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The New Phytologist Apr 2021Rare yet accumulating evidence in both plants and animals shows that whole genome duplication (WGD, leading to polyploidy) can break down reproductive barriers,... (Review)
Review
Rare yet accumulating evidence in both plants and animals shows that whole genome duplication (WGD, leading to polyploidy) can break down reproductive barriers, facilitating gene flow between otherwise isolated species. Recent population genomic studies in wild, outcrossing Arabidopsis arenosa and Arabidopsis lyrata indicate that this WGD-potentiated gene flow can be adaptive and highly specific in response to particular environmental and intracellular challenges. The mechanistic basis of WGD-mediated easing of species barrier strength seems to primarily lie in the relative dosage of each parental genome in the endosperm. While generalisations about polyploids can be fraught, this evidence indicates that the breakdown of these barriers, combined with diploid to polyploid gene flow and gene flow between polyploids, allows some polyploids to act as adaptable 'allelic sponges', enjoying increased potential to respond to challenging environments.
Topics: Animals; Arabidopsis; Diploidy; Gene Flow; Genome, Plant; Polyploidy
PubMed: 33454987
DOI: 10.1111/nph.17204 -
International Journal of Molecular... Oct 2022Plant polyploidization changes its leaf morphology and leaf development patterns. Understanding changes in leaf morphology and development patterns is a prerequisite and...
Plant polyploidization changes its leaf morphology and leaf development patterns. Understanding changes in leaf morphology and development patterns is a prerequisite and key to studying leaf development in polyploid plants. In this study, we quantified and analyzed the differences in leaf morphology, leaf growth polarity, and leaf size between diploid and tetraploid birches (), and preliminarily investigated genes involved in leaf growth and development in birch. The results showed significant changes in leaf morphology in tetraploid birches, especially the basal part of the leaf. In addition, the proximal growth rate of tetraploid leaves was altered. The changed proximal growth rate did not affect the growth polarity pattern of tetraploid leaves. The leaf area of tetraploid was significantly larger than that of diploid birch. The difference in leaf size was mainly due to differences in their growth rates in the middle and late stages of leaf development. Increased cell expansion capacity was the major reason for the enormous leaves of tetraploid birch; however, cell proliferation did not contribute to the larger tetraploid leaf. The gene expression of was associated with cell size and leaf area, and may be a critical gene affecting the leaf size in diploid and tetraploid birches. The results will provide valuable insights into plant polyploid leaf development and a theoretical basis for later investigations into the molecular mechanisms underlying the gigantism of tetraploid birch leaves.
Topics: Betula; Diploidy; Tetraploidy; Plant Leaves; Gene Expression
PubMed: 36361755
DOI: 10.3390/ijms232112966 -
Molecular Biology and Evolution Mar 2023Introgressive hybridization is widespread in wild plants and has important consequences. However, frequent hybridization between species makes the estimation of the...
Introgressive hybridization is widespread in wild plants and has important consequences. However, frequent hybridization between species makes the estimation of the species' phylogeny challenging, and little is known about the genomic landscape of introgression as it results from complex interactions of multiple evolutionary processes. Here, we reconstructed the phylogeny of ten wild diploid strawberries with whole genome resequencing data and then investigated the influence of recombination rate variation on phylogeny and introgression. We found that genomic regions with low recombination showed reduced levels of incomplete lineage sorting and introgression, and concentrated phylogenetic signals, thus contributing to the most likely species tree of wild diploid strawberries. We revealed complex and widespread introgression across the genus Fragaria, with an average proportion of approximately 4.1% of the extant genome. Introgression tends to be retained in the regions with high recombination rates and low gene density. Furthermore, we identified four SLF genes under selective sweeps that may play potential roles in the possible regain of self-incompatibility by ancient introgression. Altogether, our study yielded novel insights into the evolutionary history and genomic characteristics of introgression in wild diploid strawberries and provides evidence for the role of introgression in plant mating system transitions.
Topics: Phylogeny; Fragaria; Diploidy; Genome; Hybridization, Genetic; Recombination, Genetic
PubMed: 36864629
DOI: 10.1093/molbev/msad049 -
Cells Aug 2022Non-celiac wheat sensitivity (NCWS) is a clinical entity induced by the ingestion of gluten that leads to intestinal and/or extraintestinal symptoms, and is diagnosed... (Review)
Review
Non-celiac wheat sensitivity (NCWS) is a clinical entity induced by the ingestion of gluten that leads to intestinal and/or extraintestinal symptoms, and is diagnosed when celiac disease and wheat allergy have been ruled out. In addition to gluten, other grains' components, including amylase trypsin inhibitors (ATIs) and fermentable short-chain carbohydrates (FODMAPs), may trigger symptoms in NCWS subjects. Several studies suggest that, compared with tetraploid and hexaploid modern wheats, ancient diploid wheats species could possess a lower immunogenicity for subjects suffering from NCWS. This review aims to discuss available evidence related to the immunological features of diploid wheats compared to common wheats, and at outlining new dietary opportunities for NCWS subjects.
