Complete Sets Of Chromosomes Research Articles

Editorial: Genetics and Genomics of Polyploid Plants

Polyploidy, the condition of having more than two complete sets of chromosomes, is a widespread and influential phenomenon in the plant kingdom [...]

Integrating the Study of Polyploidy Across Organisms, Tissues, and Disease.

Polyploidy is a cellular state containing more than two complete chromosome sets. It has largely been studied as a discrete phenomenon in either organismal, tissue, or disease contexts. Increasingly, however, investigation of polyploidy across disciplines is coalescing around common principles. For example, the recent Polyploidy Across the Tree of Life meeting considered the contribution of polyploidy both in organismal evolution over millions of years and in tumorigenesis across much shorter timescales. Here, we build on this newfound integration with a unified discussion of polyploidy in organisms, cells, and disease. We highlight how common polyploidy is at multiple biological scales, thus eliminating the outdated mindset of its specialization. Additionally, we discuss rules that are likely common to all instances of polyploidy. With increasing appreciation that polyploidy is pervasive in nature and displays fascinating commonalities across diverse contexts, inquiry related to this important topic is rapidly becoming unified.

Whole-genome sequencing of allotetraploid bermudagrass reveals the origin of Cynodon and candidate genes for salt tolerance.

Bermudagrass (Cynodon dactylon) is a globally distributed, extensively used warm-season turf and forage grass with high tolerance to salinity and drought stress in alkaline environments. However, the origin of the species and genetic mechanisms for salinity tolerance in the species are basically unknown. Accordingly, we set out to study evolution divergence events in the Cynodon genome and to identify genes for salinity tolerance. We developed a 604.0 Mb chromosome-level polyploid genome sequence for bermudagrass 'A12359' (n = 18). The C. dactylon genome comprises 2 complete sets of homoeologous chromosomes, each with approximately 30 000 genes, and most genes are conserved as syntenic pairs. Phylogenetic study showed that the initial Cynodon species diverged from Oropetium thomaeum approximately 19.7-25.4 million years ago (Mya), the A and B subgenomes of C. dactylon diverged approximately 6.3-9.1 Mya, and the bermudagrass polyploidization event occurred 1.5 Mya on the African continent. Moreover, we identified 82 candidate genes associated with seven agronomic traits using a genome-wide association study, and three single-nucleotide polymorphisms were strongly associated with three salt resistance genes: RAP2-2, CNG channels, and F14D7.1. These genes may be associated with enhanced bermudagrass salt tolerance. These bermudagrass genomic resources, when integrated, may provide fundamental insights into evolution of diploid and tetraploid genomes and enhance the efficacy of comparative genomics in studying salt tolerance in Cynodon.

Gestational trophoblastic disease a contemporary review of diagnostic and pathology. Current challenge and future directions for gynecologists and obstetricians

Gestational trophoblastic disease (GTD) is a heterogenous group of disorders assosiated with abnromal proliferation of trophoblast and their course is characterized by varying degrees of malignancy. WHO classified GTD into three categories: tumor-like lesions, molar pregnancies and gestational trophoblastic neoplasms.HM is characterized by abnormal proliferation of both syncytiotrophoblast and cytotrophoblast, edema of placental villi, with or without the presence of a fetus. Complete and partial moles have been classified as two separate disease entities, and their division depends on the genetic material they contain. The complete mole has a complete set of chromosomes coming only from paternal genome, while the partial mole is triploid and the genetic material transferred comes from the father and the mother. Post-molar gestational trophoblast neoplasia (GTN) is a clinical diagnosis based on the observation of a persistent increase or persistently high hCG concentration after evacuation of the mole, requiring evaluation and treatment. Invasive hydatidiform mole, together with choriocarcinoma and placental tumor, belong to gestational trophoblast neoplasia. Currently, research has shown that short tandem repeat (STR) genotyping is the gold standard for making the correct diagnosis and this test should be performed if possible. GTD diseases originate from both syncytiotrophoblast and cytotrophoblast tissues and as a result of which they produce an extremely sensitive marker -human chorionic gonadotropin. The facts stated above and significant sensitivity to chemotherapy mean that the average cure rate for this disease currently exceeds 90%. Although the main treatment of gestational trophoblast neoplasia involves the use of cytostatics in cases with worse prognosis, i.e. those with a higher risk, surgery turns out to be an invaluable treatment method.

