-
The New Phytologist Apr 2021Polyploidy is a dominant feature of extant plant diversity. However, major research questions, including whether polyploidy is important to long-term evolution or is... (Review)
Review
Polyploidy is a dominant feature of extant plant diversity. However, major research questions, including whether polyploidy is important to long-term evolution or is just 'evolutionary noise', remain unresolved due to difficulties associated with the generation and analysis of data from polyploid lineages. Many of these difficulties have been recently overcome, such that it is now often relatively straightforward to infer the full and often reticulate phylogenetic history of groups with recently formed polyploids. This nascent field of 'polyploid phylogenetics' allows researchers to tackle long-standing questions of polyploid macroevolution, supplies the foundation for mechanistic models of ploidy change, and provides the opportunity to include a more complete and representative sample of plant taxa in our analyses in general.
Topics: Evolution, Molecular; Genome, Plant; Phylogeny; Plants; Polyploidy
PubMed: 33491778
DOI: 10.1111/nph.17105 -
Trends in Ecology & Evolution Jun 2022Polyploidy is a major driver of evolutionary change in plants, but many aspects of polyploidy in natural systems remain enigmatic. We argue that urban landscapes present... (Review)
Review
Polyploidy is a major driver of evolutionary change in plants, but many aspects of polyploidy in natural systems remain enigmatic. We argue that urban landscapes present an unprecedented opportunity to observe polyploidy in action. Integrating polyploid biology and urban evolutionary ecology, we discuss multiple factors expected to promote polyploid formation, establishment, and persistence in urban systems. We develop a predictive framework for the contemporary ecology and evolution of polyploid plants in cities, and through this novel perspective propose that studying polyploidy in an urban context could lead to breakthroughs in understanding fundamental processes in polyploid evolution. We conclude by highlighting the potential consequences of polyploidy in urban environments, and outline a roadmap for research into this currently unexplored field.
Topics: Biological Evolution; Plants; Polyploidy
PubMed: 35246321
DOI: 10.1016/j.tree.2022.02.005 -
Nature Communications Oct 2022Acute kidney injury (AKI) is frequent, often fatal and, for lack of specific therapies, can leave survivors with chronic kidney disease (CKD). We characterize the...
Acute kidney injury (AKI) is frequent, often fatal and, for lack of specific therapies, can leave survivors with chronic kidney disease (CKD). We characterize the distribution of tubular cells (TC) undergoing polyploidy along AKI by DNA content analysis and single cell RNA-sequencing. Furthermore, we study the functional roles of polyploidization using transgenic models and drug interventions. We identify YAP1-driven TC polyploidization outside the site of injury as a rapid way to sustain residual kidney function early during AKI. This survival mechanism comes at the cost of senescence of polyploid TC promoting interstitial fibrosis and CKD in AKI survivors. However, targeting TC polyploidization after the early AKI phase can prevent AKI-CKD transition without influencing AKI lethality. Senolytic treatment prevents CKD by blocking repeated TC polyploidization cycles. These results revise the current pathophysiological concept of how the kidney responds to acute injury and identify a novel druggable target to improve prognosis in AKI survivors.
Topics: Acute Kidney Injury; DNA; Disease Progression; Humans; Kidney; Polyploidy; RNA; Renal Insufficiency, Chronic; Senotherapeutics
PubMed: 36195583
DOI: 10.1038/s41467-022-33110-5 -
Methods in Molecular Biology (Clifton,... 2023Polyploidy has been observed throughout major eukaryotic clades and has played a vital role in the evolution of angiosperms. Recent polyploidizations often result in... (Review)
Review
Polyploidy has been observed throughout major eukaryotic clades and has played a vital role in the evolution of angiosperms. Recent polyploidizations often result in highly complex genome structures, posing challenges to genome assembly and phasing. Recent advances in sequencing technologies and genome assembly algorithms have enabled high-quality, near-complete chromosome-level assemblies of polyploid genomes. Advances in novel sequencing technologies include highly accurate single-molecule sequencing with HiFi reads, chromosome conformation capture with Hi-C technique, and linked reads sequencing. Additionally, new computational approaches have also significantly improved the precision and reliability of polyploid genome assembly and phasing, such as HiCanu, hifiasm, ALLHiC, and PolyGembler. Herein, we review recently published polyploid genomes and compare the various sequencing, assembly, and phasing approaches that are utilized in these genome studies. Finally, we anticipate that accurate and telomere-to-telomere chromosome-level assembly of polyploid genomes could ultimately become a routine procedure in the near future.
