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Nucleus (Austin, Tex.) Dec 2023In adult mammals, many heart muscle cells (cardiomyocytes) are polyploid, do not proliferate (post-mitotic), and, consequently, cannot contribute to heart regeneration.... (Review)
Review
In adult mammals, many heart muscle cells (cardiomyocytes) are polyploid, do not proliferate (post-mitotic), and, consequently, cannot contribute to heart regeneration. In contrast, fetal and neonatal heart muscle cells are diploid, proliferate, and contribute to heart regeneration. We have identified interdependent changes of the nuclear lamina, nuclear pore complexes, and DNA-content (ploidy) in heart muscle cell maturation. These results offer new perspectives on how cells alter their nuclear transport and, with that, their gene regulation in response to extracellular signals. We present how changes of the nuclear lamina alter nuclear pore complexes in heart muscle cells. The consequences of these changes for cellular regeneration and stress response in the heart are discussed.
Topics: Animals; Nuclear Pore; Nuclear Lamina; Ploidies; Cell Differentiation; Lamins; Mammals
PubMed: 37606283
DOI: 10.1080/19491034.2023.2246310 -
Microbiology Spectrum Feb 2024Microsporidia are obligate intracellular eukaryotic parasites with an extremely broad host range. They have both economic and public health importance. Ploidy in...
Microsporidia are obligate intracellular eukaryotic parasites with an extremely broad host range. They have both economic and public health importance. Ploidy in microsporidia is variable, with a few species formally identified as diploid and one as polyploid. Given the increase in the number of studies sequencing microsporidian genomes, it is now possible to assess ploidy levels across all currently explored microsporidian diversity. We estimate ploidy for all microsporidian data sets available on the Sequence Read Archive using k-mer-based analyses, indicating that polyploidy is widespread in Microsporidia and that ploidy change is dynamic in the group. Using genome-wide heterozygosity estimates, we also show that polyploid microsporidian genomes are relatively homozygous, and we discuss the implications of these findings on the timing of polyploidization events and their origin.IMPORTANCEMicrosporidia are single-celled intracellular parasites, distantly related to fungi, that can infect a broad range of hosts, from humans all the way to protozoans. Exploiting the wealth of microsporidian genomic data available, we use k-mer-based analyses to assess ploidy status across the group. Understanding a genome's ploidy is crucial in order to assemble it effectively and may also be relevant for better understanding a parasite's behavior and life cycle. We show that tetraploidy is present in at least six species in Microsporidia and that these polyploidization events are likely to have occurred independently. We discuss why these findings may be paradoxical, given that Microsporidia, like other intracellular parasites, have extremely small, reduced genomes.
Topics: Humans; Microsporidia; Phylogeny; Evolution, Molecular; Genome, Fungal; Polyploidy
PubMed: 38214524
DOI: 10.1128/spectrum.03669-23 -
Theriogenology Jul 2022This study describes, for the first time, the relationship between morphology and ploidy in domestic cat embryos. Blastocyst morphology and quality were assessed using... (Review)
Review
This study describes, for the first time, the relationship between morphology and ploidy in domestic cat embryos. Blastocyst morphology and quality were assessed using time-lapse recordings, while ploidy was analyzed using fluorescence in situ hybridization. Out of 54 blastocysts, clear fluorescence signals for all the molecular probes used were observed in 24 (44.4%) blastocysts, while in another 14 (25.9%) blastocysts, fluorescence signals only allowed for sex assessment. No clear signals were observed in the remaining 16 blastocysts (29.7%). Of the 24 blastocysts with clear signals, normal ploidy was detected in 10 (41.4%), 7 (29.2%) were diagnosed as haploid, and the remaining 7 blastocysts (29.2%) were mosaics. Additionally, results showed the distribution of diploid, haploid, and mosaic blastocysts in relation to the occurrence of morphological disorders and to embryo quality. The presence of abnormal embryo morphology and karyotype disorders may affect further development and the pregnancy rate. Due to the comparable proportion of good and poor quality blastocysts with disturbed ploidy, it is important to implement new methods of embryo assessment, especially when techniques used in humans, such as pronuclear observation, cannot be used.
