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Methods in Molecular Biology (Clifton,... 2023This chapter outlines an empirical analysis of genome-wide single-nucleotide polymorphism (SNP) variation and its underlying drivers among multiple natural populations...
This chapter outlines an empirical analysis of genome-wide single-nucleotide polymorphism (SNP) variation and its underlying drivers among multiple natural populations within a diploid-autopolyploid species. The aim is to reconstruct the genetic structure among natural populations of varying ploidy and infer footprints of selection in these populations, framed around specific questions that are typically encountered when analyzing a mixed-ploidy data set,e.g., addressing the relevance of natural whole-genome duplication for speciation and adaptation. We briefly review the options for the analysis of polyploid population genomic data involving variant calling, population structure, demographic history inference, and selection scanning approaches. Further, we provide suggestions for methods and associated software, possible caveats, and examples of their application to mixed-ploidy and autopolyploid data sets.
Topics: Diploidy; Metagenomics; Genomics; Ploidies; Acclimatization
PubMed: 36720820
DOI: 10.1007/978-1-0716-2561-3_16 -
Annual Review of Phytopathology Aug 2017Diverse plant biotrophs that establish a sustained site of nutrient acquisition induce localized host endoreduplication. Endoreduplication is a process by which cells... (Review)
Review
Diverse plant biotrophs that establish a sustained site of nutrient acquisition induce localized host endoreduplication. Endoreduplication is a process by which cells successively replicate their genomes without mitosis, resulting in an increase in nuclear DNA ploidy. Elevated ploidy is associated with enhanced cell size, metabolic capacity, and the capacity to differentiate. Localized host endoreduplication induced by adapted plant biotrophs promotes biotroph colonization, development, and/or proliferation. When induced host endoreduplication is limited, biotroph growth and/or development are compromised. Herein, we examine a diverse set of plant-biotroph interactions to identify (a) common host components manipulated to promote induced host endoreduplication and (b) biotroph effectors that facilitate this induced host process. Shared mechanisms to promote host endoreduplication and development of nutrient exchange/feeding sites include manipulation centered on endocycle entry at the G2-M transition as well as yet undefined roles for differentiation regulators (e.g., CLE peptides) and pectin/cell wall modification.
Topics: Endoreduplication; Gene Expression Regulation, Plant; Host-Pathogen Interactions; Mitosis; Plants; Ploidies; Symbiosis
PubMed: 28617655
DOI: 10.1146/annurev-phyto-080516-035458 -
Fertility and Sterility Aug 2023This review discusses the use of artificial intelligence (AI) algorithms in noninvasive prediction of embryo ploidy status for preimplantation genetic testing in... (Review)
Review
This review discusses the use of artificial intelligence (AI) algorithms in noninvasive prediction of embryo ploidy status for preimplantation genetic testing in in vitro fertilization procedures. The current gold standard, preimplantation genetic testing for aneuploidy, has limitations, such as an invasive biopsy, financial burden, delays in results reporting, and difficulty in results reporting, Noninvasive ploidy screening methods, including blastocoel fluid sampling, spent media testing, and AI algorithms using embryonic images and clinical parameters, are explored. Various AI models have been developed using different machine learning algorithms, such as random forest classifier and logistic regression, have shown variable performance in predicting euploidy. Static embryo imaging combined with AI algorithms have demonstrated good accuracy in ploidy prediction, with models such as Embryo Ranking Intelligent Classification Algorithm and STORK-A outperforming human grading. Time-lapse embryo imaging analyzed by AI algorithms has also shown promise in predicting ploidy status; however, the inclusion of clinical parameters is crucial to improving the predictive value of these models. Mosaicism, an important aspect of embryo classification, is often overlooked in AI algorithms and should be considered in future studies. The integration of AI algorithms into microscopy equipment and Embryoscope platforms will facilitate noninvasive genetic testing. Further development of algorithms that optimize clinical considerations and incorporate minimal-necessary covariates will also enhance the predictive value of AI in embryo selection. Artificial intelligence-based ploidy prediction has the potential to improve pregnancy rates and reduce costs in in vitro fertilization cycles.
Topics: Pregnancy; Female; Humans; Artificial Intelligence; Preimplantation Diagnosis; Genetic Testing; Ploidies; Aneuploidy; Fertilization in Vitro; Blastocyst; Retrospective Studies
PubMed: 37394089
DOI: 10.1016/j.fertnstert.2023.06.025 -
Integrative Zoology Jan 2021The analysis of molecular variance (AMOVA) is a widely used statistical method in population genetics and molecular ecology. The classic framework of AMOVA only supports...
