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Desiccation tolerance evolved recurrently across diverse plant lineages to enable survival in water-limited conditions. Many resurrection plants are polyploid, and several groups have hypothesized that polyploidy contributed to the evolution of desiccation tolerance. However, due to the vast phylogenetic distance between resurrection plant lineages, the rarity of desiccation tolerance, and the prevalence of polyploidy in plants, this hypothesis has been difficult to test. Here, we surveyed natural variation in morphological, reproductive, and desiccation tolerance traits across several cytotypes of a single species to test for links between polyploidy and increased resilience. We sampled multiple natural populations of the resurrection grass Microchloa caffra across an environmental gradient ranging from mesic to xeric in South Africa. We describe two distinct ecotypes of M. caffra that occupy different extremes of the environmental gradient and exhibit consistent differences in ploidy, morphological, reproductive, and desiccation tolerance traits in both field and common growth conditions. Interestingly, plants with more polyploid genomes exhibited consistently higher recovery from desiccation, were less reproductive, and were larger than plants with smaller genomes and lower ploidy. These data indicate that selective pressures in increasingly xeric sites may play a role in maintaining and increasing desiccation tolerance and are mediated by changes in ploidy. [ABSTRACT FROM AUTHOR]

SUMMARY While the phenomenon of uniparental silencing of 35S rDNA in interspecific hybrids and allopolyploids is well documented, there is a notable absence of information regarding whether such silencing extends to the 5S RNA component of ribosomes. To address this gap in knowledge, we analyzed the 5S and 35S rDNA expression in Cardamine (Brassicaceae) allopolyploids, namely C. × insueta (2n = 3x = 24, genome composition RRA), C. flexuosa (2n = 4x = 32, AAHH), and C. scutata (2n = 4x = 32, PPAA) which share a common diploid ancestor (AA). We employed high‐throughput sequencing of transcriptomes and genomes and phylogenetic analyses of 5S rRNA variants. The genomic organization of rDNA was further scrutinized through clustering and fluorescence in situ hybridization. In the C. × insueta allotriploid, we observed uniparental dominant expression of 5S and 35S rDNA loci. In the C. flexuosa and C. scutata allotetraploids, the expression pattern differed, with the 35S rDNA being expressed from the A subgenome, whereas the 5S rDNA was expressed from the partner subgenome. Both C. flexuosa and C. scutata but not C. × insueta showed copy and locus number changes. We conclude that in stabilized allopolyploids, transcription of ribosomal RNA components occurs from different subgenomes. This phenomenon appears to result in the formation of chimeric ribosomes comprising rRNA molecules derived from distinct parental origins. We speculate that the interplay of epigenetic silencing and rDNA rearrangements introduces an additional layer of variation in multimolecule ribosomal complexes, potentially contributing to the evolutionary success of allopolyploids. [ABSTRACT FROM AUTHOR]

Insights into the evolution of regulatory networks are emerging from studies of the 3D structure of chromatin and its role in transcriptional regulation. The development of regulome technologies has advanced our understanding of the evolutionary principles governing regulatory elements and chromatin organization. Transposons have had an important role in the evolution of cis -regulatory element (CRE) landscapes, including the formation of novel CREs and the alteration of distances between CREs and genes. The dynamics of hierarchical chromatin organization, driven by genetic variation, emerges as a critical factor in the evolution of gene regulation. This offers a promising framework for investigating the evolution of regulatory mechanisms in plant systems, their differences among species and genotypes, and following polyploidy. Development of complex traits necessitates the functioning and coordination of intricate regulatory networks involving multiple genes. Understanding 3D chromatin structure can facilitate insight into the regulation of gene expression by regulatory elements. This potential, of visualizing the role of chromatin organization in the evolution and function of regulatory elements, remains largely unexplored. Here, we describe new perspectives that arise from the dual considerations of sequence variation of regulatory elements and chromatin structure, with a special focus on whole-genome doubling or polyploidy. We underscore the significance of hierarchical chromatin organization in gene regulation during evolution. In addition, we describe strategies for exploring chromatin organization in future investigations of regulatory evolution in plants, enabling insights into the evolutionary influence of regulatory elements on gene expression and, hence, phenotypes. [ABSTRACT FROM AUTHOR]

Asexual seed reproduction, apomixis, is a relatively rare reproductive strategy in angiosperms. Its rarity is probably due to evolutionary constraints that require full and synchronous expression of all the steps that modify the ancestral sexual pathway. Therefore, the documentation of any new occurrence of apomixis, especially in taxonomic groups with no previous report, should be based on thorough and solid evidence. Here, we correct the report of suggested apomictic reproduction in two endemic hexaploid species of Senecio from Australia. Based on either excess or deficiency of expected heterozygosity across loci, over-representation of several multilocus genotypes, and segregation analysis assessed using microsatellite markers, it was suggested that apomixis together with selfing could explain the observed patterns of genetic variation in perennial S. macrocarpus and annual S. squarrosus. We used flow cytometric seed screening analyses to verify the mode of reproduction of several widespread multilocus genotypes that are considered to be apomictic. These analyses revealed that all seed progeny arose by the sexual pathway, as they exhibited a constant 3:2 endosperm to embryo ploidy ratio, typical of double fertilization of a reduced embryo sac by two reduced sperm cells. Therefore, both species reproduce sexually. We suggest that the unusual genetic patterns in both allopolyploids are caused by originally low variation in the parental species, which probably also reproduce by selfing, disomic inheritance and probably also the presence of null alleles. We call for a more careful and critical interpretation of the patterns obtained, taking into account all aspects related to apomictic reproduction. [ABSTRACT FROM AUTHOR]

New Zealand is home to 16 endemic species of Lepidium (Brassicaceae), including two species considered to have become extinct since European colonisation and an additional species shared with Australia. Previous meiotic chromosome counts suggest at least some are high polyploids. A hybrid origin has been proposed for several of them, with African and American species implicated as parents. We generated amplicon sequence data for 15 genes derived from targeted enrichment data from a selection of species endemic to New Zealand, and of African, American, and Australian origin naturalised in New Zealand. These were analysed, along with publicly available genomic data from other Lepidium species. Our results are consistent with earlier work in supporting two main groups of endemic New Zealand Lepidium, corresponding to different dominant nrDNA sequences. Our data suggest that these two groups differ in ploidy (one octoploid, the ploidy of the other uncertain). The octoploid species combine four distinguishable subgenomes and the other species may be the products of allopolyploidisation between octoploid species and a diploid species closely related to, if not, L. africanum. Previously proposed links to American Lepidium are also supported, with at least two Australasian Lepidium subgenomes related to subgenomes present in American polyploid species. The affinities of two further subgenomes present in Australasian Lepidium remain to be determined, but they may also be of American origin. One New Zealand endemic species, L. naufragorum, displays sequences broadly consistent with it being the octodecaploid product of hybridisation between octoploid and decaploid New Zealand groups. [ABSTRACT FROM AUTHOR]