Topics: Celiac Disease; Diploidy; Glutens; Humans; Intestines; Wheat Hypersensitivity
PubMed: 35954233
DOI: 10.3390/cells11152389 -
International Journal of Molecular... Feb 2024Organisms with three or more complete sets of chromosomes are designated as polyploids. Polyploidy serves as a crucial pathway in biological evolution and enriches... (Review)
Review
Organisms with three or more complete sets of chromosomes are designated as polyploids. Polyploidy serves as a crucial pathway in biological evolution and enriches species diversity, which is demonstrated to have significant advantages in coping with both biotic stressors (such as diseases and pests) and abiotic stressors (like extreme temperatures, drought, and salinity), particularly in the context of ongoing global climate deterioration, increased agrochemical use, and industrialization. Polyploid cultivars have been developed to achieve higher yields and improved product quality. Numerous studies have shown that polyploids exhibit substantial enhancements in cell size and structure, physiological and biochemical traits, gene expression, and epigenetic modifications compared to their diploid counterparts. However, some research also suggested that increased stress tolerance might not always be associated with polyploidy. Therefore, a more comprehensive and detailed investigation is essential to complete the underlying stress tolerance mechanisms of polyploids. Thus, this review summarizes the mechanism of polyploid formation, the polyploid biochemical tolerance mechanism of abiotic and biotic stressors, and molecular regulatory networks that confer polyploidy stress tolerance, which can shed light on the theoretical foundation for future research.
Topics: Humans; Biological Evolution; Polyploidy; Phenotype; Diploidy
PubMed: 38396636
DOI: 10.3390/ijms25041957 -
Cell Systems Jun 2022Physiological liver cell replacement is central to maintaining the organ's high metabolic activity, although its characteristics are difficult to study in humans. Using...
Physiological liver cell replacement is central to maintaining the organ's high metabolic activity, although its characteristics are difficult to study in humans. Using retrospective radiocarbon (C) birth dating of cells, we report that human hepatocytes show continuous and lifelong turnover, allowing the liver to remain a young organ (average age <3 years). Hepatocyte renewal is highly dependent on the ploidy level. Diploid hepatocytes show more than 7-fold higher annual birth rates than polyploid hepatocytes. These observations support the view that physiological liver cell renewal in humans is mainly dependent on diploid hepatocytes, whereas polyploid cells are compromised in their ability to divide. Moreover, cellular transitions between diploid and polyploid hepatocytes are limited under homeostatic conditions. With these findings, we present an integrated model of homeostatic liver cell generation in humans that provides fundamental insights into liver cell turnover dynamics.
Topics: Adult; Child, Preschool; Diploidy; Hepatocytes; Humans; Liver; Polyploidy; Retrospective Studies
PubMed: 35649419
DOI: 10.1016/j.cels.2022.05.001 -
Advanced Science (Weinheim,... Mar 2023Synthetic biology has been represented by the creation of artificial life forms at the genomic scale. In this work, a CRISPR-based chromosome-doubling technique is...
Synthetic biology has been represented by the creation of artificial life forms at the genomic scale. In this work, a CRISPR-based chromosome-doubling technique is designed to first construct an artificial diploid Escherichia coli cell. The stable single-cell diploid E. coli is isolated by both maximal dilution plating and flow cytometry, and confirmed with quantitative PCR, fluorescent in situ hybridization, and third-generation genome sequencing. The diploid E. coli has a greatly reduced growth rate and elongated cells at 4-5 µm. It is robust against radiation, and the survival rate after exposure to UV increased 40-fold relative to WT. As a novel life form, the artificial diploid E. coli is an ideal substrate for research fundamental questions in life science concerning polyploidy. And this technique may be applied to other bacteria.
Topics: Diploidy; Escherichia coli; In Situ Hybridization, Fluorescence; Polyploidy; Chromosomes, Plant
PubMed: 36642845
DOI: 10.1002/advs.202205855 -
Plant Biotechnology Journal Jun 2024Alfalfa (Medicago sativa L.) is one of the most important forage legumes in the world, including autotetraploid (M. sativa ssp. sativa) and diploid alfalfa...
