generate highly invasive progeny through asymmetric division. The presence of PGCCs and their progeny is pivotal in conferring resistance to chemotherapy and radiation, as well as facilitating tumor recurrence and metastasis. This review provides a comprehensive analysis of the origins, potential formation mechanisms, stressors, unique characteristics, and regulatory pathways of PGCCs, alongside therapeutic strategies targeting these cells. The objective is to enhance the understanding of PGCC initiation and progression, offering novel insights into tumor biology.

Evolution and subfunctionalization of CIPK6 homologous genes in regulating cotton drought resistance

The occurrence of whole-genome duplication or polyploidy may promote plant adaptability to harsh environments. Here, we clarify the evolutionary relationship of eight GhCIPK6 homologous genes in upland cotton (Gossypium hirsutum). Gene expression and interaction analyses indicate that GhCIPK6 homologous genes show significant functional changes after polyploidy. Among these, GhCIPK6D1 and GhCIPK6D3 are significantly up-regulated by drought stress. Functional studies reveal that high GhCIPK6D1 expression promotes cotton drought sensitivity, while GhCIPK6D3 expression promotes drought tolerance, indicating clear functional differentiation. Genetic and biochemical analyses confirm the synergistic negative and positive regulation of cotton drought resistance through GhCBL1A1-GhCIPK6D1 and GhCBL2A1-GhCIPK6D3, respectively, to regulate stomatal movement by controlling the directional flow of K+ in guard cells. These results reveal differentiated roles of GhCIPK6 homologous genes in response to drought stress in upland cotton following polyploidy. The work provides a different perspective for exploring the functionalization and subfunctionalization of duplicated genes in response to polyploidization.

Clonal growth characteristics and diversity patterns of different Clintonia udensis (Liliaceae) diploid and tetraploid cytotypes in the Hualongshan Mountains

Polyploidization plays an important role in plant evolution and biodiversity. However, intraspecific polyploidy compared to interspecific polyploidy received less attention. Clintonia udensis (Liliaceae) possess diploid (2n = 2x = 14) and autotetraploid (2n = 4x = 28) cytotypes. In the Hualongshan Mountains, the autotetraploids grew on the northern slope, while the diploids grew on the southern slopes. The clonal growth characteristics and clonal architecture were measured and analyzed by field observations and morphological methods. The diversity level and differentiation patterns for two different cytotypes were investigated using SSR markers. The results showed that the clonal growth parameters, such as the bud numbers of each rhizome node and the ratio of rhizome branches in the autotetraploids were higher than those in the diploids. Both the diploids and autotetraploids appeared phalanx clonal architectures with short internodes between ramets. However, the ramets or genets of the diploids had a relatively scattered distribution, while those of the autotetraploids were relatively clumping. The diploids and autotetraploids all allocated more biomass to their vegetative growth. The diploids had a higher allocation to reproductive organs than that of autotetraploids, which indicated that the tetraploids invested more resources in clonal reproduction than diploids. The clone diversity and genetic diversity of the autotetraploids were higher than that of the diploids. Significant genetic differentiation between two different cytotypes was observed (P < 0.01). During establishment and evolution, C. udensis autotetraploids employed more clumping phalanx clonal architecture and exhibited more genetic variation than the diploids.

Genome-wide patterns of homoeologous gene flow in allotetraploid coffee

Premise

Allopolyploidy-a hybridization-induced whole-genome duplication event-has been a major driver of plant diversification. The extent to which chromosomes pair with their proper homolog vs. with their homoeolog in allopolyploids varies across taxa, and methods to detect homoeologous gene flow (HGF) are needed to understand how HGF has shaped polyploid lineages.

Methods

The ABBA-BABA test represents a classic method for detecting introgression between closely related species, but here we developed a modified use of the ABBA-BABA test to characterize the extent and direction of HGF in allotetraploid Coffea arabica.

Results

We found that HGF is abundant in the C. arabica genome, with both subgenomes serving as donors and recipients of variation. We also found that HGF is highly maternally biased in plastid-targeted-but not mitochondrial-targeted-genes, as would be expected if plastid-nuclear incompatibilities exist between the two parent species.

Discussion

Together, our analyses provide a simple framework for detecting HGF and new evidence consistent with selection favoring overwriting of paternally derived alleles by maternally derived alleles to ameliorate plastid-nuclear incompatibilities. Natural selection therefore appears to shape the direction and intensity of HGF in allopolyploid coffee, indicating that cytoplasmic inheritance has long-term consequences for polyploid lineages.