Hybridization blurs species boundaries and leads to intertwined lineages resulting in reticulate evolution. Polyploidy, the outcome of whole genome duplication (WGD), has more recently been implicated in promoting and facilitating hybridization between polyploid species, potentially leading to adaptive introgression. However, because polyploid lineages are usually ephemeral states in the evolutionary history of life it is unclear whether WGD-potentiated hybridization has any appreciable effect on their diploid counterparts. Here, we develop a model of cytotype dynamics within mixed-ploidy populations to demonstrate that polyploidy can in fact serve as a bridge for gene flow between diploid lineages, where introgression is fully or partially hampered by the species barrier. Polyploid bridges emerge in the presence of triploid organisms, which despite critically low levels of fitness, can still allow the transfer of alleles between diploid states of independently evolving mixed-ploidy species. Notably, while marked genetic divergence prevents polyploid-mediated interspecific gene flow, we show that increased recombination rates can offset these evolutionary constraints, allowing a more efficient sorting of alleles at higher-ploidy levels before introgression into diploid gene pools. Additionally, we derive an analytical approximation for the rate of gene flow at the tetraploid level necessary to supersede introgression between diploids with nonzero introgression rates, which is especially relevant for plant species complexes, where interspecific gene flow is ubiquitous. Altogether, our results illustrate the potential impact of polyploid bridges on the (re)distribution of genetic material across ecological communities during evolution, representing a potential force behind reticulation. [ABSTRACT FROM AUTHOR]

SUMMARY: 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. [ABSTRACT FROM AUTHOR]

Motivation Major improvements in sequencing technologies and genome sequence assembly have led to a huge increase in the number of available genome sequences. In turn, these genome sequences form an invaluable source for evolutionary, ecological, and comparative studies. One kind of analysis that has become routine is the search for traces of ancient polyploidy, particularly for plant genomes, where whole-genome duplication (WGD) is rampant. Results Here, we present a major update of a previously developed tool wgd, namely wgd v2, to look for remnants of ancient polyploidy, or WGD. We implemented novel and improved previously developed tools to (a) construct K S age distributions for the whole-paranome (collection of all duplicated genes in a genome), (b) unravel intragenomic and intergenomic collinearity resulting from WGDs, (c) fit mixture models to age distributions of gene duplicates, (d) correct substitution rate variation for phylogenetic placement of WGDs, and (e) date ancient WGDs via phylogenetic dating of WGD-retained gene duplicates. The applicability and feasibility of wgd v2 for the identification and the relative and absolute dating of ancient WGDs is demonstrated using different plant genomes. Availability and implementation wgd v2 is open source and available at https://github.com/heche-psb/wgd. [ABSTRACT FROM AUTHOR]

Genome duplications and ploidy transitions have occurred in nearly every major taxon of eukaryotes, but they are far more common in plants than in animals. Due to the conservation of the nuclear:cytoplasmic volume ratio increased DNA content results in larger cells. In plants, polyploid organisms are larger than diploids as cell number remains relatively constant. Conversely, vertebrate body size does not correlate with cell size and ploidy as vertebrates compensate for increased cell size to maintain tissue architecture and body size. This has historically been explained by a simple reduction in cell number that matches the increase in cell size maintaining body size as ploidy increases, but here we show that the compensatory mechanisms that maintain body size in triploid zebrafish are tissue-specific: A) erythrocytes respond in the classical pattern with a reduced number of larger erythrocytes in circulation, B) muscle, a tissue comprised of polynucleated muscle fibers, compensates by reducing the number of larger nuclei such that myofiber and myotome size in unaffected by ploidy, and C) vascular tissue compensates by thickening blood vessel walls, possibly at the expense of luminal diameter. Understanding the physiological implications of ploidy on tissue function requires a detailed description of the specific mechanisms of morphological compensation occurring in each tissue to understand how ploidy changes affect development and physiology. [Display omitted] • Tissue-specific mechanisms compensate for changes in cell size. • Blastomere size, cleavage pattern and rate are not affected by ploidy. • Erythrocytes conform to the canonical pattern of 'fewer but larger cells'. • Multinucleate skeletal muscle cells adjust the number of nuclei to maintain size. • Vasculature is comprised of the same number and pattern of larger endothelial cells. [ABSTRACT FROM AUTHOR]

Polyploidy, resulting from whole‐genome duplication (WGD), is ubiquitous in nature and reportedly associated with extreme environments and biological invasions. However, WGD usually comes with great costs, raising questions about the establishment chance of newly formed polyploids. The surprisingly high number of polyploid and mixed‐ploidy species observed in nature may be a consequence of their continuous emergence or may reflect stable polyploid persistence and even coexistence with the ancestral ploidy under certain circumstances. However, empirical studies on contemporary polyploid establishment often neglect the cost–benefit balances of polyploid characteristics, tradeoffs between phenotypic characteristics, intercytotype interactions, recurrent polyploid formation, and stochastic processes. Here, we advocate for considering population‐level success, combining the aforementioned factors that affect polyploid establishment and long‐term coexistence with their ancestors. We approach the paradox of polyploid establishment despite high costs from a modern coexistence theory perspective and give an overview of the diversity of mechanisms and their timing that may potentially enable stable rather than transient persistence. [ABSTRACT FROM AUTHOR]

Polyploid organisms are common and can be found across the tree of life. A key question is to understand how and why these polyploid lineages become established and persist in populations, particularly since they are predicted to have a low probability of success. While the collection of papers in this special issue addresses broad questions on the evolutionary ecology of polyploids, ultimately, these studies also highlight the myriad ways that we are examining what drives the success of polyploid lineages. In this paper we consider where we've been and the challenges that we face, and then propose several directions that will allow us to continue to propel the field towards our ultimate goal of understanding the rules that govern the establishment and persistence of polyploid populations. We conclude that developing this rule set will require a combination of model systems for which we have detailed knowledge of the phylogenetic and population genetic history, expanding our perspective beyond plants to include greater taxonomic breadth, and conducting studies in ecologically relevant settings. Additionally, we argue that future research on the evolutionary ecology of polyploidy should focus on integrating theory and empirical research, providing mechanistic linkages between the effects of whole genome duplication and population demography, and build a predictive framework to understand how anthropogenic change will impact polyploid organisms. [ABSTRACT FROM AUTHOR]

Polyploidization is hypothesized to improve the freezing resistance of plants in cold regions. However, adaptive strategies and key physiological mechanisms involved in the freezing resistant ability of polyploids remain unclear. In Actinidia chinensis (kiwifruits), the tetraploids and hexaploids occupy higher altitude habitats with colder climates than the diploids, providing a study system to investigate mechanisms responsible for differentiation in freezing resistance between cytotypes. We characterized environmental conditions of their natural distribution areas, and measured leaf‐level traits of cold damages and water relations at typical sites of each cytotype along an altitudinal gradient. Polyploids showed lower semi‐lethal temperature (LT50) than ice nucleation temperature (INT), reflecting a tolerance strategy to cope with freezing events in the plateau regions. More negative turgor loss points and larger cell elastic modulus of polyploids could help to alleviate damages from freezing‐induced cell dehydration, thus strengthening their tolerance to lower subzero temperatures (lower LT50). The increased supercooling capacity of polyploids (lower INT) might correlate with less extracellular ice formation due to lower osmotic potential at full turgor, apoplastic water fraction and tissue capacitance. Our study uncovers a greater cold tolerance in polyploid kiwifruits than diploids, and suggests the potential linkage between freezing tolerance and water relations. Taken together, such a divergence in stress resistance may underlie the niche shift of polyploid plants towards harsh environments. [ABSTRACT FROM AUTHOR]