Polyploidization: A Biological Force That Enhances Stress Resistance.

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.

Polyploid tubular cells: a shortcut to stress adaptation

Tubular epithelial cells (TC) compose the majority of kidney parenchyma and play fundamental roles in maintaining homeostasis. Like other tissues, mostly immature TC with progenitor capabilities are able to replace TC lost during injury via clonal expansion and differentiation. In contrast, differentiated TC lack this capacity. However, as the kidney is frequently exposed to toxic injuries, evolution positively selected a response program that endows differentiated TC to maintain residual kidney function during kidney injury. Recently, we and others have described polyploidization of differentiated TC, a mechanism to augment the function of remnant TC after an injury by rapid hypertrophy. Polyploidy is a condition characterized by more than two complete sets of chromosomes. Polyploid cells often display an increased functional capacity and are generally more resilient to stress as evidenced by being conserved across many plants and eukaryote species from flies to mammals. Here, we discuss the occurrence of TC polyploidy in different contexts and conditions and how this integrates into existing concepts of kidney cell responses to injury. Collectively, we aim at stimulating the acquisition of novel knowledge in the kidney field as well as accelerating the translation of this basic response mechanism to the clinical sphere.

Comparing the incidence of spontaneous autopolyploidy in wild and hatchery Lake Sturgeon

AbstractObjectiveLiving species of Acipenseriformes, sturgeons and paddlefishes, are characteristically polyploid, having more than two complete sets of chromosomes (>2n). They undergo spontaneous autopolyploidy, an unintentional one and a half times increase in genome size, more frequently than any other order of fish. For Lake Sturgeon Acipenser fulvescens, which are evolutionary octoploids (8n), spontaneous autopolyploidy results in fertile dodecaploid (12n) progeny. When 12n individuals reproduce with octoploids, it is possible that resulting decaploid (10n) offspring will have poor physiological performance and survivorship. Spontaneous autopolyploidy in the wild is very low; however, incidence in fish hatcheries is greater, as seen in other 8n sturgeon species. We investigated this disparity in Lake Sturgeon, predicting to find more dodecaploid individuals in hatchery populations than in the wild.MethodsPloidy was determined using red blood cells from individuals in three hatchery and two wild populations of Lake Sturgeon in Manitoba, Canada (n = 1004). Red blood cell volume was evaluated with a Z2 Coulter counter and used to determine ploidy, based on the average of triplicate measures of the erythrocyte modal nuclei volume (fL). A subsample from each environment type was further examined using blood smear analysis (n = 130) and flow cytometry (n = 27).ResultOne 12n hatchery individual was found, along with significant differences in erythrocyte morphometry between the five populations. Fluctuations in modal nuclei volume were also observed over 169 days of repeated measurement within a single hatchery population.ConclusionThe well‐developed relationship between erythrocyte size and fishes external and physiological environment may explain the variance both between and within populations. These results demonstrate the need for ploidy monitoring in artificial hatcheries, as releasing even a single 12n fish could produce thousands of 10n offspring that, if recruited, would have a detrimental effect on the population fitness.

Tracking Karyotype Changes in Treatment-Induced Drug-Resistant Evolution.

Karyotype coding, which encompasses the complete chromosome sets and their topological genomic relationships within a given species, encodes system-level information that organizes and preserves genes' function, and determines the macroevolution of cancer. This new recognition emphasizes the crucial role of karyotype characterization in cancer research. To advance this cancer cytogenetic/cytogenomic concept and its platforms, this study outlines protocols for monitoring the karyotype landscape during treatment-induced rapid drug resistance in cancer. It emphasizes four key perspectives: combinational analyses of phenotype and karyotype, a focus on the entire evolutionary process through longitudinal analysis, a comparison of whole landscape dynamics by including various types of NCCAs (including genome chaos), and the use of the same process to prioritize different genomic scales. This protocol holds promise for studying numerous evolutionary aspects of cancers, and it further enhances the power of karyotype analysis in cancer research.

