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International Journal of Molecular... Aug 2022Polyploid cells demonstrate biological plasticity and stress adaptation in evolution; development; and pathologies, including cardiovascular diseases, neurodegeneration,... (Review)
Review
Polyploid cells demonstrate biological plasticity and stress adaptation in evolution; development; and pathologies, including cardiovascular diseases, neurodegeneration, and cancer. The nature of ploidy-related advantages is still not completely understood. Here, we summarize the literature on molecular mechanisms underlying ploidy-related adaptive features. Polyploidy can regulate gene expression via chromatin opening, reawakening ancient evolutionary programs of embryonality. Chromatin opening switches on genes with bivalent chromatin domains that promote adaptation via rapid induction in response to signals of stress or morphogenesis. Therefore, stress-associated polyploidy can activate Myc proto-oncogenes, which further promote chromatin opening. Moreover, Myc proto-oncogenes can trigger polyploidization de novo and accelerate genome accumulation in already polyploid cells. As a result of these cooperative effects, polyploidy can increase the ability of cells to search for adaptive states of cellular programs through gene regulatory network rewiring. This ability is manifested in epigenetic plasticity associated with traits of stemness, unicellularity, flexible energy metabolism, and a complex system of DNA damage protection, combining primitive error-prone unicellular repair pathways, advanced error-free multicellular repair pathways, and DNA damage-buffering ability. These three features can be considered important components of the increased adaptability of polyploid cells. The evidence presented here contribute to the understanding of the nature of stress resistance associated with ploidy and may be useful in the development of new methods for the prevention and treatment of cardiovascular and oncological diseases.
Topics: Chromatin; Epigenesis, Genetic; Gene Regulatory Networks; Humans; Polyploidy; Proto-Oncogenes
PubMed: 36077092
DOI: 10.3390/ijms23179691 -
The New Phytologist Mar 2019Polyploidy, or whole-genome duplication often with hybridization, is common in eukaryotes and is thought to drive ecological and evolutionary success, especially in...
Polyploidy, or whole-genome duplication often with hybridization, is common in eukaryotes and is thought to drive ecological and evolutionary success, especially in plants. The mechanisms of polyploid success in ecologically relevant contexts, however, remain largely unknown. We conducted an extensive test of functional trait divergence and plasticity in conferring polyploid fitness advantage in heterogeneous environments, by growing clonal replicates of a worldwide genotype collection of six allopolyploid and five diploid wild strawberry (Fragaria) taxa in three climatically different common gardens. Among leaf functional traits, we detected divergence in trait means but not plasticities between polyploids and diploids, suggesting that increased genomic redundancy in polyploids does not necessarily translate into greater trait plasticity in response to environmental change. Across the heterogeneous garden environments, however, polyploids exhibited fitness advantage, which was conferred by both trait means and adaptive trait plasticities, supporting a 'jack-and-master' hypothesis for polyploids. Our findings elucidate essential ecological mechanisms underlying polyploid adaptation to heterogeneous environments, and provide an important insight into the prevalence and persistence of polyploid plants.
Topics: Adaptation, Physiological; Diploidy; Fragaria; Oregon; Polyploidy; Quantitative Trait, Heritable
PubMed: 30281801
DOI: 10.1111/nph.15508 -
Cell Nov 2007Polyploidization, the addition of a complete set of chromosomes to the genome, represents one of the most dramatic mutations known to occur. Nevertheless, polyploidy is... (Review)
Review
Polyploidization, the addition of a complete set of chromosomes to the genome, represents one of the most dramatic mutations known to occur. Nevertheless, polyploidy is well tolerated in many groups of eukaryotes. Indeed, the majority of flowering plants and vertebrates have descended from polyploid ancestors. This Review examines the short-term effects of polyploidization on cell size, body size, genomic stability, and gene expression and the long-term effects on rates of evolution.
Topics: Animals; Biological Evolution; Body Size; Cell Size; Genes, Duplicate; Genomic Instability; Humans; Polyploidy
PubMed: 17981114
DOI: 10.1016/j.cell.2007.10.022 -
International Journal of Cell Cloning Jul 1990During the early stages of their differentiation, megakaryocytes become polyploid through repeated DNA replication and endomitotic cycles without cytokinesis. The... (Review)
Review
During the early stages of their differentiation, megakaryocytes become polyploid through repeated DNA replication and endomitotic cycles without cytokinesis. The molecular basis for the process of polyploidization remains unknown. This review summarizes available information on the cell biology of the process of endomitosis.
