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Science in China. Series C, Life... Apr 2008Polyploidy and haploid are widely employed in the studies of genetics and evolution, and great progress has been made in these fields, inspiring the enthusiasm of... (Review)
Review
Polyploidy and haploid are widely employed in the studies of genetics and evolution, and great progress has been made in these fields, inspiring the enthusiasm of scientists to explore the ploidy effects in gene expression. In this paper, we review the gene expression and its regulation in polyploids, especially in autopolyploids. We summarize some limitations in previous reports on polyploidy gene expression and its regulation, especially the limitations in the research materials. We propose an idea to create homologous ploidy series with twin-seedlings and to employ high-throughput techniques to investigate the polyploidy transcriptome and its regulation.
Topics: Gene Expression Profiling; Gene Expression Regulation, Plant; Genes, Plant; Microarray Analysis; Ploidies; Seedlings
PubMed: 18368306
DOI: 10.1007/s11427-008-0039-3 -
G3 (Bethesda, Md.) Aug 2021With the rapid rise in availability of high-quality genomes for closely related species, methods for orthology inference that incorporate synteny are increasingly...
With the rapid rise in availability of high-quality genomes for closely related species, methods for orthology inference that incorporate synteny are increasingly useful. Polyploidy perturbs the 1:1 expected frequencies of orthologs between two species, complicating the identification of orthologs. Here we present a method of ortholog inference, Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity (pSONIC). We demonstrate the utility of pSONIC using four species in the cotton tribe (Gossypieae), including one allopolyploid, and place between 75% and 90% of genes from each species into nearly 32,000 orthologous groups, 97% of which consist of at most singletons or tandemly duplicated genes-58.8% more than comparable methods that do not incorporate synteny. We show that 99% of singleton gene groups follow the expected tree topology and that our ploidy-aware algorithm recovers 97.5% identical groups when compared to splitting the allopolyploid into its two respective subgenomes, treating each as separate "species."
Topics: Algorithms; Genome; Humans; Phylogeny; Ploidies; Polyploidy; Synteny
PubMed: 33983433
DOI: 10.1093/g3journal/jkab170 -
Cytogenetic and Genome Research 2013The past decade has witnessed a tremendous increase in interest in polyploidy, which may partly be related to the development of new powerful genetic and genomic tools.... (Review)
Review
The past decade has witnessed a tremendous increase in interest in polyploidy, which may partly be related to the development of new powerful genetic and genomic tools. These have provided numerous insights into mainly genetic and genomic consequences of polyploidy, dramatically improving our understanding of the dynamics of the polyploidization process and its importance as a mechanism in animal evolution. In contrast, several other aspects of polyploidization, such as physiology, ecology and development, have received considerably less attention. Our aim is not to make an exhaustive review of current knowledge about animal polyploidy, but rather to thoroughly elaborate on some very fundamental questions which still remain open or even neglected. In particular, we show that properties of new polyploid lineages largely depend upon the proximate way in which they arose, but the evolutionary pathways to polyploidy are often unresolved. To help researchers orientate amongst the number of pathways to polyploidy, we provide an extensive review of particular scenarios proposed in distinct animal taxa. We discuss how polyploidy relates to hybridization, particularly with respect to asexuality, and elaborate on whether clonal triploids may help to overcome the constraints of aneuploidy, thereby serving as a triploid bridge towards the establishment of new polyploid species. We further show that in most animal asexual complexes clonal lineages may become established only under one ploidy level (usually either di- or triploidy), and that it is rather rare to see the coexistence of successful clones of different ploidies. We discuss why the rate of polyploidization is higher in some taxa than in others, and what tools we have to evaluate the rate of polyploidization. Finally, we review some of the immediate physiological and developmental effects of polyploidy which are related to the genome size/cell size relation and show how studies of polyploidy may enhance the study of macroecology and developmental biology. See also the sister article focusing on plants by Weiss-Schneeweiss et al. in this themed issue.
Topics: Aneuploidy; Animals; Anura; Cell Nucleus Size; Cell Size; Diploidy; Ecosystem; Evolution, Molecular; Genetic Speciation; Genome Size; Hybridization, Genetic; Phenotype; Phylogeny; Polyploidy
PubMed: 23838539
DOI: 10.1159/000353464 -
Plant Physiology Jan 2019
Topics: Cell Wall; Humans; Plant Development; Ploidies; Polyploidy
PubMed: 30610132
DOI: 10.1104/pp.18.01455 -
Methods in Molecular Biology (Clifton,... 2021Determination of the ploidy level is an essential step when trying to produce doubled haploids (DHs) in any species. Each species and method used to produce DHs has its...
Determination of the ploidy level is an essential step when trying to produce doubled haploids (DHs) in any species. Each species and method used to produce DHs has its own frequency of DH production, which means that the rest of plants produced stay haploid. Since haploids are of little use for breeding purposes, it is necessary to distinguish them from true DHs. For this, several methodologies are available, including flow cytometry, chromosome counting, chloroplast counting in stomatal guard cells, measurement of stomatal size and length, counting of nucleoli, evaluation of pollen formation and viability, analysis of cell size, and analysis of morphological markers. However, not all of them are equally easy to use, affordable, reliable, reproducible, and resolutive and therefore useful for a particular case. In this chapter, we revise these methods available to assess the ploidy level of plants, discussing their respective advantages and limitations, and provide some troubleshooting tips and hints to help decide which to choose in each case.