Development of a Set of Wheat-Rye Derivative Lines from Hexaploid Triticale with Complex Chromosomal Rearrangements to Improve Disease Resistance, Agronomic and Quality Traits of Wheat.

An elite hexaploid triticale Yukuri from Australia was used as a bridge for transferring valuable genes from Secale cereale L. into common wheat for enriching the genetic variability of cultivated wheat. Non-denaturing-fluorescence in situ hybridization (ND-FISH) identified that Yukuri was a secondary triticale with a complete set of rye chromosomes and a 6D(6A) substitution. Seed protein electrophoresis showed that Yukuri had a unique composition of glutenin subunits. A set of Yukuri-derived wheat-rye introgression lines were created from a Yukuri x wheat population, and all lines were identified by ND-FISH with multiple probes and validated by diagnostic molecular marker analysis. A total of 59 wheat-rye introgression lines including modified chromosome structural variations of wheat, and new complex recombinant chromosomes of rye were detected through ND-FISH and Oligo-FISH painting based on oligonucleotide pools derived from wheat-barley genome collinear regions. Wheat lines carrying the 1R chromosome from Yukuri displayed resistance to both stripe rust and powdery mildew, while the lines carrying the 3RL and 7RL chromosome arms showed stripe rust resistance. The chromosome 1R-derived lines were found to exhibit a significant effect on most of the dough-related parameters, and chromosome 5R was clearly associated with increased grain weight. The development of the wheat-rye cytogenetic stocks carrying disease resistances and superior agronomic traits, as well as the molecular markers and FISH probes will promote the introgression of abundant variation from rye into wheat improvement programs.

Law of precise matching and assembly chromosomes: A hypothesis for chromosome theory of inheritance and its implications in medical genetics

It is well known that chromosome abnormalities are closely related to many diseases or disorders and developmental abnormalities. However, our understanding of chromosome abnormalities and their roles in diseases or disorders and embryonic development is limited. Here, we propose a hypothesis for the chromosome theory of inheritance, and for the study of medical genetics, human embryology, and reproductive medicine. Our hypothesis is the law of precise matching and assembly chromosomes, which means that in a fertilized egg, via centromeres, haploid chromosomes with the same identity number but nonhomologous from two parents are precisely united and assembled into a complete set of diploid chromosomes. We believe that our hypothesis offers valuable insights into the study of genetics, reproduction and development, and medicine; which can be further explored and reflected upon: (1) it will help to elucidate the process and underlying molecular mechanisms and signal pathways of precise matching and assembly chromosomes, and the molecular biological underlying of chromosome abnormalities; (2) it will be helpful to discover the causes of chromosomal abnormalities and its related diseases; (3) it will be helpful to settle the issues of birth defects, spontaneous abortions, and infertility in human beings; (4) it will help to promote the revision of genetic and medical textbooks, and help train a new generation of genetic and medical talents for the benefits of all species (including human beings themselves); (5) it will help to reveal the origin, survival, reproduction, inheritance and evolution of species. Thus, our hypothesis is worthy of in-depth and extensive study and discussion in the future.

Autopolyploidy, Allopolyploidy, and Phylogenetic Networks with Horizontal Arcs

Polyploidization is an evolutionary process by which a species acquires multiple copies of its complete set of chromosomes. The reticulate nature of the signal left behind by it means that phylogenetic networks offer themselves as a framework to reconstruct the evolutionary past of species affected by it. The main strategy for doing this is to first construct a so-called multiple-labelled tree and to then somehow derive such a network from it. The following question therefore arises: How much can be said about that past if such a tree is not readily available? By viewing a polyploid dataset as a certain vector which we call a ploidy (level) profile, we show that among other results, there always exists a phylogenetic network in the form of a beaded phylogenetic tree with additional arcs that realizes a given ploidy profile. Intriguingly, the two end vertices of almost all of these additional arcs can be interpreted as having co-existed in time thereby adding biological realism to our network, a feature that is, in general, not enjoyed by phylogenetic networks. In addition, we show that our network may be viewed as a generator of ploidy profile space, a novel concept similar to phylogenetic tree space that we introduce to be able to compare phylogenetic networks that realize one and the same ploidy profile. We illustrate our findings in terms of a publicly available Viola dataset.