The analysis of molecular variance (AMOVA) is a widely used statistical method in population genetics and molecular ecology. The classic framework of AMOVA only supports haploid and diploid data, in which the number of hierarchies ranges from two to four. In practice, natural populations can be classified into more hierarchies, and polyploidy is frequently observed in extant species. The ploidy level may even vary within the same species, and/or within the same individual. We generalized the framework of AMOVA such that it can be used for any number of hierarchies and any level of ploidy. Based on this framework, we present four methods to account for data that are multilocus genotypic and allelic phenotypic (with unknown allele dosage). We use simulated datasets and an empirical dataset to evaluate the performance of our framework. We make freely available our methods in a new software package, polygene, which is freely available at https://github.com/huangkang1987/polygene.
Topics: Analysis of Variance; Genetic Techniques; Genetics, Population; Ploidies; Software
PubMed: 32648364
DOI: 10.1111/1749-4877.12460 -
Developmental Cell Jun 2017Although haploidy has not been observed in vertebrates, its natural occurrence in various eukaryotic species that had diverged from diploid ancestors suggests that there... (Review)
Review
Although haploidy has not been observed in vertebrates, its natural occurrence in various eukaryotic species that had diverged from diploid ancestors suggests that there is an innate capacity for an organism to regain haploidy and that haploidy may confer evolutionary benefits. Haploid embryonic stem cells have been experimentally generated from mouse, rat, monkey, and humans. Haploidy results in major differences in cell size and gene expression levels while also affecting parental imprinting, X chromosome inactivation, and mitochondrial metabolism genes. We discuss here haploidy in evolution and the barriers to haploidy, in particular in the human context.
Topics: Animals; Diploidy; Embryonic Stem Cells; Genomic Imprinting; Haploidy; Humans; Pluripotent Stem Cells; X Chromosome Inactivation
PubMed: 28633015
DOI: 10.1016/j.devcel.2017.04.019 -
Cytometry. Part a : the Journal of the... Dec 2023Flow cytometry (FCM) is now the most widely used method to determine ploidy levels and genome size of plants. To get reliable estimates and allow reproducibility of... (Review)
Review
Flow cytometry (FCM) is now the most widely used method to determine ploidy levels and genome size of plants. To get reliable estimates and allow reproducibility of measurements, the methodology should be standardized and follow the best practices in the field. In this article, we discuss instrument calibration and quality control and various instrument and acquisition settings (parameters, flow rate, number of events, scales, use of discriminators, peak positions). These settings must be decided before measurements because they determine the amount and quality of the data and thus influence all downstream analyses. We describe the two main approaches to raw data analysis (gating and histogram modeling), and we discuss their advantages and disadvantages. Finally, we provide a summary of best practice recommendations for data acquisition and raw data analysis in plant FCM.
Topics: Flow Cytometry; Reproducibility of Results; Calibration; Ploidies; Genome Size
PubMed: 37807676
DOI: 10.1002/cyto.a.24798 -
Science China. Life Sciences Mar 2018Distant hybridization refers to crosses between two different species, genera, or higher-ranking taxa, which can break species limits, increase genetic variation, and... (Comparative Study)
Comparative Study Review
Distant hybridization refers to crosses between two different species, genera, or higher-ranking taxa, which can break species limits, increase genetic variation, and combine the biological characteristics of existing species. It is an important way of creating genetic variation, fertile strains, and excellent characteristics in new strains and populations. Combining analyses and summaries from many inter-related documents in plants and animals, both domestic and international, including examples and long-standing research on distant hybridization in fish from our laboratory, we summarize and compare the similarities and differences in plant and animal distant hybridization. In addition, we analyze and review the biological characteristics of their different ploidy progenies and the possible causes of disparity in survival rates. Mechanisms of sterility in animal and plant distant hybrids are also discussed, and research methods for the study of biological characteristics of hybrids, including morphology, cytology, and molecular cytogenetics are presented. This paper aims to provide comprehensive research materials and to systematically compare the general and specific characteristics of plant and animal hybrids with regards to reproduction, genetics, growth traits, and other biological characteristics. It is hoped that this paper will have great theoretical and practical significance for the study of genetic breeding and biological evolution of plant and animal distant hybridization.
