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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 -
Science China. Life Sciences Apr 2012Polyploids are organisms with three or more complete chromosome sets. Polyploidization is widespread in plants and animals, and is an important mechanism of speciation.... (Review)
Review
Polyploids are organisms with three or more complete chromosome sets. Polyploidization is widespread in plants and animals, and is an important mechanism of speciation. Genome sequencing and related molecular systematics and bioinformatics studies on plants and animals in recent years support the view that species have been shaped by whole genome duplication during evolution. The stability of polyploids depends on rapid genome recombination and changes in gene expression after formation. The formation of polyploids and subsequent diploidization are important aspects in long-term evolution. Polyploids can be formed in various ways. Among them, hybrid organisms formed by distant hybridization could produce unreduced gametes and thus generate offspring with doubled chromosomes, which is a fast, efficient method of polyploidization. The formation of fertile polyploids not only promoted the interflow of genetic materials among species and enriched the species diversity, but also laid the foundation for polyploidy breeding. The study of polyploids has both important theoretical significance and valuable applications. The production and application of polyploidy breeding have brought remarkable economic and social benefits.
Topics: Animals; Breeding; Evolution, Molecular; Fertility; Genetic Variation; Genome, Plant; Hybridization, Genetic; Plants; Polyploidy
PubMed: 22566086
DOI: 10.1007/s11427-012-4310-2 -
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 -
Genes Jan 2024Cells with an abnormal number of chromosomes have been found in more than 90% of solid tumors, and among these, polyploidy accounts for about 40%. Polyploidized cells... (Review)
Review
Cells with an abnormal number of chromosomes have been found in more than 90% of solid tumors, and among these, polyploidy accounts for about 40%. Polyploidized cells most often have duplicate centrosomes as well as genomes, and thus their mitosis tends to promote merotelic spindle attachments and chromosomal instability, which produces a variety of aneuploid daughter cells. Polyploid cells have been found highly resistant to various stress and anticancer therapies, such as radiation and mitogenic inhibitors. In other words, common cancer therapies kill proliferative diploid cells, which make up the majority of cancer tissues, while polyploid cells, which lurk in smaller numbers, may survive. The surviving polyploid cells, prompted by acute environmental changes, begin to mitose with chromosomal instability, leading to an explosion of genetic heterogeneity and a concomitant cell competition and adaptive evolution. The result is a recurrence of the cancer during which the tenacious cells that survived treatment express malignant traits. Although the presence of polyploid cells in cancer tissues has been observed for more than 150 years, the function and exact role of these cells in cancer progression has remained elusive. For this reason, there is currently no effective therapeutic treatment directed against polyploid cells. This is due in part to the lack of suitable experimental models, but recently several models have become available to study polyploid cells in vivo. We propose that the experimental models in , for which genetic techniques are highly developed, could be very useful in deciphering mechanisms of polyploidy and its role in cancer progression.
Topics: Animals; Drosophila; Neoplasms; Polyploidy; Centrosome; Chromosomal Instability
PubMed: 38254985
DOI: 10.3390/genes15010096 -
Current Opinion in Plant Biology Apr 2018Polyploidy may provide adaptive advantages and is considered to be important for evolution and speciation. Polyploidy events are found throughout the evolutionary... (Review)
Review
Polyploidy may provide adaptive advantages and is considered to be important for evolution and speciation. Polyploidy events are found throughout the evolutionary history of plants, however they do not seem to be uniformly distributed along the time axis. For example, many of the detected ancient whole-genome duplications (WGDs) seem to cluster around the K/Pg boundary (∼66Mya), which corresponds to a drastic climate change event and a mass extinction. Here, we discuss more recent polyploidy events using Arabidopsis as the most developed plant model at the level of the entire genus. We review the history of the origin of allotetraploid species A. suecica and A. kamchatica, and tetraploid lineages of A. lyrata, A. arenosa and A. thaliana, and discuss potential adaptive advantages. Also, we highlight an association between recent glacial maxima and estimated times of origins of polyploidy in Arabidopsis. Such association might further support a link between polyploidy and environmental challenge, which has been observed now for different time-scales and for both ancient and recent polyploids.