Principles and dynamics of spindle assembly checkpoint signalling.

The transmission of a complete set of chromosomes to daughter cells during cell division is vital for development and tissue homeostasis. The spindle assembly checkpoint (SAC) ensures correct segregation by informing the cell cycle machinery of potential errors in the interactions of chromosomes with spindle microtubules prior to anaphase. To do so, the SAC monitors microtubule engagement by specialized structures known as kinetochores and integrates local mechanical and chemical cues such that it can signal in a sensitive, responsive and robust manner. In this Review, we discuss how SAC proteins interact to allow production of the mitotic checkpoint complex (MCC) that halts anaphase progression by inhibiting the anaphase-promoting complex/cyclosome (APC/C). We highlight recent advances aimed at understanding the dynamic signalling properties of the SAC and how it interprets various naturally occurring intermediate attachment states. Further, we discuss SAC signalling in the context of the mammalian multisite kinetochore and address the impact of the fibrous corona. We also identify current challenges in understanding how the SAC ensures high-fidelity chromosome segregation.

The effects of climate change on cytotype distributions of endemic genera in the North American Coastal Plain

ABSTRACT Background Approximately 33% of plant species face extinction due to climate change. Polyploidisation, a process resulting in more than two complete sets of chromosomes, may be promoted by periods of climate fluctuations. Ecological niche modelling (ENM) using occurrences of endemic plants in the North American Coastal Plain (NACP) biodiversity hotspot could be used to evaluate the potential effects of climate change on cytotype distributions. Aims We used known diploid and polyploid taxa endemic to the NACP to test hypotheses that diploids and polyploids differed in habitat preferences, considerable overlap existed between cytotypes, and polyploid distributions would increase under climate change projections. Methods We examined niche identity and overlap of 28 congeneric ploidy level pairs and performed ENM to evaluate how climate change could affect these groups. Results Congeneric ploidy level pairs differed significantly in niche identity, and overlap varied across genera. Eleven genera showed greater than 100% increases in habitat suitability and six genera showed almost no remaining suitable habitat in at least one future climate scenario. Conclusions With 70% of the species that showed substantial declines in projected suitable habitat being of conservation concern, we propose that future studies of these genera should be a primary focus in the NACP.

Disentangling Relationships among the Alpine Species of Luzula Sect. Luzula (Juncaceae) in the Eastern Alps

Polyploidisation, agmatoploidy and symploidy have driven the diversification of Luzula sect. Luzula. Several morphologically very similar species with different karyotypes have evolved, but their evolutionary origins and relationships are unknown. In this study, we used a combination of relative genome size and karyotype estimations as well amplified fragment length polymorphism (AFLP) fingerprinting to investigate the relationships among predominately (sub)alpine Luzula alpina, L. exspectata, L multiflora and L. sudetica in the Eastern Alps, including also some samples of L. campestris and L. taurica as outgroup. Our study revealed common co-occurrence of two or three different ploidies (di-, tetra- and hexaploids) at the same localities, and thus also common co-occurrence of different species, of which L. sudetica was morphologically, ecologically and genetically most divergent. Whereas agmatoploid L. exspectata likely originated only once from the Balkan L. taurica, and hexaploid L. multiflora once from tetraploid L. multiflora, the AFLP data suggest multiple origins of tetraploid L. multiflora, from which partly agmatoploid individuals of L. alpina likely originated recurrently by partial fragmentation of the chromosomes. In contrast to common recurrent formation of polyploids in flowering plants, populations of agmatoploids resulting by fission of complete chromosome sets appear to have single origins, whereas partial agmatoploids are formed recurrently. Whether this is a general pattern in Luzula sect. Luzula, and whether segregation of ecological niches supports the frequent co-occurrence of closely related cytotypes in mixed populations, remains the subject of ongoing research.