Origins of cancer: ain't it just mature cells misbehaving?

A pervasive view is that undifferentiated stem cells are alone responsible for generating all other cells and are the origins of cancer. However, emerging evidence demonstrates fully differentiated cells are plastic, can be coaxed to proliferate, and also play essential roles in tissue maintenance, regeneration, and tumorigenesis. Here, we review the mechanisms governing how differentiated cells become cancer cells. First, we examine the unique characteristics of differentiated cell division, focusing on why differentiated cells are more susceptible than stem cells to accumulating mutations. Next, we investigate why the evolution of multicellularity in animals likely required plastic differentiated cells that maintain the capacity to return to the cell cycle and required the tumor suppressor p53. Finally, we examine an example of an evolutionarily conserved program for the plasticity of differentiated cells, paligenosis, which helps explain the origins of cancers that arise in adults. Altogether, we highlight new perspectives for understanding the development of cancer and new strategies for preventing carcinogenic cellular transformations from occurring.

Apomixis and the paradox of sex in plants

BACKGROUND

The predominance of sex in eukaryotes, despite the high costs of meiosis and mating, remains an evolutionary enigma. Many theories have been proposed, none of them being conclusive on its own, and they are, in part, not well applicable to land plants. Sexual reproduction is obligate in embryophytes for the great majority of species.

SCOPE

This review compares the main forms of sexual and asexual reproduction in ferns and angiosperms, based on the generation cycling of sporophyte and gametophyte (leaving vegetative propagation aside). The benefits of sexual reproduction for maintenance of genomic integrity in comparison to asexuality are discussed in the light of developmental, evolutionary, genetic and phylogenetic studies.

CONCLUSIONS

Asexual reproduction represents modifications of the sexual pathway, with various forms of facultative sexuality. For sexual land plants, meiosis provides direct DNA repair mechanisms for oxidative damage in reproductive tissues. The ploidy alternations of meiosis-syngamy cycles and prolonged multicellular stages in the haploid phase in the gametophytes provide a high efficiency of purifying selection against recessive deleterious mutations. Asexual lineages might buffer effects of such mutations via polyploidy and can purge the mutational load via facultative sexuality. The role of organelle-nuclear genome compatibility for maintenance of genome integrity is not well understood. In plants in general, the costs of mating are low because of predominant hermaphroditism. Phylogenetic patterns in the archaeplastid clade suggest that high frequencies of sexuality in land plants are concomitant with a stepwise increase of intrinsic and extrinsic stress factors. Furthermore, expansion of genome size in land plants would increase the potential mutational load. Sexual reproduction appears to be essential for keeping long-term genomic integrity, and only rare combinations of extrinsic and intrinsic factors allow for shifts to asexuality.

Phased chromosome-scale genome assembly of an asexual, allopolyploid root-knot nematode reveals complex subgenomic structure

We present the chromosome-scale genome assembly of the allopolyploid root-knot nematode Meloidogyne javanica. We show that the M. javanica genome is predominantly allotetraploid, comprising two subgenomes, A and B, that most likely originated from hybridisation of two ancestral parental species. The assembly was annotated using full-length non-chimeric transcripts, comparison to reference databases, and ab initio prediction techniques, and the subgenomes were phased using ancestral k-mer spectral analysis. Subgenome B appears to show fission of chromosomal contigs, and while there is substantial synteny between subgenomes, we also identified regions lacking synteny that may have diverged in the ancestral genomes prior to or following hybridisation. This annotated and phased genome assembly forms a significant resource for understanding the origins and genetics of these globally important plant pathogens.

Single-nucleus multi-omic profiling of polyploid heart nuclei identifies fusion-derived cardiomyocytes in the human heart