Polyploidy, the state of having more than two full sets of chromosomes, has been hypothesized to provide several evolutionary advantages to flowering plants including increased ability to resist pathogens and parasites. However, studies comparing pathogen resistance in conspecific and congeneric diploids and polyploids have produced mixed results. While the supposed relationship between polyploidy and pathogen resistance has been commented on in several narrative reviews, it has never been subjected to a systematic meta‐analysis. We examined the effect of polyploidy on pathogen resistance by synthesizing 214 effect sizes from 128 studies. We find that, overall, there is no consistent effect of polyploidy on pathogen resistance. Subgroup analyses suggest that polyploids perform significantly better than diploids only in resisting hemibiotrophic pathogens, and autopolyploids tend show greater resistance than allopolyploids. This is surprising given the fact that polyploids possess extra allele copies of R‐gene alleles that provide resistance to biotrophic pathogens, and this pattern may indicate that signaling cascades needed to elicit hypersensitive responses are disrupted by polyploidy. Disruption is supported by the observation that, across all pathogens, autopolyploids show significantly greater resistance compared to diploids, whereas allopolyploids do not. This is corroborated by the observation that synthetic autopolyploids perform significantly better than their allopolyploid and established counterparts. Regarding pathogen type, diploids show greater resistance than polyploids to pathogens that are fungi or nematodes. Analyses of publication bias indicate little to no bias, and analyses of heterogeneity indicate that phylogeny explains almost none of the observed heterogeneity. These results underscore the importance of not only systematic review but also the strong degree to which the effects of polyploidy depend on ecological context. [ABSTRACT FROM AUTHOR]

Polyploidy commonly occurs in invasive species, and phenotypic plasticity (PP, the ability to alter one's phenotype in different environments) is predicted to be enhanced in polyploids and to contribute to their invasive success. However, empirical support that increased PP is frequent in polyploids and/or confers invasive success is limited. Here, we investigated if polyploids are more pre‐adapted to become invasive than diploids via the scaling of trait values and PP with ploidy level, and if post‐introduction selection has led to a divergence in trait values and PP responses between native‐ and non‐native cytotypes. We grew diploid, tetraploid (from both native North American and non‐native European ranges), and hexaploid Solidago gigantea in pots outside with low, medium, and high soil nitrogen and phosphorus (NP) amendments, and measured traits related to growth, asexual reproduction, physiology, and insects/pathogen resistance. Overall, we found little evidence to suggest that polyploidy and post‐introduction selection shaped mean trait and PP responses. When we compared diploids to tetraploids (as their introduction into Europe was more likely than hexaploids) we found that tetraploids had greater pathogen resistance, photosynthetic capacities, and water‐use efficiencies and generally performed better under NP enrichments. Furthermore, tetraploids invested more into roots than shoots in low NP and more into shoots than roots in high NP, and this resource strategy is beneficial under variable NP conditions. Lastly, native tetraploids exhibited greater plasticity in biomass accumulation, clonal‐ramet production, and water‐use efficiency. Cumulatively, tetraploid S. gigantea possesses traits that might have predisposed and enabled them to become successful invaders. Our findings highlight that trait expression and invasive species dynamics are nuanced, while also providing insight into the invasion success and cyto‐geographic patterning of S. gigantea that can be broadly applied to other invasive species with polyploid complexes. [ABSTRACT FROM AUTHOR]

Polyploidy – whole genome duplication – is common in plants. Studies over the last several decades have documented numerous mixed‐ploidy populations. Whether arising via recurrent whole genome duplication events within a population, or from secondary contact, the persistence of mixed populations is possible by niche differentiation. Specifically, one mechanism facilitating ploidy co‐occurrence is microbially‐mediated niche differentiation (MMND), wherein cytotypes occupy different niches via interactions with different sets of microbes. Inherently cryptic, MMND is underexplored in polyploid plant populations. Here, we search for evidence of MMND in creosotebush Larrea tridentata, a dominant desert shrub of the southwestern US and northern Mexico. We sequenced root‐associated fungal taxa in soils of diploid, autotetraploid, and autohexaploid plants growing in two naturally‐occurring mixed‐cytotype populations. Within populations, we found substantial fungal assemblage overlap across host plant cytotypes. However, using indicator species analysis, we identified some fungi that are differentiated by host plant cytotype, satisfying a necessarycondition for MMND. Future study is needed to determine the degree of niche differentiation conferred, if any, and whether the identified fungi play a role in the long‐term persistence of multiple cytotypes within populations. [ABSTRACT FROM AUTHOR]

Summary: 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. [ABSTRACT FROM AUTHOR]

Hybridization and polyploidization have made great contributions to speciation, heterosis, and agricultural production within plants, but there is still limited understanding and utilization in animals. Subgenome structure and expression reorganization and cooperation post hybridization and polyploidization are essential for speciation and allopolyploid success. However, the mechanisms have not yet been comprehensively assessed in animals. Here, we produced a high-fidelity reference genome sequence for common carp, a typical allotetraploid fish species cultured worldwide. This genome enabled in-depth analysis of the evolution of subgenome architecture and expression responses. Most genes were expressed with subgenome biases, with a trend of transition from the expression of subgenome A during the early stages to that of subgenome B during the late stages of embryonic development. While subgenome A evolved more rapidly, subgenome B contributed to a greater level of expression during development and under stressful conditions. Stable dominant patterns for homoeologous gene pairs both during development and under thermal stress suggest a potential fixed heterosis in the allotetraploid genome. Preferentially expressing either copy of a homoeologous gene at higher levels to confer development and response to stress indicates the dominant effect of heterosis. The plasticity of subgenomes and their shifting of dominant expression during early development, and in response to stressful conditions, provide novel insights into the molecular basis of the successful speciation, evolution, and heterosis of the allotetraploid common carp. [ABSTRACT FROM AUTHOR]

The genus Sorbus s.l. consists of small to medium‐sized trees primarily found in coastal areas, with three European hotspots of diversification: Fennoscandia, south‐east Europe and the British Isles. Taxonomic classification of Sorbus s.l. in Europe is still unresolved, and this study aims to address this issue by examining the pollen morphology of various Sorbus hybrids. Pollen morphology of 16 specimens from 13 species of Sorbus s.str., Aria and Hedlundia, some of them common, others are endemic and listed as threatened species, were studied. Measurements of the polar and equatorial axis of all pollen grains show that there are variations in pollen size and shape among different hybrids, with a correlation between ploidy levels and the equatorial diameter of the pollen. Surface structures of the pollen were observed using SEM. Principal component analysis (PCA) was performed to analyze the pollen characters, and the results show that it is possible to separate Aria from Sorbus and Hedlundia based on the length of the polar axis of the pollen grain, while the number of perforations is important for classification within Hedlundia. The study concludes that pollen morphology can be a useful tool for distinguishing between different Sorbus hybrids and can thus aid in understanding their past distributions. [ABSTRACT FROM AUTHOR]

