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PeerJ 2023Biribá ( Jacq.) is a fruit tree domesticated in Amazonia and has polyploid populations. The species presents ample phenotypic variation in fruit characteristics,...
BACKGROUND
Biribá ( Jacq.) is a fruit tree domesticated in Amazonia and has polyploid populations. The species presents ample phenotypic variation in fruit characteristics, including weight (100-4,000 g) and differences in carpel protrusions. Two cytotypes are recorded in the literature (2 = 28, 42) and genome size records are divergent (2C = 4.77, 5.42 and 6.00 pg). To decipher the role of polyploidy in the domestication of , we examined the relationships among phenotypic variation, chromosome number and genome size, and which came first, polyploidization or domestication.
METHODOLOGY
We performed chromosome counts of from central and western Brazilian Amazonia, and estimated genome size by flow cytometry. We performed phylogenetic reconstruction with publicly available data using a Bayesian framework, time divergence analysis and reconstructed the ancestral chromosome number for the genus and for .
RESULTS
We observed that variation in fruit phenotypes is not associated with variation in chromosome number and genome size. The most recent common ancestor of is inferred to be polyploid and diverged before domestication.
CONCLUSIONS
We conclude that, when domesticated, was already polyploid and we suggest that human selection is the main evolutionary force behind fruit size and fruit morphological variation in .
Topics: Humans; Phylogeny; Annona; Fruit; Brazil; Domestication; Bayes Theorem; Genome, Plant; Polyploidy; Phenotype
PubMed: 36710859
DOI: 10.7717/peerj.14659 -
International Journal of Molecular... Sep 2023Polyploidy and metastasis are associated with a low probability of disease-free survival in cancer patients. Polyploid cells are known to facilitate tumorigenesis....
Polyploidy and metastasis are associated with a low probability of disease-free survival in cancer patients. Polyploid cells are known to facilitate tumorigenesis. However, few data associate polyploidization with metastasis. Here, by generating and using diploid (2n) and tetraploid (4n) clones from malignant fibrous histiocytoma (MFH) and colon carcinoma (RKO), we demonstrate the migration and invasion advantage of tetraploid cells in vitro using several assays, including the wound healing, the OrisTM two-dimensional cell migration, single-cell migration tracking by video microscopy, the Boyden chamber, and the xCELLigence RTCA real-time cell migration. Motility advantage was observed despite tetraploid cell proliferation weakness. We could also demonstrate preferential metastatic potential in vivo for the tetraploid clone using the tail vein injection in mice and tracking metastatic tumors in the lung. Using the Mitelman Database of Chromosome Aberrations in Cancer, we found an accumulation of polyploid karyotypes in metastatic tumors compared to primary ones. This work reveals the clinical relevance of the polyploid subpopulation and the strategic need to highlight polyploidy in preclinical studies as a therapeutic target for metastasis.
Topics: Humans; Animals; Mice; Tetraploidy; Polyploidy; Chromosome Aberrations; Colonic Neoplasms
PubMed: 37762227
DOI: 10.3390/ijms241813926 -
The Journal of General and Applied... Nov 2023Thermus thermophilus is reportedly polyploid and carries four to five identical genome copies per cell, based on molecular biological experiments. To directly detect...
Thermus thermophilus is reportedly polyploid and carries four to five identical genome copies per cell, based on molecular biological experiments. To directly detect polyploidy in this bacterium, we performed live cell imaging by X-ray free-electron laser (XFEL) diffraction and observed its internal structures. The use of femtosecond XFEL pulses enables snapshots of live, undamaged cells. For successful XFEL imaging, we developed a bacterial culture method using a starch- and casein-rich medium that produces a predominance of rod-shaped cells shorter than the focused XFEL beam size, which is slightly smaller than 2 µm. When cultured in the developed medium, the length of T. thermophilus cells, which is typically ~4 µm, was less than half its usual length. We placed living cells in a micro-liquid enclosure array and successively exposed each enclosure to a single XFEL pulse. A cell image was successfully obtained by the coherent diffractive imaging technique with iterative phase retrieval calculations. The reconstructed cell image revealed five peaks, which are most likely to be nucleoids, arranged in a row in the polyploid cell without gaps. This study demonstrates that XFELs offer a novel approach for visualizing the internal nanostructures of living, micrometer-sized, polyploid bacterial cells.