Understanding the mechanisms of polyploidization in cardiomyocytes is crucial for advancing strategies to stimulate myocardial regeneration. Although endoreplication has long been considered the primary source of polyploid human cardiomyocytes, recent animal work suggests the potential for cardiomyocyte fusion. Moreover, the effects of polyploidization on the genomic-transcriptomic repertoire of human cardiomyocytes have not been studied previously. We applied single-nuclei whole genome sequencing, single nuclei RNA sequencing, and multiome ATAC + gene expression (from the same nuclei) techniques to nuclei isolated from 11 healthy hearts. Utilizing post-zygotic non-inherited somatic mutations occurring during development as "endogenous barcodes," to reconstruct lineage relationships of polyploid cardiomyocytes. Of 482 cardiomyocytes from multiple healthy donor hearts 75.7% can be sorted into several developmental clades marked by one or more somatic single-nucleotide variants (SNVs). At least ~10% of tetraploid cardiomyocytes contain cells from distinct clades, indicating fusion of lineally distinct cells, whereas 60% of higher-ploidy cardiomyocytes contain fused cells from distinct clades. Combined snRNA-seq and snATAC-seq revealed transcriptome and chromatin landscapes of polyploid cardiomyocytes distinct from diploid cardiomyocytes, and show some higher-ploidy cardiomyocytes with transcriptional signatures suggesting fusion between cardiomyocytes and endothelial and fibroblast cells. These observations provide the first evidence for cell and nuclear fusion of human cardiomyocytes, raising the possibility that cell fusion may contribute to developing or maintaining polyploid cardiomyocytes in the human heart.

Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton

Polyploidy is a prominent mechanism of plant speciation and adaptation, yet the mechanistic understandings of duplicated gene regulation remain elusive. Chromatin structure dynamics are suggested to govern gene regulatory control. Here, we characterized genome-wide nucleosome organization and chromatin accessibility in allotetraploid cotton, Gossypium hirsutum (AADD, 2n = 4X = 52), relative to its two diploid parents (AA or DD genome) and their synthetic diploid hybrid (AD), using DNS-seq. The larger A-genome exhibited wider average nucleosome spacing in diploids, and this intergenomic difference diminished in the allopolyploid but not hybrid. Allopolyploidization also exhibited increased accessibility at promoters genome-wide and synchronized cis-regulatory motifs between subgenomes. A prominent cis-acting control was inferred for chromatin dynamics and demonstrated by transposable element removal from promoters. Linking accessibility to gene expression patterns, we found distinct regulatory effects for hybridization and later allopolyploid stages, including nuanced establishment of homoeolog expression bias and expression level dominance. Histone gene expression and nucleosome organization are coordinated through chromatin accessibility. Our study demonstrates the capability to track high-resolution chromatin structure dynamics and reveals their role in the evolution of cis-regulatory landscapes and duplicate gene expression in polyploids, illuminating regulatory ties to subgenomic asymmetry and dominance.

Polyploidy in Cancer: Causal Mechanisms, Cancer-Specific Consequences, and Emerging Treatments

Drug resistance is the major determinant for metastatic disease and fatalities, across all cancers. Depending on the tissue of origin and the therapeutic course, a variety of biological mechanisms can support and sustain drug resistance. Although genetic mutations and gene silencing through epigenetic mechanisms are major culprits in targeted therapy, drug efflux and polyploidization are more global mechanisms that prevail in a broad range of pathologies, in response to a variety of treatments. There is an unmet need to identify patients at risk for polyploidy, understand the mechanisms underlying polyploidization, and to develop strategies to predict, limit, and reverse polyploidy thus enhancing efficacy of standard-of-care therapy that improve better outcomes. This literature review provides an overview of polyploidy in cancer and offers perspective on patient monitoring and actionable therapy.

Cytonuclear interplay in auto- and allopolyploids: a multifaceted perspective from the Festuca-Lolium complex

Restoring cytonuclear stoichiometry is necessary after whole-genome duplication (WGD) and interspecific/intergeneric hybridization in plants. We investigated this phenomenon in auto- and allopolyploids of the Festuca-Lolium complex providing insights into the mechanisms governing cytonuclear interactions in early polyploid and hybrid generations. Our study examined the main processes potentially involved in restoring the cytonuclear balance after WGD comparing diploids and new and well-established autopolyploids. We uncovered that both the number of chloroplasts and the number of chloroplast genome copies were significantly higher in the newly established autopolyploids and grew further in more established autopolyploids. The increase in the copy number of the chloroplast genome exceeded the rise in the number of chloroplasts and fully compensated for the doubling of the nuclear genome. In addition, changes in nuclear and organelle gene expression were insignificant. Allopolyploid Festuca × Lolium hybrids displayed potential structural conflicts in parental protein variants within the cytonuclear complexes. While biased maternal allele expression has been observed in numerous hybrids, our results suggest that its role in cytonuclear stabilization in the Festuca × Lolium hybrids is limited. This study provides insights into the restoration of the cytonuclear stoichiometry, yet it emphasizes the need for future research to explore post-transcriptional regulation and its impact on cytonuclear gene expression stoichiometry. Our findings may enhance the understanding of polyploid plant evolution, with broader implications for the study of cytonuclear interactions in diverse biological contexts.