Polyploidy and its relevance in crop improvement

Many areas of research in crop production have been geared towards crop improvement and increased yield. Crop improvement include but not restricted to; plant introduction and acclimatization, domestication, ploidy manipulation (polyploidization), recombinant DNA technology, crossing for superior selection (cultivar development), molecular genetics, etc. Polyploidy is a condition where the genome of an organism has more than the usual number of complete sets of chromosomes and the product of this phenomenon is called a Polyploid. Polyploidy occurs naturally, and can be induced chemically using antimitotic agents or physically using protoplast fusion and temperature shock. It is mostly artificially induced through a process called polyploidization. Polyploids are more advantageous in important plant attributes than the regular diploid. Relative success has been reported in the application of polyploidization for crop improvement which resulted chiefly in increased amount of beneficial secondary metabolites (phytochemicals), larger stomata and leaves,improved adaptation to stress and unfavourable conditions, to mention but a few. Therefore, it is imperative to state that polyploidy is an area of research that has been and will continually be deployed in crop improvement .

Synthetic two-species allodiploid and three-species allotetraploid Saccharomyces hybrids with euploid (complete) parental subgenomes

Combination of the genomes of Saccharomyces species has great potential for the construction of new industrial strains as well as for the study of the process of speciation. However, these species are reproductively isolated by a double sterility barrier. The first barrier is mainly due to the failure of the chromosomes to pair in allodiploid meiosis. The second barrier ensures that the hybrid remains sterile even after genome duplication, an event that can restore fertility in plant interspecies hybrids. The latter is attributable to the autodiploidisation of the allotetraploid meiosis that results in sterile allodiploid spores (return to the first barrier). Occasionally, mating-competent alloaneuploid spores arise by malsegregation of MAT-carrying chromosomes. These can mate with cells of a third species resulting in aneuploid zygotes having at least one incomplete subgenome. Here we report on the construction of euploid three-species hybrids by making use of “rare mating” between a sterile S. kudriavzevii x S. uvarum allodiploid hybrid and a diploid S. cerevisiae strain. The hybrids have allotetraploid 2nScnSk nSu genomes consisting of complete sets of parental chromosomes. This is the first report on the production of euploid three-species Saccharomyces hybrids by natural mating, without genetic manipulation. The hybrids provide possibilities for studying the interactions of three allospecific genomes and their orthologous genes present in the same cell.

Development and implementation of a metaphase DNA model for ionizing radiation induced DNA damage calculation

Objective. To develop a metaphase chromosome model representing the complete genome of a human lymphocyte cell to support microscopic Monte Carlo (MMC) simulation-based radiation-induced DNA damage studies. Approach. We first employed coarse-grained polymer physics simulation to obtain a rod-shaped chromatid segment of 730 nm in diameter and 460 nm in height to match Hi–C data. We then voxelized the segment with a voxel size of 11 nm per side and connected the chromatid with 30 types of pre-constructed nucleosomes and 6 types of linker DNAs in base pair (bp) resolutions. Afterward, we piled different numbers of voxelized chromatid segments to create 23 pairs of chromosomes of 1–5 μm long. Finally, we arranged the chromosomes at the cell metaphase plate of 5.5 μm in radius to create the complete set of metaphase chromosomes. We implemented the model in gMicroMC simulation by denoting the DNA structure in a four-level hierarchical tree: nucleotide pairs, nucleosomes and linker DNAs, chromatid segments, and chromosomes. We applied the model to compute DNA damage under different radiation conditions and compared the results to those obtained with G0/G1 model and experimental measurements. We also performed uncertainty analysis for relevant simulation parameters. Main results. The chromatid segment was successfully voxelized and connected in bps resolution, containing 26.8 mega bps (Mbps) of DNA. With 466 segments, we obtained the metaphase chromosome containing 12.5 Gbps of DNA. Applying it to compute the radiation-induced DNA damage, the obtained results were self-consistent and agreed with experimental measurements. Through the parameter uncertainty study, we found that the DNA damage ratio between metaphase and G0/G1 phase models was not sensitive to the chemical simulation time. The damage was also not sensitive to the specific parameter settings in the polymer physics simulation, as long as the produced metaphase model followed a similar contact map distribution. Significance. Experimental data reveal that ionizing radiation induced DNA damage is cell cycle dependent. Yet, DNA chromosome models, except for the G0/G1 phase, are not available in the state-of-the-art MMC simulation. For the first time, we successfully built a metaphase chromosome model and implemented it into MMC simulation for radiation-induced DNA damage computation.