Topics: Humans; Reproducibility of Results; Algorithms; Eukaryota; Eukaryotic Cells; Polyploidy
PubMed: 36720827
DOI: 10.1007/978-1-0716-2561-3_23 -
Cold Spring Harbor Perspectives in... Oct 2021Polyploidy is defined as a cell with three or more whole genome sets and enables cell growth across the kingdoms of life. Studies in model organisms have revealed that... (Review)
Review
Polyploidy is defined as a cell with three or more whole genome sets and enables cell growth across the kingdoms of life. Studies in model organisms have revealed that polyploid cell growth can be required for optimal tissue repair and regeneration. In mammals, polyploid cell growth contributes to repair of many tissues, including the liver, heart, kidney, bladder, and eye, and similar strategies have been identified in and zebrafish tissues. This review discusses the heterogeneity and versatility of polyploidy in tissue repair and regeneration. Polyploidy has been shown to restore tissue mass and maintain organ size as well as protect against oncogenic insults and genotoxic stress. Polyploid cells can also serve as a reservoir for new diploid cells in regeneration. The numerous mechanisms to generate polyploid cells provide an unlimited resource for tissues to exploit to undergo repair or regeneration.
Topics: Animals; DNA Damage; Heart; Humans; Polyploidy; Regeneration
PubMed: 34187807
DOI: 10.1101/cshperspect.a040881 -
Evolution; International Journal of... Sep 2021The effects of genetic mutations are influenced by genome structure. Polyploids have more gene or allele copies than diploids, which results in higher tolerance of...
The effects of genetic mutations are influenced by genome structure. Polyploids have more gene or allele copies than diploids, which results in higher tolerance of recessive deleterious mutations. However, this benefit may differ between autopolyploids and allopolyploids and between neopolyploids and older polyploid lineages due to the effects of hybridization and diploidization, respectively. To isolate these effects, we measured the impacts of controlled mutagenesis on reproductive fitness traits in closely related Arabidopsis diploids (A. thaliana), autotetraploids (A. thaliana), and allotetraploids (A. suecica), including both synthetic and natural polyploid lines. Overall, mutagenesis had the largest negative impacts on seed production, while its impacts on germination and survival were negligible. As expected, these effects were much stronger in diploids than in polyploids. The differences between autopolyploids, allopolyploids, and polyploids of different ages were minor-cumulative reproductive fitness did not significantly differ between the treatment and control groups for any polyploid line type. These results suggest that hybridization and polyploid age have not impacted the genomic redundancy of Arabidopsis polyploids enough to significantly alter their aggregate response to mutation, although this effect may differ in older polyploid lineages or in allopolyploids with different levels of divergence between parental subgenomes.
Topics: Aged; Arabidopsis; Diploidy; Genome, Plant; Humans; Hybridization, Genetic; Phenotype; Polyploidy
PubMed: 34251678
DOI: 10.1111/evo.14307 -
Yi Chuan = Hereditas Sep 2023Autotetraploid rice is a type of germplasm developed from the whole genome duplication of diploid rice, leading to large grains, high nutrient content, and resistance.... (Review)
Review
Autotetraploid rice is a type of germplasm developed from the whole genome duplication of diploid rice, leading to large grains, high nutrient content, and resistance. However, its low fertility has reduced yield and hampered commercialization. To address this issue, a new type of high fertility tetraploid rice was developed, which may serve as a useful germplasm for polyploid rice breeding. In this review, we summarize the progress made in understanding the cellular and molecular genetic mechanisms underlying the low fertility of autotetraploid rice and its F hybrid, as well as the main types of new tetraploid rice with high fertility. Lastly, the idea of utilizing the multi-generation heterosis of neo-tetraploid rice in the future is proposed as a reference for polyploid rice breeding.