We represent a comparative analysis of GBSS1 gene fragment sequences for a number of species related to Elymus caninus: Elymus prokudinii, Elymus viridiglumis, Elymus goloskokovii, as well as a number of morphologically deviating biotypes, inhabiting Russia and Kazakhstan. Microevolutionary relationships between species were assessed from dendrograms derived from sequences of exons and introns. In all taxa, the St subgenome was represented by St2 variants, rather typical of the North American ancestral line of Pseudoroegneria spicata than of the Asian line descending from Pseudoroegneria strigosa. All putative relatives of E. caninus had H1 subgenome variants linked around the Asian diploid carrier of the H genome from Hordeum jubatum and were divided into two subclades. One of them (H1‐1) contained most of the closely related E. caninus clones, including Elymus uralensis. Another subclade (H1‐2) consisted of five variants phylogenetically related to Elymus mutabilis. We have also studied reproductive relationships between species E. goloskokovii, E. prokudinii, and E. viridiglumis and the degree of their integration into the E. caninus complex. Biotypes included in sexual hybridization formed a single recombination gene pool, within which slight differences in reproductive compatibility were observed. A comprehensive study of microevolutionary differentiation of taxa showed the expediency of taxonomic revision. The species mentioned should probably be relegated to the infraspecific rank within E. caninus s. l. [ABSTRACT FROM AUTHOR]

Background: Transposable elements (TEs) have a profound influence on the trajectory of plant evolution, driving genome expansion and catalyzing phenotypic diversification. The pangenome, a comprehensive genetic pool encompassing all variations within a species, serves as an invaluable tool, unaffected by the confounding factors of intraspecific diversity. This allows for a more nuanced exploration of plant TE evolution. Results: Here, we constructed a pangenome for diploid A-genome cotton using 344 accessions from representative geographical regions, including 223 from China as the main component. We found 511 Mb of non-reference sequences (NRSs) and revealed the presence of 5479 previously undiscovered protein-coding genes. Our comprehensive approach enabled us to decipher the genetic underpinnings of the distinct geographic distributions of cotton. Notably, we identified 3301 presence-absence variations (PAVs) that are closely tied to gene expression patterns within the pangenome, among which 2342 novel expression quantitative trait loci (eQTLs) were found residing in NRSs. Our investigation also unveiled contrasting patterns of transposon proliferation between diploid and tetraploid cotton, with long terminal repeat (LTR) retrotransposons exhibiting a synchronized surge in polyploids. Furthermore, the invasion of LTR retrotransposons from the A subgenome to the D subgenome triggered a substantial expansion of the latter following polyploidization. In addition, we found that TE insertions were responsible for the loss of 36.2% of species-specific genes, as well as the generation of entirely new species-specific genes. Conclusions: Our pangenome analyses provide new insights into cotton genomics and subgenome dynamics after polyploidization and demonstrate the power of pangenome approaches for elucidating transposon impacts and genome evolution. [ABSTRACT FROM AUTHOR]

Natural hybridisation is now recognised as pervasive in its occurrence across the Tree of Life. Resurgent interest in natural hybridisation fuelled by developments in genomics has led to an improved understanding of the genetic factors that promote or prevent species cross‐mating. Despite this body of work overturning many widely held assumptions about the genetic barriers to hybridisation, it is still widely thought that ploidy differences between species will be an absolute barrier to hybridisation and introgression. Here, we revisit this assumption, reviewing findings from surveys of polyploidy and hybridisation in the wild. In a case study in the British flora, 203 hybrids representing 35% of hybrids with suitable data have formed via cross‐ploidy matings, while a wider literature search revealed 59 studies (56 in plants and 3 in animals) in which cross‐ploidy hybridisation has been confirmed with genetic data. These results show cross‐ploidy hybridisation is readily overlooked, and potentially common in some groups. General findings from these studies include strong directionality of hybridisation, with introgression usually towards the higher ploidy parent, and cross‐ploidy hybridisation being more likely to involve allopolyploids than autopolyploids. Evidence for adaptive introgression across a ploidy barrier and cases of cross‐ploidy hybrid speciation shows the potential for important evolutionary outcomes. [ABSTRACT FROM AUTHOR]

Summary: Angiosperms, which inhabit diverse environments across all continents, exhibit significant variation in genome sizes, making them an excellent model system for examining hypotheses about the global distribution of genome size. These include the previously proposed large genome constraint, mutational hazard, polyploidy‐mediated, and climate‐mediated hypotheses.We compiled the largest genome size dataset to date, encompassing 16 017 (> 5% of known) angiosperm species, and analyzed genome size distribution using a comprehensive geographic distribution dataset for all angiosperms.We observed that angiosperms with large range sizes generally had small genomes, supporting the large genome constraint hypothesis. Climate was shown to exert a strong influence on genome size distribution along the global latitudinal gradient, while the frequency of polyploidy and the type of growth form had negligible effects. In contrast to the unimodal patterns along the global latitudinal gradient shown by plant size traits and polyploid proportions, the increase in angiosperm genome size from the equator to 40–50°N/S is probably mediated by different (mostly climatic) mechanisms than the decrease in genome sizes observed from 40 to 50°N northward.Our analysis suggests that the global distribution of genome sizes in angiosperms is mainly shaped by climatically mediated purifying selection, genetic drift, relaxed selection, and environmental filtering. [ABSTRACT FROM AUTHOR]

The genetic diversity that exists in natural populations of Arachis duranensis, the wild diploid donor of the A subgenome of cultivated tetraploid peanut, has the potential to improve crop adaptability, resilience to major pests and diseases, and drought tolerance. Despite its potential value for peanut improvement, limited research has been focused on the association between allelic variation, environmental factors, and response to early (ELS) and late leaf spot (LLS) diseases. The present study implemented a landscape genomics approach to gain a better understanding of the genetic variability of A. duranensis represented in the ex-situ peanut germplasm collection maintained at the U.S. Department of Agriculture, which spans the entire geographic range of the species in its center of origin in South America. A set of 2810 single nucleotide polymorphism (SNP) markers allowed a high-resolution genome-wide characterization of natural populations. The analysis of population structure showed a complex pattern of genetic diversity with five putative groups. The incorporation of bioclimatic variables for genotype-environment associations, using the latent factor mixed model (LFMM2) method, provided insights into the genomic signatures of environmental adaptation, and led to the identification of SNP loci whose allele frequencies were correlated with elevation, temperature, and precipitation-related variables (q < 0.05). The LFMM2 analysis for ELS and LLS detected candidate SNPs and genomic regions on chromosomes A02, A03, A04, A06, and A08. These findings highlight the importance of the application of landscape genomics in ex situ collections of peanut and other crop wild relatives to effectively identify favorable alleles and germplasm for incorporation into breeding programs. We report new sources of A. duranensis germplasm harboring adaptive allelic variation, which have the potential to be utilized in introgression breeding for a single or multiple environmental factors, as well as for resistance to leaf spot diseases. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The cellular and molecular mechanisms governing sexual reproduction are conserved across eukaryotes. Nevertheless, hybridization can disrupt these mechanisms, leading to asexual reproduction, often accompanied by polyploidy. In this study, we investigate how ploidy level and ratio of parental genomes in hybrids affect their reproductive mode. We analyze the gametogenesis of sexual species and their diploid and triploid hybrids from the freshwater fish family Cobitidae, using newly developed cytogenetic markers. We find that diploid hybrid females possess oogonia and oocytes with original (diploid) and duplicated (tetraploid) ploidy. Diploid oocytes cannot progress beyond pachytene due to aberrant pairing. However, tetraploid oocytes, which emerge after premeiotic genome endoreplication, exhibit normal pairing and result in diploid gametes. Triploid hybrid females possess diploid, triploid, and haploid oogonia and oocytes. Triploid and haploid oocytes cannot progress beyond pachytene checkpoint due to aberrant chromosome pairing, while diploid oocytes have normal pairing in meiosis, resulting in haploid gametes. Diploid oocytes emerge after premeiotic elimination of a single-copied genome. Triploid hybrid males are sterile due to aberrant pairing and the failure of chromosomal segregation during meiotic divisions. Thus, changes in ploidy and genome dosage may lead to cyclical alteration of gametogenic pathways in hybrids. The cytogenetic analysis of gonial cells and meiocytes on Korean loach complex suggest that instant switch between sexual to asexual reproduction in hybrids depend on their ploidy and genome dosage. [ABSTRACT FROM AUTHOR]