Impact of polyploidy on plant tolerance to abiotic and biotic stresses.

Polyploidy, defined as the coexistence of three or more complete sets of chromosomes in an organism’s cells, is considered as a pivotal moving force in the evolutionary history of vascular plants and has played a major role in the domestication of several crops. In the last decades, improved cultivars of economically important species have been developed artificially by inducing autopolyploidy with chemical agents. Studies on diverse species have shown that the anatomical and physiological changes generated by either natural or artificial polyploidization can increase tolerance to abiotic and biotic stresses as well as disease resistance, which may positively impact on plant growth and net production. The aim of this work is to review the current literature regarding the link between plant ploidy level and tolerance to abiotic and biotic stressors, with an emphasis on the physiological and molecular mechanisms responsible for these effects, as well as their impact on the growth and development of both natural and artificially generated polyploids, during exposure to adverse environmental conditions. We focused on the analysis of those types of stressors in which more progress has been made in the knowledge of the putative morpho-physiological and/or molecular mechanisms involved, revealing both the factors in common, as well as those that need to be addressed in future research.

Dosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maize

The genomic imbalance caused by varying the dosage of individual chromosomes or chromosomal segments (aneuploidy) has more detrimental effects than altering the dosage of complete chromosome sets (ploidy). Previous analysis of maize (Zea mays) aneuploids revealed global modulation of gene expression both on the varied chromosome (cis) and the remainder of the genome (trans). However, little is known regarding the role of microRNAs (miRNAs) under genomic imbalance. Here, we report the impact of aneuploidy and polyploidy on the expression of miRNAs. In general, cis miRNAs in aneuploids present a predominant gene-dosage effect, whereas trans miRNAs trend toward the inverse level, although other types of responses including dosage compensation, increased effect, and decreased effect also occur. By contrast, polyploids show less differential miRNA expression than aneuploids. Significant correlations between expression levels of miRNAs and their targets are identified in aneuploids, indicating the regulatory role of miRNAs on gene expression triggered by genomic imbalance.

Castration-resistant prostate cancer patient presenting with whole genome doubling with CDK-12 mutation

BackgroundThe use of whole-genome sequencing in clinical practice has revealed variable genomic characteristics across cancer types, one of which is whole-genome doubling (WGD), which describes the duplication of a complete set of chromosomes. Yet it is relatively rare in prostate cancer and no such case has ever been reported in Japanese patients.Case presentationA 54-year-old patient with prostatic adenocarcinoma with bone and lymph node metastases was started on androgen-deprivation therapy. As the prostate cancer turned castration-resistant, multimodal therapies including taxane- and platinum-based chemotherapy, androgen-receptor antagonist inhibitors, radiotherapy and radium-233 were introduced. Good controls of serum prostate-specific antigen (PSA) level and bone metastases were achieved for more than 13 years since after the initial treatment. During the treatment, a metastatic lymph node biopsy was performed to confirm the tumor histology, and spinal decompression surgery were performed for spinal compression due to lumber vertebral metastases. The immunohistochemical analysis identified PSA and androgen receptor positive tumor cells in both metastatic lesions, while no variable cancer cells were detected in the prostate on second biopsy. Whole-genome sequencing was performed on the biopsied metastatic lymph node in search for another possible treatment and it revealed that the tumor had WGD and CDK12 mutation. The WGD-positive tumor cells contained large and polymorphic nucleus, presumably reflecting on the ploidy abnormality of the chromosomes.ConclusionsThis report is the first case of a Japanese patient presenting with WGD, who survived more than 13 years with multimodal chemotherapies and radiotherapies.