Topics: Crosses, Genetic; Haploidy; Plant Breeding; Ploidies; Seeds; Zea mays
PubMed: 34270026
DOI: 10.1007/978-1-0716-1315-3_4 -
PLoS Pathogens Dec 2022
Topics: Humans; Ploidies; Reproduction
PubMed: 36480532
DOI: 10.1371/journal.ppat.1010954 -
Journal of Mathematical Biology Sep 2022Polyploidization, whereby an organism inherits multiple copies of the genome of their parents, is an important evolutionary event that has been observed in plants and...
Polyploidization, whereby an organism inherits multiple copies of the genome of their parents, is an important evolutionary event that has been observed in plants and animals. One way to study such events is in terms of the ploidy number of the species that make up a dataset of interest. It is therefore natural to ask: How much information about the evolutionary past of the set of species that form a dataset can be gleaned from the ploidy numbers of the species? To help answer this question, we introduce and study the novel concept of a ploidy profile which allows us to formalize it in terms of a multiplicity vector indexed by the species the dataset is comprised of. Using the framework of a phylogenetic network, we present a closed formula for computing the hybrid number (i.e. the minimal number of polyploidization events required to explain a ploidy profile) of a large class of ploidy profiles. This formula relies on the construction of a certain phylogenetic network from the simplification sequence of a ploidy profile and the hybrid number of the ploidy profile with which this construction is initialized. Both of them can be computed easily in case the ploidy numbers that make up the ploidy profile are not too large. To help illustrate the applicability of our approach, we apply it to a simplified version of a publicly available Viola dataset.
Topics: Animals; Genome; Phylogeny; Ploidies
PubMed: 36114394
DOI: 10.1007/s00285-022-01792-6 -
Methods in Molecular Biology (Clifton,... 2023In this chapter, we present the use of Spirodela polyrhiza in experiments designed to study the evolutionary impact of whole-genome duplication (WGD). We shortly...
In this chapter, we present the use of Spirodela polyrhiza in experiments designed to study the evolutionary impact of whole-genome duplication (WGD). We shortly introduce this duckweed species and explain why it is a suitable model for experimental evolution. Subsequently, we discuss the most relevant steps and methods in the design of a ploidy-related duckweed experiment. These steps include strain selection, ploidy determination, different methods of making polyploid duckweeds, replication, culturing conditions, preservation, and the ways to quantify phenotypic and transcriptomic change.
Topics: Gene Duplication; Araceae; Gene Expression Profiling; Ploidies; Polyploidy
PubMed: 36720823
DOI: 10.1007/978-1-0716-2561-3_19 -
International Journal of Molecular... Jul 2022Sexual vs. asexual reproduction-unisexual vs. bisexual populations-diploid vs. polyploid biotypes-genetic vs. environmental sex determination: all these natural... (Review)
Review
Sexual vs. asexual reproduction-unisexual vs. bisexual populations-diploid vs. polyploid biotypes-genetic vs. environmental sex determination: all these natural phenomena are associated with the genus of teleost fish, . This review places emphasis on two entities with completely different biological characteristics: one globally widespread and invasive , and the other with a decreasing trend of natural occurrence. Comprehensive biological and cytogenetic knowledge of both entities, including the physical interactions between them, can help to balance the advantages of highly invasive and disadvantages of threatened species. For example, the benefits of a wide-ranged colonization can lead to the extinction of native species or be compensated by parasitic enemies and lead to equilibrium. This review emphasizes the comprehensive biology and cytogenetic knowledge and the importance of the genus as one of the most useful experimental vertebrate models for evolutionary biology and genetics. Secondly, the review points out that effective molecular cytogenetics should be used for the identification of various species, ploidy levels, and hybrids. The proposed investigation of these hallmark characteristics in may be applied in conservation efforts to sustain threatened populations in their native ranges. Furthermore, the review focuses on the consequences of the co-occurrence of native and non-native species and outlines future perspectives of research.
Topics: Animals; Cyprinidae; Cytogenetic Analysis; Cytogenetics; Diploidy; Ploidies
PubMed: 35897665
DOI: 10.3390/ijms23158095 -
Advanced Science (Weinheim,... Jun 2024Polyploidization and depolyploidization are critical processes in the normal development and tissue homeostasis of diploid organisms. Recent investigations have revealed... (Review)
Review
Polyploidization and depolyploidization are critical processes in the normal development and tissue homeostasis of diploid organisms. Recent investigations have revealed that polyaneuploid cancer cells (PACCs) exploit this ploidy variation as a survival strategy against anticancer treatment and for the repopulation of tumors. Unscheduled polyploidization and chromosomal instability in PACCs enhance malignancy and treatment resistance. However, their inability to undergo mitosis causes catastrophic cellular death in most PACCs. Adaptive ploid reversal mechanisms, such as multipolar mitosis, centrosome clustering, meiosis-like division, and amitosis, counteract this lethal outcome and drive cancer relapse. The purpose of this work is to focus on PACCs induced by cytotoxic therapy, highlighting the latest discoveries in ploidy dynamics in physiological and pathological contexts. Specifically, by emphasizing the role of "poly-depolyploidization" in tumor progression, the aim is to identify novel therapeutic targets or paradigms for combating diseases associated with aberrant ploidies.
Topics: Humans; Neoplasms; Polyploidy; Animals
PubMed: 38629780
DOI: 10.1002/advs.202306318