Topics: Animals; Blastocyst; Cats; Female; In Situ Hybridization, Fluorescence; Ploidies; Pregnancy; Pregnancy Rate
PubMed: 35462315
DOI: 10.1016/j.theriogenology.2022.03.030 -
Methods in Molecular Biology (Clifton,... 2023Analyzing autopolyploid genetic data still presents numerous challenges due to, e.g., missing dosage information of genotypes and the presence of multiple ploidy levels...
Analyzing autopolyploid genetic data still presents numerous challenges due to, e.g., missing dosage information of genotypes and the presence of multiple ploidy levels within species or populations, but also because the choice of software is limited when compared to what is available for diploid data. However, over the last years, the number of software programs that can deal with polyploid data is slowly increasing. The software GENODIVE is one of the most widely used programs for the analysis of polyploid genetic data, presenting a wide array of different methods. In this chapter, I outline several frequently used types of population genetic analyses and explain how these apply to polyploid data, including possible pitfalls and biases. I then explain how GENODIVE approaches these analyses and whether and how it can overcome possible biases. Specifically, I focus on analyses of genetic diversity, Hardy-Weinberg equilibrium, quantifying population differentiation, clustering, and calculation of genetic distances. GENODIVE can be downloaded freely from http://www.patrickmeirmans.com/software .
Topics: Humans; Cluster Analysis; Diploidy; Genotype; Ploidies; Polyploidy
PubMed: 36720818
DOI: 10.1007/978-1-0716-2561-3_14 -
Current Opinion in Microbiology Aug 2015Variation is the spice of life or, in the case of evolution, variation is the necessary material on which selection can act to enable adaptation. Karyotypic variation in... (Review)
Review
Variation is the spice of life or, in the case of evolution, variation is the necessary material on which selection can act to enable adaptation. Karyotypic variation in ploidy (the number of homologous chromosome sets) and aneuploidy (imbalance in the number of chromosomes) are fundamentally different than other types of genomic variants. Karyotypic variation emerges through different molecular mechanisms than other mutational events, and unlike mutations that alter the genome at the base pair level, rapid reversion to the wild type chromosome number is often possible. Although karyotypic variation has long been noted and discussed by biologists, interest in the importance of karyotypic variants in evolutionary processes has spiked in recent years, and much remains to be discovered about how karyotypic variants are produced and subsequently selected.
Topics: Cell Physiological Phenomena; Genetic Variation; Karyotype; Ploidies; Selection, Genetic
PubMed: 26321163
DOI: 10.1016/j.mib.2015.06.010 -
The New Phytologist Nov 2023
Topics: Ploidies; Plants; Polyploidy; Genome, Plant
PubMed: 37337836
DOI: 10.1111/nph.19057 -
International Journal of Molecular... Mar 2022DNA replication during cell proliferation is 'vertical' copying, which reproduces an initial amount of genetic information. Polyploidy, which results from whole-genome... (Review)
Review
DNA replication during cell proliferation is 'vertical' copying, which reproduces an initial amount of genetic information. Polyploidy, which results from whole-genome duplication, is a fundamental complement to vertical copying. Both organismal and cell polyploidy can emerge via premature cell cycle exit or via cell-cell fusion, the latter giving rise to polyploid hybrid organisms and epigenetic hybrids of somatic cells. Polyploidy-related increase in biological plasticity, adaptation, and stress resistance manifests in evolution, development, regeneration, aging, oncogenesis, and cardiovascular diseases. Despite the prevalence in nature and importance for medicine, agri- and aquaculture, biological processes and epigenetic mechanisms underlying these fundamental features largely remain unknown. The evolutionarily conserved features of polyploidy include activation of transcription, response to stress, DNA damage and hypoxia, and induction of programs of morphogenesis, unicellularity, and longevity, suggesting that these common features confer adaptive plasticity, viability, and stress resistance to polyploid cells and organisms. By increasing cell viability, polyploidization can provide survival under stressful conditions where diploid cells cannot survive. However, in somatic cells it occurs at the expense of specific function, thus promoting developmental programming of adult cardiovascular diseases and increasing the risk of cancer. Notably, genes arising via evolutionary polyploidization are heavily involved in cancer and other diseases. Ploidy-related changes of gene expression presumably originate from chromatin modifications and the derepression of bivalent genes. The provided evidence elucidates the role of polyploidy in evolution, development, aging, and carcinogenesis, and may contribute to the development of new strategies for promoting regeneration and preventing cardiovascular diseases and cancer.