Genome-wide DNA methylation dynamics following recent polyploidy in the allotetraploid Tragopogon miscellus (Asteraceae)

Polyploidy is an important evolutionary force, yet epigenetic mechanisms, such as DNA methylation, that regulate genome-wide expression of duplicated genes remain largely unknown. Here, we use Tragopogon (Asteraceae) as a model system to discover patterns and temporal dynamics of DNA methylation in recently formed polyploids. The naturally occurring allotetraploid Tragopogon miscellus formed in the last 95-100 yr from parental diploids Tragopogon dubius and T. pratensis. We profiled the DNA methylomes of these three species using whole-genome bisulfite sequencing. Genome-wide methylation levels in T. miscellus were intermediate between its diploid parents. However, nonadditive CG and CHG methylation occurred in transposable elements (TEs), with variation among TE types. Most differentially methylated regions (DMRs) showed parental legacy, but some novel DMRs were detected in the polyploid. Differentially methylated genes (DMGs) were also identified and characterized. This study provides the first assessment of both overall and locus-specific patterns of DNA methylation in a recent natural allopolyploid and shows that novel methylation variants can be generated rapidly after polyploid formation. Together, these results demonstrate that mechanisms to regulate duplicate gene expression may arise soon after allopolyploid formation and that these mechanisms vary among genes.

Whole-genome duplication in the Multicellularity Long Term 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. 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 undergo spontaneous WGD. From its origin within the first 50 days of the experiment, tetraploids persist for the next 950 days (nearly 5,000 generations, the current leading edge of our experiment) in ten replicate populations, despite being genomically unstable. Using synthetic reconstruction, biophysical modeling, and counter-selection experiments, we found that tetraploidy evolved because it confers immediate fitness benefits in this environment, 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, playing 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.

Polyploidy Promotes Hypertranscription, Apoptosis Resistance, and Ciliogenesis in Cancer Cells and Mesenchymal Stem Cells of Various Origins: Comparative Transcriptome In Silico Study

Mesenchymal stem cells (MSC) attract an increasing amount of attention due to their unique therapeutic properties. Yet, MSC can undergo undesirable genetic and epigenetic changes during their propagation in vitro. In this study, we investigated whether polyploidy can compromise MSC oncological safety and therapeutic properties. For this purpose, we compared the impact of polyploidy on the transcriptome of cancer cells and MSC of various origins (bone marrow, placenta, and heart). First, we identified genes that are consistently ploidy-induced or ploidy-repressed through all comparisons. Then, we selected the master regulators using the protein interaction enrichment analysis (PIEA). The obtained ploidy-related gene signatures were verified using the data gained from polyploid and diploid populations of early cardiomyocytes (CARD) originating from iPSC. The multistep bioinformatic analysis applied to the cancer cells, MSC, and CARD indicated that polyploidy plays a pivotal role in driving the cell into hypertranscription. It was evident from the upregulation of gene modules implicated in housekeeping functions, stemness, unicellularity, DNA repair, and chromatin opening by means of histone acetylation operating via DNA damage associated with the NUA4/TIP60 complex. These features were complemented by the activation of the pathways implicated in centrosome maintenance and ciliogenesis and by the impairment of the pathways related to apoptosis, the circadian clock, and immunity. Overall, our findings suggest that, although polyploidy does not induce oncologic transformation of MSC, it might compromise their therapeutic properties because of global epigenetic changes and alterations in fundamental biological processes. The obtained results can contribute to the development and implementation of approaches enhancing the therapeutic properties of MSC by removing polyploid cells from the cell population.