Cytogenetics can be used as a tool to study the evolution of polyploidy and taxonomy. Here we focus on aquatic African pipids, dwarf clawed frogs (Hymenochirus). Our study reveals that dwarf clawed frogs, present for decades in captivity, are best referred to as Hymenochirus sp. instead of the commonly used name ' H. boettgeri ' or sometimes ' H. curtipes '. We present the first karyotype from a morphologically identified specimen of H. boettgeri with a known locality in the north-western Congo, which is tetraploid with 2n = 36. The captive Hymenochirus species has been found diploid in previous studies with different reported chromosome numbers; here we reveal 2n = 20A + 1B chromosomes. Our findings suggest that the tetraploid H. boettgeri karyotype evolved through fusion of two biarmed chromosomes and subsequent allotetraploidization, and is functionally diploid, similar to the origin of tetraploid clawed frogs in the subgenus Xenopus. We observed the stable presence of a single B chromosome in both sexes of our individuals from the captive population of Hymenochirus sp. However, additional investigation is necessary to clarify whether there is variation in the number of A and B chromosomes among populations, individuals, and/or tissues. Further research is also needed to understand the evolution and taxonomy of the genus Hymenochirus. [ABSTRACT FROM AUTHOR]

Neoteny is a developmental strategy wherein an organism reaches sexual maturity without associated adult characteristics. In salamanders, neoteny takes the form of individuals retaining aquatic larval characteristics such as external gills upon maturation. Mole salamanders (Ambystoma) occupy a wide range of habitats and areas across the North American continent, and display examples of non‐neotenic, facultatively neotenic and obligate neotenic species, providing high variation for investigating the factors influencing the evolution of neoteny. Here, we use phylogenetic comparative methods to test existing hypotheses that neoteny is associated with elevational and latitudinal distribution, cave‐associated isolation, and hybridisation‐related polyploidy. We also test if neoteny influences the diversity of habitats a species can occupy, since the restriction to an aquatic life should constrain the availability of different niches. We find that neoteny tends to occur in a narrow latitudinal band between 20–30° North, with particularly narrow latitudinal ranges for obligate compared to facultative neotenic species (16–52° North). We also find that facultatively neotenic species occur at elevations more than twice as high as other species on average, and that species with a higher frequency of neoteny typically have lower habitat diversity. Our results suggest that evolutionary transitions between non‐neotenic and facultative neoteny states occur at relatively high and approximately equal rates. Moreover, we estimate that obligate neoteny cannot evolve directly from non‐neotenic species (and vice versa), such that facultative neoteny acts as an evolutionary 'stepping stone' to and from obligate neoteny. However, our transition rate estimates suggest that obligate neoteny is lost >4‐times faster than it evolves, partly explaining the rarity of obligate species. These results support the hypothesis that low latitudes favour the evolution of neoteny, presumably linked to more stable (aquatic) environments due to reduced seasonality, but once evolved it may constrain the diversity of habitats. [ABSTRACT FROM AUTHOR]

Knowledge of the function of growth-regulating factors (GRFs) in sugarcane (Saccharum officinarum and S. spontaneum) growth and development could assist breeders in selecting desirable plant architectures. However, limited information about GRFs is available in Saccharum due to their polyploidy. In this study, 22 GRFs were identified in the two species and their conserved domains, gene structures, chromosome location, and synteny were characterized. GRF7 expression varied among tissues and responded to diurnal rhythm. SsGRF7-YFPwas localized preferentially in the nucleus and appears to act as a transcriptional cofactor. SsGRF7positively regulated the size and lengthof rice leaves, possibly by regulating cell size and plant hormones. Of seven potential transcription factors binding to the SsGRF7 promoter in S. spontaneum, four showed positive expression patterns, and two showed negative expression patterns relative to SsGRF7. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

High-throughput sequencing-based methods for bulked segregant analysis (BSA) allow for the rapid identification of genetic markers associated with traits of interest. BSA studies have successfully identified qualitative (binary) and quantitative trait loci (QTLs) using QTL mapping. However, most require population structures that fit the models available and a reference genome. Instead, high-throughput short-read sequencing can be combined with BSA of k-mers (BSA-k-mer) to map traits that appear refractory to standard approaches. This method can be applied to any organism and is particularly useful for species with genomes diverged from the closest sequenced genome. It is also instrumental when dealing with highly heterozygous and potentially polyploid genomes without phased haplotype assemblies and for which a single haplotype can control a trait. Finally, it is flexible in terms of population structure. Here, we apply the BSA-k-mer method for the rapid identification of candidate regions related to seed spot and seed size in diploid potato. Using a mixture of F1 and F2 individuals from a cross between 2 highly heterozygous parents, candidate sequences were identified for each trait using the BSA-k-mer approach. Using parental reads, we were able to determine the parental origin of the loci. Finally, we mapped the identified k-mers to a closely related potato genome to validate the method and determine the genomic loci underlying these sequences. The location identified for the seed spot matches with previously identified loci associated with pigmentation in potato. The loci associated with seed size are novel. Both loci are relevant in future breeding toward true seeds in potato. [ABSTRACT FROM AUTHOR]

