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Genomics May 2022Phasing, and in particular polyploid phasing, have been challenging problems held back by the limited read length of high-throughput short read sequencing methods which... (Review)
Review
Phasing, and in particular polyploid phasing, have been challenging problems held back by the limited read length of high-throughput short read sequencing methods which can't overcome the distance between heterozygous sites and labor high cost of alternative methods such as the physical separation of chromosomes for example. Recently developed single molecule long-read sequencing methods provide much longer reads which overcome this previous limitation. Here we review the alignment-based methods of polyploid phasing that rely on four main strategies: population inference methods, which leverage the genetic information of several individuals to phase a sample; objective function minimization methods, which minimize a function such as the Minimum Error Correction (MEC); graph partitioning methods, which represent the read data as a graph and split it into k haplotype subgraphs; cluster building methods, which iteratively grow clusters of similar reads into a final set of clusters that represent the haplotypes. We discuss the advantages and limitations of these methods and the metrics used to assess their performance, proposing that accuracy and contiguity are the most meaningful metrics. Finally, we propose the field of alignment-based polyploid phasing would greatly benefit from the use of a well-designed benchmarking dataset with appropriate evaluation metrics. We consider that there are still significant improvements which can be achieved to obtain more accurate and contiguous polyploid phasing results which reflect the complexity of polyploid genome architectures.
Topics: Humans; Genome, Human; Sequence Analysis, DNA; Haplotypes; Algorithms; Polyploidy; High-Throughput Nucleotide Sequencing
PubMed: 35483655
DOI: 10.1016/j.ygeno.2022.110369 -
Development (Cambridge, England) Jul 2018Polyploid cells, which contain multiple copies of the typically diploid genome, are widespread in plants and animals. Polyploidization can be developmentally programmed... (Review)
Review
Polyploid cells, which contain multiple copies of the typically diploid genome, are widespread in plants and animals. Polyploidization can be developmentally programmed or stress induced, and arises from either cell-cell fusion or a process known as endoreplication, in which cells replicate their DNA but either fail to complete cytokinesis or to progress through M phase entirely. Polyploidization offers cells several potential fitness benefits, including the ability to increase cell size and biomass production without disrupting cell and tissue structure, and allowing improved cell longevity through higher tolerance to genomic stress and apoptotic signals. Accordingly, recent studies have uncovered crucial roles for polyploidization in compensatory cell growth during tissue regeneration in the heart, liver, epidermis and intestine. Here, we review current knowledge of the molecular pathways that generate polyploidy and discuss how polyploidization is used in tissue repair and regeneration.
Topics: Animals; Cell Division; DNA Replication; Humans; Organ Specificity; Polyploidy; Regeneration; Stress, Physiological
PubMed: 30021843
DOI: 10.1242/dev.156034 -
Seminars in Cancer Biology Jun 2022Polyploidy, a cell status defined as more than two sets of genomic DNA, is a conserved strategy across species that can increase cell size and biosynthetic production,... (Review)
Review
Polyploidy, a cell status defined as more than two sets of genomic DNA, is a conserved strategy across species that can increase cell size and biosynthetic production, but the functional aspects of polyploidy are nuanced and vary across cell types. Throughout Drosophila developmental stages (embryo, larva, pupa and adult), polyploid cells are present in numerous organs and help orchestrate development while contributing to normal growth, well-being and homeostasis of the organism. Conversely, increasing evidence has shown that polyploid cells are prevalent in Drosophila tumors and play important roles in tumor growth and invasiveness. Here, we summarize the genes and pathways involved in polyploidy during normal and tumorigenic development, the mechanisms underlying polyploidization, and the functional aspects of polyploidy in development, homeostasis and tumorigenesis in the Drosophila model.
Topics: Animals; DNA; Drosophila; Homeostasis; Humans; Neoplasms; Polyploidy
PubMed: 34562587
DOI: 10.1016/j.semcancer.2021.09.011 -
Current Opinion in Plant Biology Oct 2022Recent advances in the genomics of polyploid species answer some of the long-standing questions about the role of polyploidy in crop species. Here, we summarize the... (Review)
Review
Recent advances in the genomics of polyploid species answer some of the long-standing questions about the role of polyploidy in crop species. Here, we summarize the current literature to reexamine scenarios in which polyploidy played a role both before and after domestication. The prevalence of polyploidy can help to explain environmental robustness in agroecosystems. This review also clarifies the molecular basis of some agriculturally advantageous traits of polyploid crops, including yield increments in polyploid cotton via subfunctionalization, modification of a separated sexuality to selfing in polyploid persimmon via neofunctionalization, and transition to a selfing system via nonfunctionalization combined with epistatic interaction between duplicated S-loci. The rapid progress in genomics and genetics is discussed along with how this will facilitate functional studies of understudied polyploid crop species.
Topics: Crops, Agricultural; Domestication; Genome, Plant; Genomics; Polyploidy
PubMed: 35870416
DOI: 10.1016/j.pbi.2022.102255 -
Trends in Cell Biology Jun 2018To battle adverse internal and external conditions and maintain homeostasis, diploid organisms employ various cellular processes, such as proliferation and apoptosis. In... (Review)
Review
To battle adverse internal and external conditions and maintain homeostasis, diploid organisms employ various cellular processes, such as proliferation and apoptosis. In some tissues, an alternative mechanism, endoreplication, is employed toward similar goals. Endoreplication is an evolutionarily conserved cell cycle program during which cells replicate their genomes without division, resulting in polyploid cells. Importantly, endoreplication is reported to be indispensable for normal development and organ formation across various organisms, from fungi to humans. In recent years, more attention has been drawn to delineating its connections to wound healing and tumorigenesis. In this Review, we discuss mechanisms of endoreplication and polyploidization, their essential and positive roles in normal development and tissue homeostasis, and the relationship between polyploidy and cancer.