Topics: Adaptation, Physiological; Carcinogenesis; Cardiovascular Diseases; Diploidy; Humans; Neoplasms; Polyploidy
PubMed: 35408902
DOI: 10.3390/ijms23073542 -
Biology Letters Dec 2022Whole-genome duplication is a common mutation in eukaryotes with far-reaching phenotypic effects, the resulting morphological and fitness consequences and how they... (Meta-Analysis)
Meta-Analysis
Whole-genome duplication is a common mutation in eukaryotes with far-reaching phenotypic effects, the resulting morphological and fitness consequences and how they affect the survival of polyploid lineages are intensively studied. Another important factor may also determine the probability of establishment and success of polyploid lineages: inbreeding depression. Inbreeding depression is expected to play an important role in the establishment of neopolyploid lineages, their capacity to colonize new environments, and in the simultaneous evolution of ploidy and other life-history traits such as self-fertilization. Both theoretically and empirically, there is no consensus on the consequences of polyploidy on inbreeding depression. In this meta-analysis, we investigated the effect of polyploidy on the evolution of inbreeding depression, by performing a meta-analysis within angiosperm species. The main results of our study are that the consequences of polyploidy on inbreeding depression are complex and depend on the time since polyploidization. We found that young polyploid lineages have a much lower amount of inbreeding depression than their diploid relatives and their established counterparts. Natural polyploid lineages are intermediate and have a higher amount of inbreeding depression than synthetic neopolyploids, and a smaller amount than diploids, suggesting that the negative effect of polyploidy on inbreeding depression decreases with time since polyploidization.
Topics: Inbreeding Depression; Polyploidy; Diploidy; Inbreeding; Magnoliopsida
PubMed: 36514955
DOI: 10.1098/rsbl.2022.0477 -
Trends in Plant Science Mar 2015Endoreduplication, the replication of the genome without mitosis, leads to an increase in the cellular ploidy of an organism over its lifetime, a condition termed... (Review)
Review
Endoreduplication, the replication of the genome without mitosis, leads to an increase in the cellular ploidy of an organism over its lifetime, a condition termed 'endopolyploidy'. Endopolyploidy is thought to play significant roles in physiology and development through cellular, metabolic, and genetic effects. While the occurrence of endopolyploidy has been observed widely across taxa, studies have only recently begun to characterize and manipulate endopolyploidy with a focus on its ecological and evolutionary importance. No compilation of these examples implicating endoreduplication as a generalized response to stress has thus far been made, despite the growing evidence supporting this notion. We review here the recent literature of stress-induced endopolyploidy and suggest that plants employ endoreduplication as an adaptive, plastic response to mitigate the effects of stress.
Topics: Endoreduplication; Plant Physiological Phenomena; Plants; Ploidies; Stress, Physiological
PubMed: 25534217
DOI: 10.1016/j.tplants.2014.11.007 -
Cytometry. Part a : the Journal of the... Sep 2022Flow cytometry (FCM) is currently the most widely-used method to establish nuclear DNA content in plants. Since simple, 1-3-parameter, flow cytometers, which are... (Review)
Review
Flow cytometry (FCM) is currently the most widely-used method to establish nuclear DNA content in plants. Since simple, 1-3-parameter, flow cytometers, which are sufficient for most plant applications, are commercially available at a reasonable price, the number of laboratories equipped with these instruments, and consequently new FCM users, has greatly increased over the last decade. This paper meets an urgent need for comprehensive recommendations for best practices in FCM for different plant science applications. We discuss advantages and limitations of establishing plant ploidy, genome size, DNA base composition, cell cycle activity, and level of endoreduplication. Applications of such measurements in plant systematics, ecology, molecular biology research, reproduction biology, tissue cultures, plant breeding, and seed sciences are described. Advice is included on how to obtain accurate and reliable results, as well as how to manage troubleshooting that may occur during sample preparation, cytometric measurements, and data handling. Each section is followed by best practice recommendations; tips as to what specific information should be provided in FCM papers are also provided.
Topics: DNA, Plant; Flow Cytometry; Genome Size; Genome, Plant; Plants; Ploidies
PubMed: 34585818
DOI: 10.1002/cyto.a.24499