Premature endocycling of Drosophila follicle cells causes pleiotropic defects in oogenesis

Endocycling cells grow and repeatedly duplicate their genome without dividing. Cells switch from mitotic cycles to endocycles in response to developmental signals during the growth of specific tissues in a wide range of organisms. The purpose of switching to endocycles, however, remains unclear in many tissues. Additionally, cells can switch to endocycles in response to conditional signals, which can have beneficial or pathological effects on tissues. However, the impact of these unscheduled endocycles on development is underexplored. Here, we use Drosophila ovarian somatic follicle cells as a model to examine the impact of unscheduled endocycles on tissue growth and function. Follicle cells normally switch to endocycles at mid-oogenesis. Inducing follicle cells to prematurely switch to endocycles resulted in the lethality of the resulting embryos. Analysis of ovaries with premature follicle cell endocycles revealed aberrant follicular epithelial structure and pleiotropic defects in oocyte growth, developmental gene amplification, and the migration of a special set of follicle cells known as border cells. Overall, these findings reveal how unscheduled endocycles can disrupt tissue growth and function to cause aberrant development.

Polyploid tubular cells: a shortcut to stress adaptation

Tubular epithelial cells (TCs) compose the majority of kidney parenchyma and play fundamental roles in maintaining homeostasis. Like other tissues, mostly immature TC with progenitor capabilities are able to replace TC lost during injury via clonal expansion and differentiation. In contrast, differentiated TC lack this capacity. However, as the kidney is frequently exposed to toxic injuries, evolution positively selected a response program that endows differentiated TC to maintain residual kidney function during kidney injury. Recently, we and others have described polyploidization of differentiated TC, a mechanism to augment the function of remnant TC after injury by rapid hypertrophy. Polyploidy is a condition characterized by >2 complete sets of chromosomes. Polyploid cells often display an increased functional capacity and are generally more resilient to stress as evidenced by being conserved across many plants and eukaryote species from flies to mammals. Here, we discuss the occurrence of TC polyploidy in different contexts and conditions and how this integrates into existing concepts of kidney cell responses to injury. Collectively, we aim at stimulating the acquisition of novel knowledge in the kidney field as well as accelerating the translation of this basic response mechanism to the clinical sphere.

Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics

Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these technologies are gaining traction in plant molecular and developmental biology for elucidating the transcriptional changes across cell types in a specific tissue or organ, upon treatments, in response to biotic and abiotic stresses, or between genotypes. Despite the rapidly accelerating use of these technologies, collective and standardized experimental and analytical procedures to support the acquisition of high-quality data sets are still missing. In this commentary, we discuss common challenges associated with the use of single-cell transcriptomics in plants and propose general guidelines to improve reproducibility, quality, comparability, and interpretation and to make the data readily available to the community in this fast-developing field of research.

The antagonistic relationship between apoptosis and polyploidy in development and cancer

One of the important functions of regulated cell death is to prevent cells from inappropriately acquiring extra copies of their genome, a state known as polyploidy. Apoptosis is the primary cell death mechanism that prevents polyploidy, and defects in this apoptotic response can result in polyploid cells whose subsequent error-prone chromosome segregation are a major contributor to genome instability and cancer progression. Conversely, some cells actively repress apoptosis to become polyploid as part of normal development or regeneration. Thus, although apoptosis prevents polyploidy, the polyploid state can actively repress apoptosis. In this review, we discuss progress in understanding the antagonistic relationship between apoptosis and polyploidy in development and cancer. Despite recent advances, a key conclusion is that much remains unknown about the mechanisms that link apoptosis to polyploid cell cycles. We suggest that drawing parallels between the regulation of apoptosis in development and cancer could help to fill this knowledge gap and lead to more effective therapies.

An unscheduled switch to endocycles induces a reversible senescent arrest that impairs growth of the Drosophila wing disc

A programmed developmental switch to G / S endocycles results in tissue growth through an increase in cell size. Unscheduled, induced endocycling cells (iECs) promote wound healing but also contribute to cancer. Much remains unknown, however, about how these iECs affect tissue growth. Using the D. melanogasterwing disc as model, we find that populations of iECs initially increase in size but then subsequently undergo a heterogenous arrest that causes severe tissue undergrowth. iECs acquired DNA damage and activated a Jun N-terminal kinase (JNK) pathway, but, unlike other stressed cells, were apoptosis-resistant and not eliminated from the epithelium. Instead, iECs entered a JNK-dependent and reversible senescent-like arrest. Senescent iECs promoted division of diploid neighbors, but this compensatory proliferation did not rescue tissue growth. Our study has uncovered unique attributes of iECs and their effects on tissue growth that have important implications for understanding their roles in wound healing and cancer.