Topics: Animals; Chromosomes; DNA Replication; Humans; Megakaryocytes; Polyploidy
PubMed: 2205660
DOI: 10.1002/stem.5530080405 -
Genetics Sep 2022Theoretical population genetics has been mostly developed for sexually reproducing diploid and for monoploid (haploid) organisms, focusing on eukaryotes. The evolution...
Theoretical population genetics has been mostly developed for sexually reproducing diploid and for monoploid (haploid) organisms, focusing on eukaryotes. The evolution of bacteria and archaea is often studied by models for the allele dynamics in monoploid populations. However, many prokaryotic organisms harbor multicopy replicons-chromosomes and plasmids-and theory for the allele dynamics in populations of polyploid prokaryotes remains lacking. Here, we present a population genetics model for replicons with multiple copies in the cell. Using this model, we characterize the fixation process of a dominant beneficial mutation at 2 levels: the phenotype and the genotype. Our results show that depending on the mode of replication and segregation, the fixation of the mutant phenotype may precede genotypic fixation by many generations; we term this time interval the heterozygosity window. We furthermore derive concise analytical expressions for the occurrence and length of the heterozygosity window, showing that it emerges if the copy number is high and selection strong. Within the heterozygosity window, the population is phenotypically adapted, while both alleles persist in the population. Replicon ploidy thus allows for the maintenance of genetic variation following phenotypic adaptation and consequently for reversibility in adaptation to fluctuating environmental conditions.
Topics: Alleles; Chromosomes; Haploidy; Humans; Plasmids; Polyploidy
PubMed: 35959975
DOI: 10.1093/genetics/iyac121 -
Genetics Nov 2018Detecting and quantifying the differences in individual genomes (, genotyping), plays a fundamental role in most modern bioinformatics pipelines. Many scientists now use...
Detecting and quantifying the differences in individual genomes (, genotyping), plays a fundamental role in most modern bioinformatics pipelines. Many scientists now use reduced representation next-generation sequencing (NGS) approaches for genotyping. Genotyping diploid individuals using NGS is a well-studied field, and similar methods for polyploid individuals are just emerging. However, there are many aspects of NGS data, particularly in polyploids, that remain unexplored by most methods. Our contributions in this paper are fourfold: (i) We draw attention to, and then model, common aspects of NGS data: sequencing error, allelic bias, overdispersion, and outlying observations. (ii) Many datasets feature related individuals, and so we use the structure of Mendelian segregation to build an empirical Bayes approach for genotyping polyploid individuals. (iii) We develop novel models to account for preferential pairing of chromosomes, and harness these for genotyping. (iv) We derive oracle genotyping error rates that may be used for read depth suggestions. We assess the accuracy of our method in simulations, and apply it to a dataset of hexaploid sweet potato (). An R package implementing our method is available at https://cran.r-project.org/package=updog.
Topics: Alleles; Genotyping Techniques; High-Throughput Nucleotide Sequencing; Ipomoea batatas; Models, Genetic; Polymorphism, Single Nucleotide; Polyploidy
PubMed: 30185430
DOI: 10.1534/genetics.118.301468 -
Medecine Sciences : M/S 2019Polyploidy (alias whole genome amplification) refers to organisms containing more than two basic sets of chromosomes. Polyploidy was first observed in plants more than a... (Review)
Review
Polyploidy (alias whole genome amplification) refers to organisms containing more than two basic sets of chromosomes. Polyploidy was first observed in plants more than a century ago, and it is known that such processes occur in many eukaryotes under a variety of circumstances. In mammals, the development of polyploid cells can contribute to tissue differentiation and therefore possibly a gain of function. Alternately, it can be associated with development of disease such as cancer. Polyploidy can occur because of cell fusion or abnormal cell division. Polyploidy is a common characteristic of the mammalian liver. Polyploidization occurs notably during liver development, but also in adults because of cellular stress. Recent progresses have unraveled the mechanisms and functional consequences of hepatocytes polyploidization during normal and pathological liver growth.
