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Chen et al. identified 132 whole-genome duplications (WGDs) clustered around environmental crises. We highlight how, over longer evolutionary timescales, ancient WGDs convergently retained MADS-box, MYB, WRKY and HSF transcription factors, building stress-adaptation networks. These insights guide climate-resilient crop improvement through comparative genomics and CRISPR engineering.
The ploidy of myocardiocytes nuclei in the left ventricle was determined stereometrically and microspectrophotometrically in 20 cases of ischemic heart disease (IHD) and 9 control cases. An increase in the number of nuclei and the degree of their ploidy and their correlation with the myocardium mass were established. The number of polyploid nuclei was particularly high in the periphery of postinfarction scars. These data indirectly indicate the participation of polyploidization and amitosis of myocardiocytes nuclei in the development of myocardial regenerative hypertrophy.
The satellite DNAs of Drosophila virilis have been examined in diploid and polyploid tissues by isopycnic ultracentrifugation and thermal denaturation experiments. Previous work has established that the satellite DNAs are underreplicated in the polytene chromosomes of the salivary glands of D. virilis. The results of the present experiments demonstrate that this underreplication also takes place in the ovaries which contain nurse cells and follicle cells. These tissues are polyploid but do not show polytene chromosomes.
Observation on meiotic diplotene chromosomes from oocytes of Xenopus species and subspecies hybrids are reported. Species interrelationships are established on the basis of the number of bivalent in the respective hybrids. Polyploid oocytes were found and their origin by supplementary endoreduplication placed at the differentiation stage of gametogenesis when oogonia become oocytes. The significance of polyploid oocytes for speciation is discussed.
This study, the third in a three-part series, investigates whether chromosomal instability persists in cultivated peanut. The allotetraploid peanut (Arachis hypogaea; genome type AABB) originated from the hybridization and polyploidization of A. duranensis (AA) and A. ipaënsis (BB). Our first study established that this was an extremely narrow genetic origin, likely from a single hybridization event. This raised a paradox: how did such narrow genetics give rise to the phenotypic diversity seen in cultivated peanut? The second study addressed this, showing that a single neoallotetraploid spontaneously generates striking diversity, and that homoeologous exchanges-abundant in early generations following polyploidy-are a key mechanism in creating this diversity. In contrast to this early-generation instability, cultivated peanut is generally considered to be genetically stable, presumably due to selection. This third study tests whether residual instability still occurs in modern peanut. From a single plant of the highly selfed 'genome stock' of the cultivar 'Tifrunner', we advanced lineages through seven generations in a pollinator-free greenhouse. Among 233 plants, we identified three new large-scale chromosomal instability events: a large deletion on chromosome B01, associated with reduced pod width and seed weight, and two ABBB compositions involving chromosomes A02/B02 and A05/B05. With these observations in hand, we reinterpreted previously published data from two recombinant inbred populations. Together, these results indicate that at least 1% of pure pedigree A. hypogaea plants exhibit spontaneous large-scale chromosomal changes-a surprising frequency of instability that likely contributes to peanut's long-term adaptability and evolution.
It was established by cytophotometry that the amount of DNA in intestinal-epithelium cells rises from the diploid to a tetraploid level during the early postnatal ontogeny of ascarids so that eventually nuclei with a diploid quantity of DNA practically disappear. Apart from this, there appear cells with a higher DNA content: 8c, 16c, 32c, and even 64c. Pictures of anomalous mitotic processes, as well as polypoid meta- and anaphases, were also observed. A result of the polyploidization is an increased size of nuclei and cells, but nucleus size is not always correlated with the DNA content. The previously established sixfold increase in the mean volume of intestinal cells during postnatal ontogeny of the ascarid is due to their transition to the new ploidy level and additional "paragenomic" growth of the polypoid cells.