Water stress modulates terpene biosynthesis and morphophysiology at different ploidal levels in Lippia alba (Mill.) N. E. Brown (Verbenaceae)

Monoterpenes are the main component in essential oils of Lippia alba. In this species, the chemical composition of essential oils varies with genome size: citral (geraniol and neral) is dominant in diploids and tetraploids, and linalool in triploids. Because environmental stress impacts various metabolic pathways, we hypothesized that stress responses in L. alba could alter the relationship between genome size and essential oil composition. Water stress affects the flowering, production, and reproduction of plants. Here, we evaluated the effect of water stress on morphophysiology, essential oil production, and the expression of genes related to monoterpene synthesis in diploid, triploid, and tetraploid accessions of L. alba cultivated in vitro for 40 days. First, using transcriptome data, we performed de novo gene assembly and identified orthologous genes using phylogenetic and clustering-based approaches. The expression of candidate genes related to terpene biosynthesis was estimated by real-time quantitative PCR. Next, we assessed the expression of these genes under water stress conditions, whereby 1% PEG-4000 was added to MS medium. Water stress modulated L. alba morphophysiology at all ploidal levels. Gene expression and essential oil production were affected in triploid accessions. Polyploid accessions showed greater growth and metabolic tolerance under stress compared to diploids. These results confirm the complex regulation of metabolic pathways such as the production of essential oils in polyploid genomes. In addition, they highlight aspects of genotype and environment interactions, which may be important for the conservation of tropical biodiversity.

Polyploidization: A Biological Force That Enhances Stress Resistance

Organisms with three or more complete sets of chromosomes are designated as polyploids. Polyploidy serves as a crucial pathway in biological evolution and enriches species diversity, which is demonstrated to have significant advantages in coping with both biotic stressors (such as diseases and pests) and abiotic stressors (like extreme temperatures, drought, and salinity), particularly in the context of ongoing global climate deterioration, increased agrochemical use, and industrialization. Polyploid cultivars have been developed to achieve higher yields and improved product quality. Numerous studies have shown that polyploids exhibit substantial enhancements in cell size and structure, physiological and biochemical traits, gene expression, and epigenetic modifications compared to their diploid counterparts. However, some research also suggested that increased stress tolerance might not always be associated with polyploidy. Therefore, a more comprehensive and detailed investigation is essential to complete the underlying stress tolerance mechanisms of polyploids. Thus, this review summarizes the mechanism of polyploid formation, the polyploid biochemical tolerance mechanism of abiotic and biotic stressors, and molecular regulatory networks that confer polyploidy stress tolerance, which can shed light on the theoretical foundation for future research.

Polyploid Cancer Cell Models in Drosophila

Cells with an abnormal number of chromosomes have been found in more than 90% of solid tumors, and among these, polyploidy accounts for about 40%. Polyploidized cells most often have duplicate centrosomes as well as genomes, and thus their mitosis tends to promote merotelic spindle attachments and chromosomal instability, which produces a variety of aneuploid daughter cells. Polyploid cells have been found highly resistant to various stress and anticancer therapies, such as radiation and mitogenic inhibitors. In other words, common cancer therapies kill proliferative diploid cells, which make up the majority of cancer tissues, while polyploid cells, which lurk in smaller numbers, may survive. The surviving polyploid cells, prompted by acute environmental changes, begin to mitose with chromosomal instability, leading to an explosion of genetic heterogeneity and a concomitant cell competition and adaptive evolution. The result is a recurrence of the cancer during which the tenacious cells that survived treatment express malignant traits. Although the presence of polyploid cells in cancer tissues has been observed for more than 150 years, the function and exact role of these cells in cancer progression has remained elusive. For this reason, there is currently no effective therapeutic treatment directed against polyploid cells. This is due in part to the lack of suitable experimental models, but recently several models have become available to study polyploid cells in vivo. We propose that the experimental models in Drosophila, for which genetic techniques are highly developed, could be very useful in deciphering mechanisms of polyploidy and its role in cancer progression.

PloiDB: the plant ploidy database

See also the Commentary on this article by Spoelhof et al., 240: 909–911.

