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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 -
The Plant Cell Jul 2022Bread wheat (Triticum aestivum, genome BBAADD) is a young hexaploid species formed only 8,500-9,000 years ago through hybridization between a domesticated...
Bread wheat (Triticum aestivum, genome BBAADD) is a young hexaploid species formed only 8,500-9,000 years ago through hybridization between a domesticated free-threshing tetraploid progenitor, genome BBAA, and Aegilops tauschii, the diploid donor of the D subgenome. Very soon after its formation, it spread globally from its cradle in the fertile crescent into new habitats and climates, to become a staple food of humanity. This extraordinary global expansion was probably enabled by allopolyploidy that accelerated genetic novelty through the acquisition of new traits, new intergenomic interactions, and buffering of mutations, and by the attractiveness of bread wheat's large, tasty, and nutritious grain with high baking quality. New genome sequences suggest that the elusive donor of the B subgenome is a distinct (unknown or extinct) species rather than a mosaic genome. We discuss the origin of the diploid and tetraploid progenitors of bread wheat and the conflicting genetic and archaeological evidence on where it was formed and which species was its free-threshing tetraploid progenitor. Wheat experienced many environmental changes throughout its evolution, therefore, while it might adapt to current climatic changes, efforts are needed to better use and conserve the vast gene pool of wheat biodiversity on which our food security depends.
Topics: Bread; Diploidy; Evolution, Molecular; Genome, Plant; Hybridization, Genetic; Polyploidy; Tetraploidy; Triticum
PubMed: 35512194
DOI: 10.1093/plcell/koac130 -
Cell Mar 2021Cultivated rice varieties are all diploid, and polyploidization of rice has long been desired because of its advantages in genome buffering, vigorousness, and...
Cultivated rice varieties are all diploid, and polyploidization of rice has long been desired because of its advantages in genome buffering, vigorousness, and environmental robustness. However, a workable route remains elusive. Here, we describe a practical strategy, namely de novo domestication of wild allotetraploid rice. By screening allotetraploid wild rice inventory, we identified one genotype of Oryza alta (CCDD), polyploid rice 1 (PPR1), and established two important resources for its de novo domestication: (1) an efficient tissue culture, transformation, and genome editing system and (2) a high-quality genome assembly discriminated into two subgenomes of 12 chromosomes apiece. With these resources, we show that six agronomically important traits could be rapidly improved by editing O. alta homologs of the genes controlling these traits in diploid rice. Our results demonstrate the possibility that de novo domesticated allotetraploid rice can be developed into a new staple cereal to strengthen world food security.
Topics: CRISPR-Cas Systems; Crops, Agricultural; Domestication; Food Security; Gene Editing; Genetic Variation; Genome, Plant; Oryza; Polyploidy
PubMed: 33539781
DOI: 10.1016/j.cell.2021.01.013 -
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 -
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 -
Genome Biology Apr 2021High-quality chromosome-scale haplotype sequences of diploid genomes, polyploid genomes, and metagenomes provide important insights into genetic variation associated... (Review)
Review
High-quality chromosome-scale haplotype sequences of diploid genomes, polyploid genomes, and metagenomes provide important insights into genetic variation associated with disease and biodiversity. However, whole-genome short read sequencing does not yield haplotype information spanning whole chromosomes directly. Computational assembly of shorter haplotype fragments is required for haplotype reconstruction, which can be challenging owing to limited fragment lengths and high haplotype and repeat variability across genomes. Recent advancements in long-read and chromosome-scale sequencing technologies, alongside computational innovations, are improving the reconstruction of haplotypes at the level of whole chromosomes. Here, we review recent and discuss methodological progress and perspectives in these areas.
Topics: Chromosomes; Computational Biology; Diploidy; Genomics; Haplotypes; High-Throughput Nucleotide Sequencing; Humans; Metagenome; Metagenomics; Polyploidy; Sequence Analysis, DNA
PubMed: 33845884
DOI: 10.1186/s13059-021-02328-9 -
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 -
Genomics, Proteomics & Bioinformatics Jun 2020Lycophytes and seed plants constitute the typical vascular plants. Lycophytes have been thought to have no paleo-polyploidization although the event is known to be...
Lycophytes and seed plants constitute the typical vascular plants. Lycophytes have been thought to have no paleo-polyploidization although the event is known to be critical for the fast expansion of seed plants. Here, genomic analyses including the homologous gene dot plot analysis detected multiple paleo-polyploidization events, with one occurring approximately 13-15 million years ago (MYA) and another about 125-142 MYA, during the evolution of the genome of Selaginella moellendorffii, a model lycophyte. In addition, comparative analysis of reconstructed ancestral genomes of lycophytes and angiosperms suggested that lycophytes were affected by more paleo-polyploidization events than seed plants. Results from the present genomic analyses indicate that paleo-polyploidization has contributed to the successful establishment of both lineages-lycophytes and seed plants-of vascular plants.
Topics: Evolution, Molecular; Genome, Plant; Genomics; Phylogeny; Polyploidy; Selaginellaceae
PubMed: 33157303
DOI: 10.1016/j.gpb.2020.10.002 -
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 -
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