Topics: Arabidopsis; Evolution, Molecular; Genetic Variation; Genome, Plant; Phylogeny; Polyploidy
PubMed: 29448159
DOI: 10.1016/j.pbi.2018.01.005 -
The Journal of Heredity Mar 2018Though polyploidy is an important aspect of the evolutionary genetics of both plants and animals, the development of population genetic theory of polyploids has... (Review)
Review
Though polyploidy is an important aspect of the evolutionary genetics of both plants and animals, the development of population genetic theory of polyploids has seriously lagged behind that of diploids. This is unfortunate since the analysis of polyploid genetic data-and the interpretation of the results-requires even more scrutiny than with diploid data. This is because of several polyploidy-specific complications in segregation and genotyping such as tetrasomy, double reduction, and missing dosage information. Here, we review the theoretical and statistical aspects of the population genetics of polyploids. We discuss several widely used types of inferences, including genetic diversity, Hardy-Weinberg equilibrium, population differentiation, genetic distance, and detecting population structure. For each, we point out how the statistical approach, expected result, and interpretation differ between different ploidy levels. We also discuss for each type of inference what biases may arise from the polyploid-specific complications and how these biases can be overcome. From our overview, it is clear that the statistical toolbox that is available for the analysis of genetic data is flexible and still expanding. Modern sequencing techniques will soon be able to overcome some of the current limitations to the analysis of polyploid data, though the techniques are lagging behind those available for diploids. Furthermore, the availability of more data may aggravate the biases that can arise, and increase the risk of false inferences. Therefore, simulations such as we used throughout this review are an important tool to verify the results of analyses of polyploid genetic data.
Topics: Animals; Cluster Analysis; Gene Frequency; Genetic Variation; Genetics, Population; Heterozygote; Models, Genetic; Multivariate Analysis; Polyploidy; Reproduction
PubMed: 29385510
DOI: 10.1093/jhered/esy006 -
American Journal of Physiology. Cell... Oct 2023Polyploidization of tubular cells (TC) is triggered by acute kidney injury (AKI) to allow survival in the early phase after AKI, but in the long run promotes fibrosis...
Polyploidization of tubular cells (TC) is triggered by acute kidney injury (AKI) to allow survival in the early phase after AKI, but in the long run promotes fibrosis and AKI-chronic kidney disease (CKD) transition. The molecular mechanism governing the link between polyploid TC and kidney fibrosis remains to be clarified. In this study, we demonstrate that immediately after AKI, expression of cell cycle markers mostly identifies a population of DNA-damaged polyploid TC. Using transgenic mouse models and single-cell RNA sequencing we show that, unlike diploid TC, polyploid TC accumulate DNA damage and survive, eventually resting in the G1 phase of the cell cycle. In vivo and in vitro single-cell RNA sequencing along with sorting of polyploid TC shows that these cells acquire a profibrotic phenotype culminating in transforming growth factor (TGF)-β1 expression and that TGF-β1 directly promotes polyploidization. This demonstrates that TC polyploidization is a self-sustained mechanism. Interactome analysis by single-cell RNA sequencing revealed that TGF-β1 signaling fosters a reciprocal activation loop among polyploid TC, macrophages, and fibroblasts to sustain kidney fibrosis and promote CKD progression. Collectively, this study contributes to the ongoing revision of the paradigm of kidney tubule response to AKI, supporting the existence of a tubulointerstitial cross talk mediated by TGF-β1 signaling produced by polyploid TC following DNA damage. Polyploidization in tubular epithelial cells has been neglected until recently. Here, we showed that polyploidization is a self-sustained mechanism that plays an important role during chronic kidney disease development, proving the existence of a cross talk between infiltrating cells and polyploid tubular cells. This study contributes to the ongoing revision of kidney adaptation to injury, posing polyploid tubular cells at the center of the process.