Polyploidy-associated autophagy promotes larval tracheal histolysis at Drosophila metamorphosis

Polyploidy is an extended phenomenon in biology. However, its physiological significance and whether it defines specific cell behaviors is not well understood. Here we study its connection to macroautophagy/autophagy, using the larval respiratory system of Drosophila as a model. This system comprises cells with the same function yet with notably different ploidy status, namely diploid progenitors and their polyploid larval counterparts, the latter destined to die during metamorphosis. We identified an association between polyploidy and autophagy and found that higher endoreplication status correlates with elevated autophagy. Finally, we report that tissue histolysis in the trachea during Drosophila metamorphosis is mediated by autophagy, which triggers the apoptosis of polyploid cells.Abbreviations: APF: after pupa formation; Atg: autophagy related; btl: breathless; CycE: Cyclin E; DT: dorsal trunk; fzr: fizzy-related; L3: larval stage 3; PBS: phosphate-buffered saline; RI: RNAi; Tr: tracheal metamere; yki: yorkie.

Plant neopolyploidy and genetic background differentiate the microbiome of duckweed across a variety of natural freshwater sources

Whole-genome duplication has long been appreciated for its role in driving phenotypic novelty in plants, often altering the way organisms interface with the abiotic environment. Only recently, however, have we begun to investigate how polyploidy influences interactions of plants with other species, despite the biotic niche being predicted as one of the main determinants of polyploid establishment. Nevertheless, we lack information about how polyploidy affects the diversity and composition of the microbial taxa that colonize plants, and whether this is genotype-dependent and repeatable across natural environments. This information is a first step towards understanding whether the microbiome contributes to polyploid establishment. We, thus, tested the immediate effect of polyploidy on the diversity and composition of the bacterial microbiome of the aquatic plant Spirodela polyrhiza using four pairs of diploids and synthetic autotetraploids. Under controlled conditions, axenic plants were inoculated with pond waters collected from 10 field sites across a broad environmental gradient. Autotetraploids hosted 4%-11% greater bacterial taxonomic and phylogenetic diversity than their diploid progenitors. Polyploidy, along with its interactions with the inoculum source and genetic lineage, collectively explained 7% of the total variation in microbiome composition. Furthermore, polyploidy broadened the core microbiome, with autotetraploids having 15 unique bacterial taxa in addition to the 55 they shared with diploids. Our results show that whole-genome duplication directly leads to novelty in the plant microbiome and importantly that the effect is dependent on the genetic ancestry of the polyploid and generalizable over many environmental contexts.

Creating Polyploid Escherichia Coli and Its Application in Efficient L-Threonine Production

Prokaryotic genomes are generally organized in haploid. In synthetic biological research, efficient chassis cells must be constructed to produce bio-based products. Here, the essential division of the ftsZ gene to create functional polyploid E. coli is regulated. The artificial polyploid E. coli containing 2-4 chromosomes is confirmed through PCR amplification, terminator localization, and flow cytometry. The polyploid E. coli exhibits a larger cell size, and its low pH tolerance and acetate resistance are stronger than those of haploid E. coli. Transcriptome analysis shows that the genes of the cell's main functional pathways are significantly upregulated in the polyploid E. coli. These advantages of the polyploid E. coli results in the highest reported L-threonine yield (160.3 g L-1 ) in fed-batch fermentation to date. In summary, an easy and convenient method for constructing polyploid E. coli and demonstrated its application in L-threonine production is developed. This work provides a new approach for creating an excellent host strain for biochemical production and studying the evolution of prokaryotes and their chromosome functions.

Characterization of the horse chestnut genome reveals the evolution of aescin and aesculin biosynthesis

Horse chestnut (Aesculus chinensis) is an important medicinal tree that contains various bioactive compounds, such as aescin, barrigenol-type triterpenoid saponins (BAT), and aesculin, a glycosylated coumarin. Herein, we report a 470.02 Mb genome assembly and characterize an Aesculus-specific whole-genome duplication event, which leads to the formation and duplication of two triterpenoid biosynthesis-related gene clusters (BGCs). We also show that AcOCS6, AcCYP716A278, AcCYP716A275, and AcCSL1 genes within these two BGCs along with a seed-specific expressed AcBAHD6 are responsible for the formation of aescin. Furthermore, we identify seven Aesculus-originated coumarin glycoside biosynthetic genes and achieve the de novo synthesis of aesculin in E. coli. Collinearity analysis shows that the collinear BGC segments can be traced back to early-diverging angiosperms, and the essential gene-encoding enzymes necessary for BAT biosynthesis are recruited before the splitting of Aesculus, Acer, and Xanthoceras. These findings provide insight on the evolution of gene clusters associated with medicinal tree metabolites.