Topics: Humans; Thermus thermophilus; X-Rays; X-Ray Diffraction; Lasers; Polyploidy
PubMed: 37302826
DOI: 10.2323/jgam.2023.06.002 -
Annals of Botany Feb 2023Most, if not all, green plant (Virdiplantae) species including angiosperms and ferns are polyploids themselves or have ancient polyploid or whole genome duplication...
BACKGROUND
Most, if not all, green plant (Virdiplantae) species including angiosperms and ferns are polyploids themselves or have ancient polyploid or whole genome duplication signatures in their genomes. Polyploids are not only restricted to our major crop species such as wheat, maize, potato and the brassicas, but also occur frequently in wild species and natural habitats. Polyploidy has thus been viewed as a major driver in evolution, and its influence on genome and chromosome evolution has been at the centre of many investigations. Mechanistic models of the newly structured genomes are being developed that incorporate aspects of sequence evolution or turnover (low-copy genes and regulatory sequences, as well as repetitive DNAs), modification of gene functions, the re-establishment of control of genes with multiple copies, and often meiotic chromosome pairing, recombination and restoration of fertility.
SCOPE
World-wide interest in how green plants have evolved under different conditions - whether in small, isolated populations, or globally - suggests that gaining further insight into the contribution of polyploidy to plant speciation and adaptation to environmental changes is greatly needed. Forward-looking research and modelling, based on cytogenetics, expression studies, and genomics or genome sequencing analyses, discussed in this Special Issue of the Annals of Botany, consider how new polyploids behave and the pathways available for genome evolution. They address fundamental questions about the advantages and disadvantages of polyploidy, the consequences for evolution and speciation, and applied questions regarding the spread of polyploids in the environment and challenges in breeding and exploitation of wild relatives through introgression or resynthesis of polyploids.
CONCLUSION
Chromosome number, genome size, repetitive DNA sequences, genes and regulatory sequences and their expression evolve following polyploidy - generating diversity and possible novel traits and enabling species diversification. There is the potential for ever more polyploids in natural, managed and disturbed environments under changing climates and new stresses.
Topics: Genome, Plant; Evolution, Molecular; Chromosomes; Plants; Polyploidy
PubMed: 36282971
DOI: 10.1093/aob/mcac132 -
Nature Ecology & Evolution Oct 2021Most diploid organisms have polyploid ancestors. The evolutionary process of polyploidization is poorly understood but has frequently been conjectured to involve some...
Most diploid organisms have polyploid ancestors. The evolutionary process of polyploidization is poorly understood but has frequently been conjectured to involve some form of 'genome shock', such as genome reorganization and subgenome expression dominance. Here we study polyploidization in Arabidopsis suecica, a post-glacial allopolyploid species formed via hybridization of Arabidopsis thaliana and Arabidopsis arenosa. We generated a chromosome-level genome assembly of A. suecica and complemented it with polymorphism and transcriptome data from all species. Despite a divergence around 6 million years ago (Ma) between the ancestral species and differences in their genome composition, we see no evidence of a genome shock: the A. suecica genome is colinear with the ancestral genomes; there is no subgenome dominance in expression; and transposon dynamics appear stable. However, we find changes suggesting gradual adaptation to polyploidy. In particular, the A. thaliana subgenome shows upregulation of meiosis-related genes, possibly to prevent aneuploidy and undesirable homeologous exchanges that are observed in synthetic A. suecica, and the A. arenosa subgenome shows upregulation of cyto-nuclear processes, possibly in response to the new cytoplasmic environment of A. suecica, with plastids maternally inherited from A. thaliana. These changes are not seen in synthetic hybrids, and thus are likely to represent subsequent evolution.