Aim: Apomixis is a widespread trait in extreme environments worldwide, yet phylogeographical studies for species exhibiting these complex reproductive systems are still limited to temperate zones in the Northern Hemisphere. Through analyses of a combination of adult plants and seedlings, and nuclear and chloroplast DNA, we assessed the contemporary genetic outcomes of apomixis and phylogeographical patterns in an arid unglaciated landscape to understand the evolutionary trajectory of apomictic species. Location: Pilbara bioregion, north‐western Australia. Taxon: Senna glutinosa subsp. glutinosa. Materials and Methods: Spatial patterns of genetic diversity and differentiation in three chloroplast regions and 17 nuclear microsatellite markers were evaluated in 480 plants from 20 populations of S. glutinosa subsp. glutinosa across the Pilbara bioregion. We also germinated and genotyped seed for a progeny analysis to quantify polyembryony and the relative frequency of asexual versus sexual reproduction. Results: We found frequent polyembryony and a high proportion of asexual offspring (84.56%), resulting in low within‐population genotypic diversity. The nuclear dataset identified 72 multilocus lineages (MLLs) with moderate pairwise population genetic fixation and low differentiation among populations with no geographically structured genetic clustering. Chloroplast DNA showed high haplotype diversity and a widespread distribution of haplotypes. Only one peripheral population presented a single unique haplotype and MLL. Main Conclusions: Analysis of this woody perennial in an arid landscape shows the influence of apomixis on genetic patterns and species persistence. Haplotype diversity was indicative of long‐term persistence within the ancient Pilbara region. Widespread distribution of haplotypes and sharing of several nuclear MLLs among distant populations indicated extensive seed dispersal throughout the study area. The combination of polyploidy, facultative apomixis and extensive seed dispersal maintains genetic variability within local populations and promotes the spread of advantageous genotypes across wide geographical distances. Therefore, apomixis, rather than an evolutionary 'dead‐end', can be regarded as a mechanism facilitating evolutionary success of apomictic species in extreme and complex environments. [ABSTRACT FROM AUTHOR]

Background: Alfalfa, the most economically important forage legume worldwide, features modest genetic progress due to long selection cycles and the extent of the non-additive genetic variance associated with its autotetraploid genome. Methods: To improve the efficiency of genomic selection in alfalfa, we explored the effects of genome parametrization (as tetraploid and diploid dosages, plus allele ratios) and SNP marker subsetting (all available SNPs, only genic regions, and only non-genic regions) on genomic regressions, together with various levels of filtering on reading depth and missing rates. We used genotyping by sequencing-generated data and focused on traits of different genetic complexity, i.e., dry biomass yield in moisture-favorable (FE) and drought stress (SE) environments, leaf size, and the onset of flowering, which were assessed in 143 genotyped plants from a genetically broad European reference population and their phenotyped half-sib progenies. Results: On average, the allele ratio improved the predictive ability compared with other genome parametrizations (+7.9% vs. tetraploid dosage, +12.6% vs. diploid dosage), while using all the SNPs offered an advantage compared with any specific SNP subsetting (+3.7% vs. genic regions, +7.6% vs. non-genic regions). However, when focusing on specific traits, different combinations of genome parametrization and subsetting achieved better performances. We also released Legpipe2, an SNP calling pipeline tailored for reduced representation (GBS, RAD) in medium-sized genotyping experiments. [ABSTRACT FROM AUTHOR]

This study investigated the differences in gene expression profiles of diploid and autotetraploid in cowpea, and provided theoretical basis for screening key genes of differential expression and ploidy breeding. The phenotypes and contents of chlorophyll, soluble sugar and soluble protein of diploid and autotetraploid of cowpea were compared and transcriptome sequencing was performed. The autotetraploid leaves of cowpea were thicker and darker green than diploid leaves, and the contents of chlorophyll, soluble sugar and soluble protein in leaves were higher. A total of 2678 differentially expressed genes (DEGs) were analyzed in the diploid and autotetraploid of cowpea. Among them, there were 421 genes with higher expression of tetraploid than diploid, and 2257 genes with lower expression of tetraploid than diploid. All 2678 DEGs were annotated into the Gene Ontology (GO) functional library. The DEGs were mainly concentrated in metabolism and cell composition. Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway analysis showed that cowpea diploid and autotetraploid have significant differences in flavonoid biosynthesis, degradation of other glycan, phenylpropane biosynthesis, starch sucrose metabolism, keratin, amber and wax biosynthesis, circadian rhythm and plant pathways. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Polyploidy is typically described as the condition wherein a cell or organism has more than two complete sets of chromosomes. Occurrence of polyploidy is a naturally occurring phenomenon in the body's development and differentiation processes under normal physiological conditions. However, in pathological conditions, the occurrence of polyploidy is documented in numerous disorders, including cancer, aging and diabetes. Due to the frequent association that the polyploidy has with these pathologies and physiological process, understanding the cause and consequences of polyploidy would be beneficial to develop potential therapeutic applications. Many of the genetic and epigenetic alterations leading to cancer, diabetes and aging are linked to signaling pathways. Nonetheless, the specific signaling pathway associated with the cause and consequences of polyploidy still remains largely unknown. Mammalian/mechanistic target of rapamycin (mTOR) plays a key role in the coordination between eukaryotic cell growth and metabolism, thereby simultaneously respond to various environmental inputs including nutrients and growth factors. Extensive research over the past two decades has established a central role for mTOR in the regulation of many fundamental cellular processes that range from protein synthesis to autophagy. Dysregulated mTOR signaling has been found to be implicated in various disease progressions. Importantly, there is a strong correlation between the hallmarks of polyploidy and dysregulated mTOR signaling. In this review, we explore and discuss the molecular connection between mTOR signaling and polyploidy along with its association with cancer, diabetes and aging. Additionally, we address some unanswered questions and provide recommendations to further advance our understanding of the intricate relationship between mTOR signaling and polyploidy. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Background: Capsella bursa-pastoris, a cosmopolitan weed of hybrid origin, is an emerging model object for the study of early consequences of polyploidy, being a fast growing annual and a close relative of Arabidopsis thaliana. The development of this model is hampered by the absence of a reference genome sequence. Results: We present here a subgenome-resolved chromosome-scale assembly and a genetic map of the genome of Capsella bursa-pastoris. It shows that the subgenomes are mostly colinear, with no massive deletions, insertions, or rearrangements in any of them. A subgenome-aware annotation reveals the lack of genome dominance—both subgenomes carry similar number of genes. While most chromosomes can be unambiguously recognized as derived from either paternal or maternal parent, we also found homeologous exchange between two chromosomes. It led to an emergence of two hybrid chromosomes; this event is shared between distant populations of C. bursa-pastoris. The whole-genome analysis of 119 samples belonging to C. bursa-pastoris and its parental species C. grandiflora/rubella and C. orientalis reveals introgression from C. orientalis but not from C. grandiflora/rubella. Conclusions: C. bursa-pastoris does not show genome dominance. In the earliest stages of evolution of this species, a homeologous exchange occurred; its presence in all present-day populations of C. bursa-pastoris indicates on a single origin of this species. The evidence coming from whole-genome analysis challenges the current view that C. grandiflora/rubella was a direct progenitor of C. bursa-pastoris; we hypothesize that it was an extinct (or undiscovered) species sister to C. grandiflora/rubella. [ABSTRACT FROM AUTHOR]