Topics: Animals; Breeding; Fishes; Genetic Variation; Hybridization, Genetic; Phenotype; Plant Physiological Phenomena; Plants; Ploidies; Reproduction; Reproductive Isolation
PubMed: 28861869
DOI: 10.1007/s11427-017-9094-2 -
Current Issues in Molecular Biology 2016This article proposes the concept of genome network, describes different variations of the somatic genome network, and reviews the agricultural implications of such... (Review)
Review
This article proposes the concept of genome network, describes different variations of the somatic genome network, and reviews the agricultural implications of such variations. All genetic materials in a cell constitute the genome network of the cell and can jointly influence the cell's function and fate. The somatic genome of a plant is the genome network of cells in somatic tissues and of nonreproductive cells in pollen and ovules. Somatic genome variation (SGV, approximately equivalent to somagenetic variation) occurs at multiple levels, including stoichiometric, ploidy, and sequence variations. For a multicellular organism, the term "somatic genome variation" covers both the variation in part of the organism and the generation of new genotype individuals through somatic means from a sexually produced original genotype. For unicellular organisms, genome variation in somatic nuclei occurs at the whole organism level because there is only a single cell per individual. Growth, development and evolution of living organisms require both stability and instability of their genomes. Somatic genome variation displays many more attributes than genetic mutation and has strong implications for agriculture.
Topics: Agriculture; Animals; Evolution, Molecular; Genetic Variation; Genome; Humans; Livestock; Models, Genetic; Mutation; Ploidies
PubMed: 26636317
DOI: No ID Found -
Methods (San Diego, Calif.) Apr 2020Whole genome duplications (WGD) occur widely in plants, but the effects of these events impact all branches of life. WGD events have major evolutionary impacts, often... (Review)
Review
Whole genome duplications (WGD) occur widely in plants, but the effects of these events impact all branches of life. WGD events have major evolutionary impacts, often leading to major structural changes within the chromosomes and massive changes in gene expression that facilitate rapid speciation and gene diversification. Even for species that currently have diploid genomes, the impact of ancestral duplication events is still present in the genomes, especially in the context of highly similar gene families that are retained from WGD. However, the impact of these ploidies on various bioinformatics workflows has not been studied well. In this review, we overview biological significance of polyploidy in different organisms. We describe the impact of having polyploid transcriptomes on bioinformatics analyses, especially focusing on transcriptome assembly and transcript quantification. We discuss the benefits of using simulated benchmarking data when we examine the performance of various methods. We also present an example strategy to generate simulated allopolyploid transcriptomes and RNAseq datasets and how these benchmark datasets can be used to assess the performance of transcript assembly and quantification methods. Our benchmarking study shows that all transcriptome assembly methods are affected by having polyploid genomes. Quantification accuracy is also impacted by polyploidy depending on the method. These simulated datasets can be adapted for testing, such as, read mapping, variant calling, and differential expression using biologically realistic conditions.
Topics: Computational Biology; Polyploidy; RNA-Seq; Sequence Alignment; Transcriptome
PubMed: 31176772
DOI: 10.1016/j.ymeth.2019.06.001 -
FEMS Microbiology Reviews Sep 2021Changes in ploidy are a significant type of genetic variation, describing the number of chromosome sets per cell. Ploidy evolves in natural populations, clinical... (Review)
Review
Changes in ploidy are a significant type of genetic variation, describing the number of chromosome sets per cell. Ploidy evolves in natural populations, clinical populations, and lab experiments, particularly in unicellular fungi. Predicting how ploidy will evolve has proven difficult, despite a long history of theoretical work on this topic, as it is often unclear why one ploidy state outperforms another. Here, we review what is known about contemporary ploidy evolution in diverse fungal species through the lens of population genetics. As with typical genetic variants, ploidy evolution depends on the rate that new ploidy states arise by mutation, natural selection on alternative ploidy states, and random genetic drift. However, ploidy variation also has unique impacts on evolution, with the potential to alter chromosomal stability, the rate and patterns of point mutation, and the nature of selection on all loci in the genome. We discuss how ploidy evolution depends on these general and unique factors and highlight areas where additional experimental evidence is required to comprehensively explain the ploidy transitions observed in the field, the clinic, and the lab.
Topics: Fungi; Genetics, Population; Mutation; Ploidies; Selection, Genetic
PubMed: 33503232
DOI: 10.1093/femsre/fuab006