Topics: Arabidopsis; Diploidy; Genome, Plant; Humans; Hybridization, Genetic; Polyploidy
PubMed: 34413506
DOI: 10.1038/s41559-021-01525-w -
BMC Plant Biology Jun 2023Cymbidium aloifolium is a popular ornamental flower in Thailand with both economic and medical values. Polyploid induction techniques are used to improve plant quality....
BACKGROUND
Cymbidium aloifolium is a popular ornamental flower in Thailand with both economic and medical values. Polyploid induction techniques are used to improve plant quality. This study identified polyploidy levels of C. aloifolium induction by colchicine. Protocorms of C. aloifolium were treated on solid New Dogashima Medium (NDM) with various concentrations of colchicine (0, 0.01, 0.02, 0.03, 0.04 and 0.05% w/v) for 2, 4 and 8 weeks.
RESULTS
Colchicine effectively induced plant polyploidy. Tetraploid plants were found after treatment with 0.03% and 0.04% colchicine for 8 weeks, while at increased concentration and duration, survival, response and growth performance decreased. Tetraploid plants showed the lowest growth performance but highest size of stomatal and epidermal cells. Growth performance and leaf surface anatomy data were analyzed by Pearson's correlation and PCA. Results showed that stomatal and epidermal cell sizes had strongly negative correlations with other variables, while HCA revealed that stomatal and epidermal cell sizes of tetraploid plantlets were larger but stomatal and epidermal cell densities decreased when compared with the diploids.
CONCLUSION
Colchicine at suitable concentrations and duration produced polyploid plants with alteration of morphological and anatomical traits. This study provides potential information to support orchid quality production as ornamental plants and a source of pharmaceutical raw materials.
Topics: Tetraploidy; Polyploidy; Plant Leaves; Flowers; Colchicine
PubMed: 37264309
DOI: 10.1186/s12870-023-04314-8 -
Seminars in Cancer Biology Jun 2022The aberrant biology of polyploid giant cancer cells (PGCC) includes dysregulation of the cell cycle, induction of stress responses, and dedifferentiation, all of which... (Review)
Review
The aberrant biology of polyploid giant cancer cells (PGCC) includes dysregulation of the cell cycle, induction of stress responses, and dedifferentiation, all of which are likely accompanied by adaptations in biophysical properties and metabolic activity. Sphingolipids are the second largest class of membrane lipids and play important roles in many aspects of cell biology that are potentially relevant to polyploidy. We have recently shown that the function of the sphingolipid enzyme acid ceramidase (ASAH1) is critical for the ability of PGCC to generate progeny by depolyploidization but mechanisms by which sphingolipids contribute to polyploidy and generation of offspring with stem-like properties remain elusive. This review discusses the role of sphingolipids during embryonic development, cell cycle regulation, and stem cells in an effort to highlight parallels to polyploidy.
Topics: Cell Cycle; Embryonic Development; Humans; Neoplasms; Polyploidy; Sphingolipids
PubMed: 33429049
DOI: 10.1016/j.semcancer.2020.12.027 -
UGDR: a generic pipeline to detect recombined regions in polyploid and complex hybrid yeast genomes.BMC Bioinformatics Dec 2022In eukaryotes, homologous recombination between the parental genomes frequently occurs during the evolutionary conserved process of meiosis, generating the genetic...
MOTIVATION
In eukaryotes, homologous recombination between the parental genomes frequently occurs during the evolutionary conserved process of meiosis, generating the genetic diversity transmitted by the gametes. The genome-wide determination of the frequency and location of the recombination events can now be efficiently performed by genotyping the offspring's polymorphic markers. However, genotyping recombination in complex hybrid genomes with existing methods remains challenging because of their strain and ploidy specificity and the degree of diversity and complexity of the parental genomes, especially in [Formula: see text] polyploids.