Alfalfa (Medicago sativa L.) is one of the most important forage legumes in the world, including autotetraploid (M. sativa ssp. sativa) and diploid alfalfa (M. sativa ssp. caerulea, progenitor of autotetraploid alfalfa). Here, we reported a high-quality genome of ZW0012 (diploid alfalfa, 769 Mb, contig N50 = 5.5 Mb), which was grouped into the Northern group in population structure analysis, suggesting that our genome assembly filled a major gap among the members of M. sativa complex. During polyploidization, large phenotypic differences occurred between diploids and tetraploids, and the genetic information underlying its massive phenotypic variations remains largely unexplored. Extensive structural variations (SVs) were identified between ZW0012 and XinJiangDaYe (an autotetraploid alfalfa with released genome). We identified 71 ZW0012-specific PAV genes and 1296 XinJiangDaYe-specific PAV genes, mainly involved in defence response, cell growth, and photosynthesis. We have verified the positive roles of MsNCR1 (a XinJiangDaYe-specific PAV gene) in nodulation using an Agrobacterium rhizobia-mediated transgenic method. We also demonstrated that MsSKIP23_1 and MsFBL23_1 (two XinJiangDaYe-specific PAV genes) regulated leaf size by transient overexpression and virus-induced gene silencing analysis. Our study provides a high-quality reference genome of an important diploid alfalfa germplasm and a valuable resource of variation landscape between diploid and autotetraploid, which will facilitate the functional gene discovery and molecular-based breeding for the cultivars in the future.
Topics: Medicago sativa; Genome, Plant; Diploidy; Chromosomes, Plant; Genetic Variation
PubMed: 38288521
DOI: 10.1111/pbi.14300 -
Biology Open Nov 2020The near-haploid human cell line HAP1 recently became a popular subject for CRISPR/Cas9 editing, since only one allele requires modification. Through the gene-editing...
The near-haploid human cell line HAP1 recently became a popular subject for CRISPR/Cas9 editing, since only one allele requires modification. Through the gene-editing service at Horizon Discovery, there are at present more than 7500 edited cell lines available and the number continuously increases. The haploid nature of HAP1 is unstable as cultures become diploid with time. Here, we demonstrated some fundamental differences between haploid and diploid HAP1 cells, hence underlining the need for taking control over ploidy status in HAP1 cultures prior to phenotyping. Consequently, we optimized a procedure to determine the ploidy of HAP1 by flow cytometry in order to obtain diploid cultures and avoid ploidy status as an interfering variable in experiments. Furthermore, in order to facilitate this quality control, we validated a size-based cell sorting procedure to obtain the diploid culture more rapidly. Hence, we provide here two streamlined protocols for quality controlling the ploidy of HAP1 cells and document their validity and necessity.This article has an associated First Person interview with the co-first authors of the paper.
Topics: CRISPR-Cas Systems; Cell Line; Cells, Cultured; Diploidy; Flow Cytometry; Gene Editing; Gene Knockdown Techniques; Haploidy; Humans; Nerve Tissue Proteins; Ploidies
PubMed: 33184093
DOI: 10.1242/bio.057174 -
PloS One 2023Polyploidization results in significant changes in the morphology and physiology of plants, with increased growth rate and genetic gains as the number of chromosomes...
Polyploidization results in significant changes in the morphology and physiology of plants, with increased growth rate and genetic gains as the number of chromosomes increases. In this study, the leaf functional traits, photosynthetic characteristics, leaf cell structure and transcriptome of Camellia sinensis were analyzed. The results showed that triploid tea had a significant growth advantage over diploid tea, the leaf area was 59.81% larger, and the photosynthetic capacity was greater. The morphological structure of triploid leaves was significantly different, the xylem of the veins was more developed, the cell gap between the palisade tissue and the sponge tissue was larger and the stomata of the triploid leaves were also larger. Transcriptome sequencing analysis revealed that in triploid tea, the changes in leaf morphology and physiological characteristics were affected by the expression of certain key regulatory genes. We identified a large number of genes that may play important roles in leaf development, especially genes involved in photosynthesis, cell division, hormone synthesis and stomata development. This research will enhance our understanding of the molecular mechanism underlying tea and stomata development and provide a basis for molecular breeding of high-quality and high-yield tea varieties.
Topics: Transcriptome; Camellia sinensis; Diploidy; Triploidy; Tea; Plant Leaves; Gene Expression Regulation, Plant
PubMed: 36800382
DOI: 10.1371/journal.pone.0275652