Topics: Oryza; Tetraploidy; Plant Breeding; Cytoplasm; Polyploidy
PubMed: 37731232
DOI: 10.16288/j.yczz.23-074 -
Protein & Cell Aug 2023Polyploid cells, which contain more than one set of chromosome pairs, are very common in nature. Polyploidy can provide cells with several potential benefits over their...
Polyploid cells, which contain more than one set of chromosome pairs, are very common in nature. Polyploidy can provide cells with several potential benefits over their diploid counterparts, including an increase in cell size, contributing to organ growth and tissue homeostasis, and improving cellular robustness via increased tolerance to genomic stress and apoptotic signals. Here, we focus on why polyploidy in the cell occurs and which stress responses and molecular signals trigger cells to become polyploid. Moreover, we discuss its crucial roles in cell growth and tissue regeneration in the heart, liver, and other tissues.
Topics: Humans; Liver; Hepatocytes; Cell Cycle; Polyploidy; Homeostasis
PubMed: 37526344
DOI: 10.1093/procel/pwac064 -
Annual Review of Physiology Feb 2020In mammals, most cardiomyocytes (CMs) become polyploid (they have more than two complete sets of chromosomes). The purpose of this review is to evaluate assumptions... (Review)
Review
In mammals, most cardiomyocytes (CMs) become polyploid (they have more than two complete sets of chromosomes). The purpose of this review is to evaluate assumptions about CM ploidy that are commonly discussed, even if not experimentally demonstrated, and to highlight key issues that are still to be resolved. Topics discussed here include () technical and conceptual difficulties in defining a polyploid CM, () the candidate role of reactive oxygen as a proximal trigger for the onset of polyploidy, () the relationship between polyploidization and other aspects of CM maturation, () recent insights related to the regenerative role of the subpopulation of CMs that are not polyploid, and () speculations as to why CMs become polyploid at all. New approaches to experimentally manipulate CM ploidy may resolve some of these long-standing and fundamental questions.
Topics: Cell Proliferation; Humans; Myocardium; Myocytes, Cardiac; Polyploidy; Regeneration
PubMed: 31585517
DOI: 10.1146/annurev-physiol-021119-034618 -
Seminars in Liver Disease Nov 2023The liver's unique chromosomal variations, including polyploidy and aneuploidy, influence hepatocyte identity and function. Among the most well-studied mammalian... (Review)
Review
The liver's unique chromosomal variations, including polyploidy and aneuploidy, influence hepatocyte identity and function. Among the most well-studied mammalian polyploid cells, hepatocytes exhibit a dynamic interplay between diploid and polyploid states. The ploidy state is dynamic as hepatocytes move through the "ploidy conveyor," undergoing ploidy reversal and re-polyploidization during proliferation. Both diploid and polyploid hepatocytes actively contribute to proliferation, with diploids demonstrating an enhanced proliferative capacity. This enhanced potential positions diploid hepatocytes as primary drivers of liver proliferation in multiple contexts, including homeostasis, regeneration and repopulation, compensatory proliferation following injury, and oncogenic proliferation. This review discusses the influence of ploidy variations on cellular activity. It presents a model for ploidy-associated hepatocyte proliferation, offering a deeper understanding of liver health and disease with the potential to uncover novel treatment approaches.
Topics: Animals; Humans; Liver Regeneration; Liver; Hepatocytes; Cell Proliferation; Polyploidy; Mammals
PubMed: 37967885
DOI: 10.1055/a-2211-2144