Topics: Animals; Mice; Transforming Growth Factor beta1; Acute Kidney Injury; Epithelial Cells; Polyploidy; Fibrosis
PubMed: 37642236
DOI: 10.1152/ajpcell.00081.2023 -
Current Opinion in Plant Biology Oct 2022The prevalence of polyploidy in wild and crop species has stimulated debate over its evolutionary advantages and disadvantages. Previous studies have focused on changes... (Review)
Review
The prevalence of polyploidy in wild and crop species has stimulated debate over its evolutionary advantages and disadvantages. Previous studies have focused on changes occurring at the polyploidization events, including genome-wide changes termed "genome shock," as well as ancient polyploidy. Recent bioinformatics advances and empirical studies of Arabidopsis and wheat relatives are filling a research gap: the functional evolutionary study of polyploid species using RNA-seq, DNA polymorphism, and epigenomics. Polyploid species can become generalists in natura through environmental robustness by inheriting and merging parental stress responses. Their evolvability is enhanced by mutational robustness working on inherited standing variation. The identification of key genes responsible for gradual adaptive evolution will encourage synthetic biological approaches to transfer polyploid advantages to other species.
Topics: Arabidopsis; Evolution, Molecular; Genome, Plant; Polyploidy; Triticum
PubMed: 36063635
DOI: 10.1016/j.pbi.2022.102292 -
Current Opinion in Plant Biology Apr 2018The large wave of polyploidization following the Cretaceous-Paleogene (K-Pg) mass extinction has been explained by enhanced polyploid persistence arising from adaptive... (Review)
Review
The large wave of polyploidization following the Cretaceous-Paleogene (K-Pg) mass extinction has been explained by enhanced polyploid persistence arising from adaptive properties of the polyploids themselves, as well as an increase in unreduced gamete production and diploid hybridization. We propose that the demise of diploids afforded opportunities for polyploid establishment and expansion into novel habitats. Augmented polyploid gene pools from diploid and polyploid relatives, in association with their multiple and independent origins (of both autopolyploids and allopolyploids), facilitated their subsequent diversification. Their ability to recruit genetic variation from their diploid relatives or from products of recurrent origins sharing their genome(s) ostensibly contributed to polyploid persistence. Concomitantly, we propose that the number of congeneric diploid species dramatically contracted disproportionally to polyploids during the K-Pg interval (i.e. a diploid trough), resulting in a reduction in the rate of diploid speciation. Accordingly, the preponderance of neopolyploids was likely autopolyploids.
Topics: DNA, Plant; Diploidy; Ecosystem; Genetic Variation; Hybridization, Genetic; Phylogeny; Polyploidy
PubMed: 29107221
DOI: 10.1016/j.pbi.2017.09.010 -
Seminars in Liver Disease Jan 2021Hepatocytes are the primary functional cells of the liver that perform essential roles in homeostasis, regeneration, and injury. Most mammalian somatic cells are diploid... (Review)
Review
Hepatocytes are the primary functional cells of the liver that perform essential roles in homeostasis, regeneration, and injury. Most mammalian somatic cells are diploid and contain pairs of each chromosome, but there are also polyploid cells containing additional sets of chromosomes. Hepatocytes are among the best described polyploid cells, with polyploids comprising more than 25 and 90% of the hepatocyte population in humans and mice, respectively. Cellular and molecular mechanisms that regulate hepatic polyploidy have been uncovered, and in recent years, diploid and polyploid hepatocytes have been shown to perform specialized functions. Diploid hepatocytes accelerate liver regeneration induced by resection and may accelerate compensatory regeneration after acute injury. Polyploid hepatocytes protect the liver from tumor initiation in hepatocellular carcinoma and promote adaptation to tyrosinemia-induced chronic injury. This review describes how ploidy variations influence cellular activity and presents a model for context-specific functions for diploid and polyploid hepatocytes.
Topics: Animals; Diploidy; Hepatocytes; Humans; Liver; Liver Neoplasms; Mice; Polyploidy
PubMed: 33764484
DOI: 10.1055/s-0040-1719175