Background: RNA-seq is a fundamental technique in genomics, yet reference bias, where transcripts derived from non-reference alleles are quantified less accurately, can undermine the accuracy of RNA-seq quantification and thus the conclusions made downstream. Reference bias in RNA-seq analysis has yet to be explored in complex polyploid genomes despite evidence that they are often a complex mosaic of wild relative introgressions, which introduce blocks of highly divergent genes. Results: Here we use hexaploid wheat as a model complex polyploid, using both simulated and experimental data to show that RNA-seq alignment in wheat suffers from widespread reference bias which is largely driven by divergent introgressed genes. This leads to underestimation of gene expression and incorrect assessment of homoeologue expression balance. By incorporating gene models from ten wheat genome assemblies into a pantranscriptome reference, we present a novel method to reduce reference bias, which can be readily scaled to capture more variation as new genome and transcriptome data becomes available. Conclusions: This study shows that the presence of introgressions can lead to reference bias in wheat RNA-seq analysis. Caution should be exercised by researchers using non-sample reference genomes for RNA-seq alignment and novel methods, such as the one presented here, should be considered. [ABSTRACT FROM AUTHOR]

Nonapomictic citrus tetraploids are desirable in citrus breeding for the production of triploid, seedless varieties, and polyploid rootstocks. However, only a few lines have been reported, and they were all generated using chemical methods. A 2x + 4 × cytochimera of the nonapomictic citrus variety 'Orah' mandarin, which developed from a bud mutant, was found due to its morphology differing from that of diploid plants and characterised via ploidy analysis combining flow cytometry and chromosome observation. The chimaera was stable, and there were 1.86–1.90 times as tetraploid cells as diploid cells. Anatomical structure observation revealed that the 'Orah' chimaera may be a periclinal chimaera with diploid cells in the L1 layer and tetraploid cells in the L2 and L3 layers. The chimaera showed some typical traits of polyploid plants, including thicker shoots, wider and thicker leaves, larger flowers and fruits, and fewer but larger seeds in fruits than in diploid plants. Almost all the seeds of the chimaera were monoembryonic. Most of the self-pollinated progenies of the chimaera were identified as tetraploids, and some triploid, pentaploid, and hexaploid plants were found. As a female, the chimaera produced allotriploids when crossed with Australian finger lime. In addition, 6 plants developed from polyembryonic seeds of the chimaera were identified as sexual tetraploid progenies with low-level recombinant genomes. Therefore, the 'Orah' 2x + 4 × chimaera can be used as a female parent to produce hybrid triploid and tetraploid citrus plants with high efficiency. Identification of the chimaera demonstrated that tetraploid citrus plants, especially nonapomictic varieties, can be generated from shoot bud mutants. [ABSTRACT FROM AUTHOR]

Fishes of the genus Carassius are useful experimental vertebrate models for the study of evolutionary biology and cytogenetics. Carassius demonstrates diverse biological characteristics, such as variation in ploidy levels and chromosome numbers, and presence of microchromosomes. Those Carassius polyploids with ≥ 150 chromosomes have microchromosomes, but the origin of microchromosomes, especially in European populations, is unknown. We used cytogenetics to study evolution of tandem repeats (U1 and U2 small nuclear DNAs and H3 histone) and microchromosomes in Carassius from the Czech Republic. We tested the hypotheses whether the number of tandem repeats was affected by polyploidization or divergence between species and what mechanism drives evolution of microchromosomes. Tandem repeats were found in tetraploid and hexaploid Carassius gibelio , and tetraploid Carassius auratus and Carassius carassius in conserved numbers, with the exception of U1 small nuclear DNA in C. auratus. This conservation indicates reduction and/or loss in the number of copies per locus in hexaploids and may have occurred by divergence rather than polyploidization. To study the evolution of microchromosomes, we used the whole microchromosome painting probe from hexaploid C. gibelio and hybridized it to tetraploid and hexaploid C. gibelio , and tetraploid C. auratus and C. carassius. Our results revealed variation in the number of microchromosomes in hexaploids and indicated that the evolution of the Carassius karyotype is governed by macrochromosome fissions followed by segmental duplication in pericentromeric areas. These are potential mechanisms responsible for the presence of microchromosomes in Carassius hexaploids. Differential efficacy of one or both of these mechanisms in different tetraploids could ensure variability in chromosome number in polyploids in general. [ABSTRACT FROM AUTHOR]

Polyploid cells contain multiple genome copies and arise in many animal tissues as a regulated part of development. However, polyploid cells can also arise due to cell division failure, DNA damage or tissue damage. Although polyploidization is crucial for the integrity and function of many tissues, the cellular and tissue-wide consequences of polyploidy can be very diverse. Nonetheless, many polyploid cell types and tissues share a remarkable similarity in function, providing important information about the possible contribution of polyploidy to cell and tissue function. Here, we review studies on polyploid cells in development, underlining parallel functions between different polyploid cell types, as well as differences between developmentally-programmed and stress-induced polyploidy. [ABSTRACT FROM AUTHOR]

Summary: Combining two or more related homoeologous genomes in a single nucleus, newly formed allopolyploids must rapidly adapt meiosis to restore balanced chromosome segregation, production of euploid gametes and fertility. The poor fertility of such neo‐allopolyploids thus strongly selects for the limitation or avoidance of genetic crossover formation between homoeologous chromosomes.In this study, we have reproduced the interspecific hybridization between Arabidopsis thaliana and Arabidopsis arenosa leading to the allotetraploid Arabidopsis suecica and have characterized the first allopolyploid meioses.First‐generation neo‐allopolyploid siblings vary considerably in fertility, meiotic behavior and levels of homoeologous recombination. We show that centromere dynamics at early meiosis is altered in synthetic neo‐allopolyploids compared with evolved A. suecica, with a significant increase in homoeologous centromere interactions at zygotene. At metaphase I, the presence of multivalents involving homoeologous chromosomes confirms that homoeologous recombination occurs in the first‐generation synthetic allopolyploid plants and this is associated with a significant reduction in homologous recombination, compared to evolved A. suecica.Together, these data strongly suggest that the fidelity of recombination partner choice, likely during the DNA invasion step, is strongly impaired during the first meiosis of neo‐allopolyploids and requires subsequent adaptation. [ABSTRACT FROM AUTHOR]

Premise: The western North American fern genus Pentagramma (Pteridaceae) is characterized by complex patterns of ploidy variation, an understanding of which is critical to comprehending both the evolutionary processes within the genus and its current diversity. Methods: We undertook a cytogeographic study across the range of the genus, using a combination of chromosome counts and flow cytometry to infer ploidy level. Bioclimatic variables and elevation were used to compare niches. Results: We found that diploids and tetraploids are common and widespread, and triploids are rare and sporadic; in contrast with genome size inferences in earlier studies, no hexaploids were found. Diploids and tetraploids show different geographic ranges: only tetraploids were found in the northernmost portion of the range (Washington, Oregon, and British Columbia) and only diploids were found in the Sierra Nevada of California. Diploid, triploid, and tetraploid cytotypes were found to co‐occur in relatively few localities: in the southern (San Diego County, California) and desert Southwest (Arizona) parts of the range, and along the Pacific Coast of California. Conclusions: Tetraploids occupy a wider bioclimatic niche than diploids both within P. triangularis and at the genus‐wide scale. It is unknown whether the wider niche of tetraploids is due to their expansion upon the diploid niche, if diploids have contracted their niche due to competition or changing abiotic conditions, or if this wider niche occupancy is due to multiple origins of tetraploids. [ABSTRACT FROM AUTHOR]