Topics: Adult; Animals; Cell Division; Cell Fusion; Hepatocytes; Humans; Liver; Polyploidy
PubMed: 31274081
DOI: 10.1051/medsci/2019094 -
Genes Jan 2022Newly formed polyploids often show extensive meiotic defects, resulting in aneuploid gametes, and thus reduced fertility. However, while many neopolyploids are... (Review)
Review
Newly formed polyploids often show extensive meiotic defects, resulting in aneuploid gametes, and thus reduced fertility. However, while many neopolyploids are meiotically unstable, polyploid lineages that survive in nature are generally stable and fertile; thus, those lineages that survive are those that are able to overcome these challenges. Several genes that promote polyploid stabilization are now known in plants, allowing speculation on the evolutionary origin of these meiotic adjustments. Here, I discuss results that show that meiotic stability can be achieved through the differentiation of certain alleles of certain genes between ploidies. These alleles, at least sometimes, seem to arise by novel mutation, while standing variation in either ancestral diploids or related polyploids, from which alleles can introgress, may also contribute. Growing evidence also suggests that the coevolution of multiple interacting genes has contributed to polyploid stabilization, and in allopolyploids, the return of duplicated genes to single copies (genome fractionation) may also play a role in meiotic stabilization. There is also some evidence that epigenetic regulation may be important, which can help explain why some polyploid lineages can partly stabilize quite rapidly.
Topics: Epigenesis, Genetic; Genome, Plant; Meiosis; Plants; Polyploidy
PubMed: 35052487
DOI: 10.3390/genes13010147 -
Single Nucleotide Polymorphism Identification in Polyploids: A Review, Example, and Recommendations.Molecular Plant Jun 2015Understanding the relationship between genotype and phenotype is a major biological question and being able to predict phenotypes based on molecular genotypes is... (Review)
Review
Understanding the relationship between genotype and phenotype is a major biological question and being able to predict phenotypes based on molecular genotypes is integral to molecular breeding. Whole-genome duplications have shaped the history of all flowering plants and present challenges to elucidating the relationship between genotype and phenotype, especially in neopolyploid species. Although single nucleotide polymorphisms (SNPs) have become popular tools for genetic mapping, discovery and application of SNPs in polyploids has been difficult. Here, we summarize common experimental approaches to SNP calling, highlighting recent polyploid successes. To examine the impact of software choice on these analyses, we called SNPs among five peanut genotypes using different alignment programs (BWA-mem and Bowtie 2) and variant callers (SAMtools, GATK, and Freebayes). Alignments produced by Bowtie 2 and BWA-mem and analyzed in SAMtools shared 24.5% concordant SNPs, and SAMtools, GATK, and Freebayes shared 1.4% concordant SNPs. A subsequent analysis of simulated Brassica napus chromosome 1A and 1C genotypes demonstrated that, of the three software programs, SAMtools performed with the highest sensitivity and specificity on Bowtie 2 alignments. These results, however, are likely to vary among species, and we therefore propose a series of best practices for SNP calling in polyploids.
Topics: Arachis; Brassica napus; High-Throughput Nucleotide Sequencing; Plant Proteins; Polymorphism, Single Nucleotide; Polyploidy
PubMed: 25676455
DOI: 10.1016/j.molp.2015.02.002 -
Kidney International Apr 2024Tubular epithelial cells (TCs) compose the majority of kidney parenchyma and play fundamental roles in maintaining homeostasis. Like other tissues, mostly immature TC...
Tubular epithelial cells (TCs) compose the majority of kidney parenchyma and play fundamental roles in maintaining homeostasis. Like other tissues, mostly immature TC with progenitor capabilities are able to replace TC lost during injury via clonal expansion and differentiation. In contrast, differentiated TC lack this capacity. However, as the kidney is frequently exposed to toxic injuries, evolution positively selected a response program that endows differentiated TC to maintain residual kidney function during kidney injury. Recently, we and others have described polyploidization of differentiated TC, a mechanism to augment the function of remnant TC after injury by rapid hypertrophy. Polyploidy is a condition characterized by >2 complete sets of chromosomes. Polyploid cells often display an increased functional capacity and are generally more resilient to stress as evidenced by being conserved across many plants and eukaryote species from flies to mammals. Here, we discuss the occurrence of TC polyploidy in different contexts and conditions and how this integrates into existing concepts of kidney cell responses to injury. Collectively, we aim at stimulating the acquisition of novel knowledge in the kidney field as well as accelerating the translation of this basic response mechanism to the clinical sphere.
Topics: Animals; Hepatocytes; Cell Differentiation; Epithelial Cells; Polyploidy; Kidney; Mammals
PubMed: 38199322
DOI: 10.1016/j.kint.2023.10.036