BACKGROUND AND AIMS: Complex genomic histories shaped by hybridisation and polyploidy can influence traits related to plant defence, stress tolerance and toxicity, particularly in Amaranthaceae, which includes crops such as quinoa and spinach. Within this family, white goosefoot (Chenopodium album), a widespread agricultural weed and traditional food resource, belongs to a diploid-polyploid aggregate with extensive phylogenetic discordance. Clarifying its evolutionary history provides context for interpreting ecologically and agronomically relevant trait variation across the aggregate. Building on the established genome-lineage framework, we tested whether discordance persists when constituent genome-lineage components are represented separately and whether the remaining signal is compatible with reticulate evolution. METHODS: We analysed 2,298 conserved nuclear BUSCO families across 27 assembly-level terminals using tree- and network-based approaches. Genome-lineage-aware analyses used 2,156 families after separating polyploid Chenopodium into A-H components, with Dysphania ambrosioides as outgroup. HyDe tested site-pattern asymmetry under global false-discovery-rate correction. KEY RESULTS: Assembly-level analyses grouped the Danish C. album aggregate accession Ca6-1 with hexaploid C. album sensu stricto dcCheAlbu1.1, whereas relationships among surrounding Chenopodium taxa were less stable. Genome-lineage-aware analyses recovered the expected B-, C- and D-affinity relationships, but substantial gene-family heterogeneity persisted. Reticulate network models fitted the assembly-level data better than bifurcating models, although inferred patterns differed between methods. HyDe detected significant site-pattern asymmetry in a small subset of loci, with most retained signal shared between the focal assemblies. CONCLUSIONS: Gene-tree discordance persists in the C. album aggregate after genome-lineage separation. The established genome-lineage framework captures the dominant phylogenomic structure, while residual heterogeneity is compatible with both tree-like and reticulate processes without identifying direct progenitors or a unique hybridisation history. This framework supports future analyses of lineage-specific and trait-associated loci related to plant defence, food quality and toxicity in C. album and related Amaranthaceae.
The precision of CRISPR/Cas systems is fundamental to their application in plant and animal biotechnology. However, comprehensive sequence-based off-target candidate discovery remains a computational bottleneck, particularly in large and complex genomes. Here we developed SpacerScope, an off-target candidate discovery framework that enables unbiased, genome-wide discovery by leveraging binary vectorization, bitwise filtering, and right-end-anchored alignment. Benchmarking against human CIRCLE-seq data demonstrated that SpacerScope recovered 100% of validated off-target sites (6142/6142), matching the sensitivity of exhaustive algorithms. Crucially, SpacerScope achieved this maximum candidate recovery while substantially reducing computational overhead. In large-genome evaluations, SpacerScope maintained low peak memory usage of 2.20 GiB and achieved substantial runtime improvements over indel-aware comparator tools, including more than 50-fold speedup relative to Cas-OFFinder 3 (544 s versus 29 185 s). Furthermore, comparative analyses in polyploid species, such as the octoploid strawberry, revealed that SpacerScope identified larger sequence-compatible candidate burdens than standard web-based design platforms. Our results establish SpacerScope as a high-speed framework for sequence-based genome-wide off-target candidate discovery across diverse and highly repetitive genomic landscapes. The source code and program was publicly available at https://github.com/charlesqu666/SpacerScope. Short Abstract CRISPR/Cas sequence-based off-target candidate discovery remains computationally challenging in large, repetitive, and polyploid genomes. Existing tools either miss indel-containing candidate sites or incur prohibitive runtime and memory costs. We developed SpacerScope, a binary-vectorized framework that enables unbiased, genome-wide off-target candidate discovery without pre-selected candidate sites. By integrating bitwise filtering with right-end-anchored alignment, SpacerScope recovered 100% of validated off-target sites in human CIRCLE-seq data while using only 2.20 GiB of memory and achieving more than 10-fold speedup over indel-aware alternatives. Evaluation in plant genomes, including rice and octoploid strawberry, further demonstrated SpacerScope's capacity to identify larger sequence-compatible candidate burdens overlooked by standard tools. SpacerScope thus provides a high-speed framework for sequence-based genome-wide off-target candidate discovery across diverse and highly repetitive genomic landscapes, supporting downstream prioritization.
The patterns of DNA synthesis and kinetics of cell population in the rat and mouse embryos were studied by means of 3H-thymidine autoradiography and cytofluorimetry. The rat and mouse embryos during the period of cleavage consist of a heterogenous population of blastomeres. At all the stages under study, all phases of the cell cycle occur in the blastomeres: G1, S, G2 and mitosis. The embryonic cells were distributed into groups containing 2c, 3c, 4c and more DNA. The ratio of cell number in these groups differed in the mouse and rat embryos. The mouse embryos are characterized by the appearance of a considerable amount of polyploid cells in S phase at the morula stage. The stage and species specific quantitative and qualitative patterns were established for DNA synthesis and kinetics of the cell population of blastomeres.
Gastric mucosa was obtained from 126 patients by endoscopic biopsy and subsequent cell brushing for histological, cytological and DNA cytophotometric studies. 23 cases were carcinomatous. DNA histogram evaluation for each case was carried out with special consideration of the position of the DNA stem line and the scatter of the measured DNA values. Additionally, DNA distribution characteristics were established for clinical or cytological diagnostic groups. By ascertaining relative mean ploidy values (U values) and relative frequency of euploid and polyploid values (Z values) in the sample populations, cell nuclear DNA determination was used as a criteria for differentiating between benign and malignant alterations of the stomach. The results allow optimistic prognosis concerning the use of cell nuclear DNA content as a significant, though not as the only measuring factor in automated diagnostic procedures.