RESULTS
We present UGDR, a pipeline to genotype the polymorphisms of complex hybrid yeast genomes. It is based on optimal mapping strategies of NGS reads, comparative analyses of the allelic ratio variation and read depth coverage. We tested the UGDR pipeline with sequencing reads from recombined hybrid diploid yeast strains and various clinical strains exhibiting different degrees of ploidy. UGDR allows to plot the markers distribution and recombination profile per chromosome.
CONCLUSION
UGDR detects and plots recombination events in haploids and polyploid yeasts, which facilitates the discovery and understanding of the yeast genetic recombination map and identify new out-performing recombinants.
Topics: Genome; Polyploidy; Ploidies; Diploidy; Polymorphism, Genetic; Yeasts
PubMed: 36544090
DOI: 10.1186/s12859-022-05113-y -
American Journal of Botany Aug 2022Whole-genome duplication is common in plants and is considered to have a broad range of effects on individuals' phenotypes and genomes and to be an important driver of...
Whole-genome duplication is common in plants and is considered to have a broad range of effects on individuals' phenotypes and genomes and to be an important driver of plant adaptation and speciation. Despite their increased capacity to cope with challenging environments, polyploid lineages are generally as prone to extinction, and sometimes more prone, than their diploid progenitors. Although several explanations have been proposed to explain the short- and long-term disadvantages of polyploidy on the survival probability of populations, the consequences of whole-genome doubling on the heritable variance remain poorly studied. Whole-genome doubling can have major effects not only on the genetics, but also on the ecology and life history of the populations. Modifications of other properties of populations can reverse the effects of polyploidization per se on heritable variance. In this synthesis, I summarize the empirical and theoretical knowledge about the multifarious consequences of genome doubling on the heritable variance of quantitative traits and on the evolutionary potential of polyploid populations compared to their diploid progenitors. I propose several ways to decipher the consequences of whole-genome doubling on survival probability and to study the further consequences of shifting the ecological niche and life-history traits of a population. I also highlight some practical considerations for comparing the heritable variance of a trait among different cytotypes. Such investigations appear to be timely and necessary to understand more about the paradoxical aspects of polyploidization and to understand the evolutionary potential of polyploid lineages in a global warming context.
Topics: Biological Evolution; Diploidy; Genome, Plant; Plants; Polyploidy
PubMed: 35862788
DOI: 10.1002/ajb2.16029 -
American Journal of Botany Nov 2021Whole-genome duplication (WGD) is ubiquitous in plants. Recent reviews and meta-analyses, aiming to understand how such phenotypic transition could facilitate... (Meta-Analysis)
Meta-Analysis
PREMISE
Whole-genome duplication (WGD) is ubiquitous in plants. Recent reviews and meta-analyses, aiming to understand how such phenotypic transition could facilitate neopolyploid establishment, demonstrated multifarious immediate effects of WGD on fitness and reproductive traits. Yet, little is known about how short-term modifications evolve through time. Such a comparison among new and established polyploid lineages is crucial to understand which effects of WGD promote or impede polyploid survival.
METHODS
We performed a meta-analysis to determine how WGD affects morphological, cellular, and fitness traits in autotetraploid individuals compared to their diploid progenitors. We studied how established tetraploids differed from diploids compared to neotetraploids, to further learn about the fate of WGD-associated phenotypic effects during polyploid establishment.
RESULTS
The short-term effects of WGD were an increase in size of morphological traits and cells, accompanied by a decrease in fitness and the number of cells. After establishment, the morphological effect persisted, but cellular and fitness components reverted back to the values observed in the diploid ancestors.
CONCLUSIONS
Our results suggest that the larger morphology of autotetraploids is not a constraint to establishment. However, other observable effects of genome doubling disappeared with time, suggesting that solving cellular and fitness constraints are critical aspects for polyploid establishment.
Topics: Diploidy; Gene Duplication; Genome, Plant; Polyploidy; Tetraploidy
PubMed: 34618350
DOI: 10.1002/ajb2.1759