Topics: Cell Cycle; Cell Differentiation; Cell Division; Endoreduplication; Homeostasis; Humans; Neoplasms; Polyploidy
PubMed: 29567370
DOI: 10.1016/j.tcb.2018.02.006 -
Cellular and Molecular Gastroenterology... 2020
Topics: Diploidy; Gene Expression Profiling; Hepatocytes; Humans; Ploidies; Polyploidy; Stem Cells; Transcriptome
PubMed: 31654613
DOI: 10.1016/j.jcmgh.2019.09.008 -
Transgenic Research Aug 2021Plant breeding aims to develop improved crop varieties. Many crops have a polyploid and often highly heterozygous genome, which may make breeding of polyploid crops a... (Review)
Review
Plant breeding aims to develop improved crop varieties. Many crops have a polyploid and often highly heterozygous genome, which may make breeding of polyploid crops a real challenge. The efficiency of traditional breeding based on crossing and selection has been improved by using marker-assisted selection (MAS), and MAS is also being applied in polyploid crops, which helps e.g. for introgression breeding. However, methods such as random mutation breeding are difficult to apply in polyploid crops because there are multiple homoeologous copies (alleles) of each gene. Genome editing technology has revolutionized mutagenesis as it enables precisely selecting targets. The genome editing tool CRISPR/Cas is especially valuable for targeted mutagenesis in polyploids, as all alleles and/or copies of a gene can be targeted at once. Even multiple genes, each with multiple alleles, may be targeted simultaneously. In addition to targeted mutagenesis, targeted replacement of undesirable alleles by desired ones may become a promising application of genome editing for the improvement of polyploid crops, in the near future. Several examples of the application of genome editing for targeted mutagenesis are described here for a range of polyploid crops, and achievements and bottlenecks are highlighted.
Topics: CRISPR-Cas Systems; Crops, Agricultural; Gene Editing; Genome, Plant; Plant Breeding; Plants, Genetically Modified; Polyploidy
PubMed: 33846956
DOI: 10.1007/s11248-021-00251-0 -
Cell Cycle (Georgetown, Tex.) Jun 2019Polyploid cells contain more than two homologous sets of chromosomes. The original observations of liver polyploidy date back to the 1940s, but functional roles for... (Review)
Review
Polyploid cells contain more than two homologous sets of chromosomes. The original observations of liver polyploidy date back to the 1940s, but functional roles for polyploid cells are still unclear. Liver polyploidy may influence regeneration, stress response, and cancer, although little evidence has established direct causal links between polyploidy and these biological phenotypes. In this review, we will introduce broad concepts about polyploidy including its distribution in nature and how polyploids form in normal and pathological situations. Then we will examine recent discoveries that have begun to clarify functionality and disease relevance of liver polyploidy. Finally, we will discuss implications and future directions of research about polyploidy in the liver.
Topics: Animals; Carcinogenesis; Hepatocytes; Humans; Liver; Models, Biological; Polyploidy
PubMed: 31096847
DOI: 10.1080/15384101.2019.1618123 -
Development (Cambridge, England) Mar 2024Polyploid cells contain multiple genome copies and arise in many animal tissues as a regulated part of development. However, polyploid cells can also arise due to cell... (Review)
Review
Polyploid cells contain multiple genome copies and arise in many animal tissues as a regulated part of development. However, polyploid cells can also arise due to cell division failure, DNA damage or tissue damage. Although polyploidization is crucial for the integrity and function of many tissues, the cellular and tissue-wide consequences of polyploidy can be very diverse. Nonetheless, many polyploid cell types and tissues share a remarkable similarity in function, providing important information about the possible contribution of polyploidy to cell and tissue function. Here, we review studies on polyploid cells in development, underlining parallel functions between different polyploid cell types, as well as differences between developmentally-programmed and stress-induced polyploidy.
Topics: Animals; Cell Division; DNA Damage; Polyploidy
PubMed: 38415794
DOI: 10.1242/dev.202392 -
Philosophical Transactions of the Royal... Aug 2014Nearly four decades ago, Roose & Gottlieb (Roose & Gottlieb 1976 Evolution 30, 818-830. (doi:10.2307/2407821)) showed that the recently derived allotetraploids... (Review)
Review
Nearly four decades ago, Roose & Gottlieb (Roose & Gottlieb 1976 Evolution 30, 818-830. (doi:10.2307/2407821)) showed that the recently derived allotetraploids Tragopogon mirus and T. miscellus combined the allozyme profiles of their diploid parents (T. dubius and T. porrifolius, and T. dubius and T. pratensis, respectively). This classic paper addressed the link between genotype and biochemical phenotype and documented enzyme additivity in allopolyploids. Perhaps more important than their model of additivity, however, was their demonstration of novelty at the biochemical level. Enzyme multiplicity-the production of novel enzyme forms in the allopolyploids-can provide an extensive array of polymorphism for a polyploid individual and may explain, for example, the expanded ranges of polyploids relative to their diploid progenitors. In this paper, we extend the concept of evolutionary novelty in allopolyploids to a range of genetic and ecological features. We observe that the dynamic nature of polyploid genomes-with alterations in gene content, gene number, gene arrangement, gene expression and transposon activity-may generate sufficient novelty that every individual in a polyploid population or species may be unique. Whereas certain combinations of these features will undoubtedly be maladaptive, some unique combinations of newly generated variation may provide tremendous evolutionary potential and adaptive capabilities.
Topics: Adaptation, Biological; Biological Evolution; Enzymes; Genetic Variation; Models, Genetic; Phenotype; Polyploidy; Tragopogon
PubMed: 24958924
DOI: 10.1098/rstb.2013.0351