While polyploids are common in nature, existing models suggest that polyploid establishment should be difficult and rare. We explore this apparent paradox by focussing on the role of unreduced gametes, as their union is the main route for the formation of neopolyploids. Production of such gametes is affected by genetic and environmental factors, resulting in variation in the formation rate of unreduced gametes (u). Once formed, neopolyploids face minority cytotype exclusion (MCE) due to a lack of viable mating opportunities. More than a dozen theoretical models have explored factors that could permit neopolyploids to overcome MCE and become established. Until now, however, none have explored variability in u and its consequences for the rate of polyploid establishment. Here, we determine the distribution that best fits the available empirical data on u. We perform a global sensitivity analysis exploring the consequences of using empirical distributions of u to investigate effects on polyploid establishment. We determined that in many cases, u is best fit by a log-normal distribution. We found environmental stochasticity in u dramatically impacts model predictions when compared to a static u. Our results help reconcile previous modelling results suggesting high barriers to the polyploid establishment with the observation that polyploids are common in nature. [ABSTRACT FROM AUTHOR]

Purpose: Post prostatectomy PSA kinetics and General Grade Groups (GGG) are the strongest prognostic markers of biochemical recurrence (BCR) and prostate cancer (PCa)-specific mortality after radical prostatectomy. Despite having low-risk PCa, some patients will experience BCR, for some, clinically significant BCR. There is a need for an objective prognostic marker at the time of prostatectomy to improve risk stratification within this population. In this study, we investigated the prognostic potential of DNA ploidy. Materials and Methods: Prostatectomy samples from 97 patients with GGG1 and GGG2 with a low-risk CAPRA-S score were included in this study. PCa tissue with the worst Gleason pattern underwent tissue disaggregation, cell isolation and staining with a DNA stoichiometric stain. Using image cytometry, DNA ploidy was measured and a Ploidy Score (PS) was generated. Results: Among the 97 patients, 79 had no BCR, 18 experienced BCR, of which 14 had a PSA doubling time (PSA-DT) >1 year (low-risk group) and 4 had a PSA-DT of <1 year (high-risk group). Using Logistic regression analysis, only pathological T stage (pT) and PS independently predicted BCR with PS being the most significant (p = 0.001). The number of aneuploid cells was significantly higher in the high-risk group compared to the other groups (p = 1.7x10-11). PS combined with GGG diagnosis further stratified risk groups of biochemical recurrence free survival within CAPRA-S low-risk cohort. Conclusion: DNA ploidy is an independent prognostic marker of BCR in low-risk PCa after radical prostatectomy, which could early on identify potentially aggressive PCa recurrences and introduce a more personalized approach to salvage treatments. [ABSTRACT FROM AUTHOR]

[Objectives]Polyploidy is widespread in plants kingdom. However, the lack of reference genes has severely limited the research progress of polyploidy-related gene expression. The present study aimed to improve the accuracy and reproducibility of gene expression analyses in polyploids by establishing a set of stable reference genes. [Methods]The abundance of 10 candidate reference genes(UBI-ep, ACT, ACT3, TUA, EF-1α, CACS, TIP41, F-box, CYP and UBQ)were compared by real-time fluorescence quantitative analysis(qPCR)at different ploidy levels of Cucumis including artificial allotetraploid, their diploid parents and triploid offsprings. The stability of these candidate reference genes expression was analyzed by geNorm and NormFinder software. Furthermore, the correlation of relative transcript abundance estimated by qPCR analysis and transcriptome sequencing(RNA-seq)data was calculated to evaluate the stability of candidate reference genes. [Results]The qPCR results showed that the reference gene CYP in cucumber had the highest expression with a CT value of 15.8, and the reference gene F-box in tetraploid material had the lowest expression with a CT value of 30.5. Four stable reference genes were selected by combining the results of geNorm and NormFinder, which were F-box, TIP41, ACT3 and ACT. Among them, F-box and TIP41 had a lower stability value M than ACT3 and ACT genes at the polyploid level, but their expression abundance were low. When ACT3 was used as the internal reference, the relative transcript abundance correlation coefficient between qPCR and RNA-seq was extremely significant(R2=0.844, P<0.01). But the correlation was minimum when F-box was an internal parameter. [Conclusions]Attention should be paid to the selection of reference genes when comparing transcript abundance across different ploidy levels. TIP41 could be selected as the internal reference gene for the low abundance expression genes of multiple ploidy materials in melon. For highly expressed genes, ACT3 could be used as an internal reference gene. [ABSTRACT FROM AUTHOR]

Plants in German states Thuringia and Bavaria previously thought to belong to Potentilla thuringiaca belong to at least three different taxa. Most populations in Thuringia and Bavaria are rather uniform and have a ploidy of 2n = 10x. These populations belong to P. thuringiaca as originally described. A lectotype and an epitype are designated for P. thuringiaca. In an isolated range in Eastern Thuringia, we found octoploids (2n = 8x), which are characterized mainly by a higher number of flowering stems. These populations are described as Potentilla saalae T. Gregor & Korsch. Decaploid (2n = 10x) plants from a very small range in the Bavarian Rhoen with more rounded central leaves are probably of independent origin. The relationship of German P. thuringiaca populations to those in the Alps, the Balkans, the Carpathians, and Eastern Europe is unresolved. [ABSTRACT FROM AUTHOR]

Background and Aims The development and morphology of crop plants have been profoundly altered by evolution under cultivation, initially through unconscious selection, without deliberate foresight, and later by directed breeding. Wild wheats remain an important potential source of variation for modern breeders; however, the sequence and timing of morphological changes during domestication are not fully resolved. Methods We grew and measured 142 wheat accessions representing different stages in wheat evolution, including three independent domestication events, and compared their morphological traits to define the morphospace of each group. Key Results The results show that wild and domesticated wheats have overlapping morphospaces, but each also occupies a distinct area of morphospace from one another. Polyploid formation in wheat increased leaf biomass and seed weight but had its largest effects on tiller loss. Domestication continued to increase the sizes of wheat leaves and seeds and made wheat grow taller, with more erect architecture. Associated changes to the biomass of domesticated wheats generated more grains and achieved higher yields. Landrace improvement subsequently decreased the numbers of tillers and spikes, to focus resource allocation to the main stem, accompanied by a thicker main stem and larger flag leaves. During the Green Revolution, wheat height was reduced to increase the harvest index and therefore yield. Modern wheats also have more erect leaves and larger flower biomass proportions than landraces. Conclusions Quantitative trait history in wheat differs by trait. Some trait values show progressive changes in the same direction (e.g. leaf size, grain weight), whereas others change in a punctuated way at particular stages (e.g. canopy architecture), and other trait values switch directions during wheat evolution (e.g. plant height, flower biomass proportion). Agronomically valued domestication traits arose during different stages of wheat history, such that modern wheats are the product of >10 000 years of morphological evolution. [ABSTRACT FROM AUTHOR]