Nonbacterial thrombotic endocarditis (NBTE) is a rare condition characterized by sterile platelet-fibrin vegetations on cardiac valves in the absence of systemic infection. The pathogenesis of marantic endocarditis is driven by endothelial dysfunction and a systemic hypercoagulable state. In contrast to infective endocarditis, vegetations in NBTE lack significant inflammatory infiltrates and do not yield positive blood cultures. NBTE typically comes to clinical attention via systemic embolic events, with cerebrovascular accidents serving as a clinical hallmark and constituting over 50% of cases. While NBTE is commonly associated with mucin-producing adenocarcinomas of the lung, pancreas, and gastrointestinal tract, its occurrence secondary to hematological malignancies or precursor plasma cell dyscrasias like monoclonal gammopathy of undetermined significance (MGUS) is exceedingly rare, particularly in young individuals. We report the case of a previously healthy 35-year-old woman who presented with acute-onset blurred vision. Neuroimaging via magnetic resonance imaging (MRI) revealed an acute left occipital infarct along with multiple chronic infarcts, raising a strong suspicion of a recurrent embolic process. A transesophageal echocardiogram (TEE) demonstrated two vegetations on the aortic valve with moderate transvalvular regurgitation; in the context of persistent negative blood cultures, these findings supported the diagnosis of NBTE. The patient was managed with systemic anticoagulation. A comprehensive hypercoagulable and autoimmune workup revealed an elevated lambda free light chain level with a decreased kappa/lambda ratio. Subsequent bone marrow biopsy and cytogenetic analysis established a diagnosis of MGUS featuring high-risk genomic aberrations, specifically an immunoglobulin heavy chain/musculoaponeurotic fibrosarcoma (IGH/MAF) rearrangement and the loss of chromosome 13 in a polyploid (3n, 4n) background, findings consistent with plasma cell neoplasia. The prevalence of MGUS in individuals under the age of 40 is exceptionally low, estimated at less than 0.3%. This case underscores NBTE as a critical finding that can unmask underlying, atypical plasma cell neoplasms. It highlights the necessity of an exhaustive diagnostic evaluation for occult hematological disorders and high-risk cytogenetic features in young patients presenting with multi-territory embolic strokes.
Changes of a destructive and adaptational character have been revealed in the extraplacental coats in late toxicoses of pregnant women by histological, histochemical and spectrophotometrical methods. The intesity of the apotomical way of the glucose oxidation decreased in the aminiotic epithelium. While the activity of enzymes converting the lipid decomposition products into glycolysis increased. The glucose utilization in the chorial epithelium occurs mainly due to anaerobic glycolysis. Histochemical methods have established a high content of acid glucoaminoglycanes in the smooth chorion under these pathological conditions and the appearance of fibrinoid deposits on the border with the decidual tissue. The number of polyploid cells containing a considerable amount of RNA has been found to increase in the amniotic and chorial epithelium by spectrophotometric methods. The possible role of the extraplacental coats of the fetus in pathogenesis of late toxicoses is discussed.
Whole-genome duplication (WGD) events create genetic redundancy, posing the evolutionary challenge of how paralogs escape functional overlap to drive innovation. Here, we demonstrate that the MIR164 family in Brassica oleracea resolves this redundancy through spatiotemporal niche partitioning. Following WGD, the family expanded to eight members, which subsequently underwent divergent selection-some preserved under purifying selection, while others showed signals of positive selection. This led to expression divergence, with Bol-MIR164a1 emerging as a key universally expressed paralog. CRISPR-Cas9 mutagenesis of Bol-MIR164a1 revealed its essential role in coordinating two pivotal traits: leaf serration and leaf coloration. Mutants exhibited enhanced leaf serration due to spatial deregulation of CUC2 at organ boundaries, concurrently with yellow-green leaves and elevated flavonoid accumulation. We mechanistically linked the metabolic phenotype to direct transactivation of the anthocyanidin reductase (ANR) promoter by NAC100, alongside its upregulation of chlorophyll catabolism genes. Our findings establish a paradigm in which spatial segregation of target gene expression domains enables a single, widely expressed miRNA paralog to resolve genetic redundancy by independently orchestrating distinct regulatory programs. This provides a fundamental framework for understanding complex trait evolution in polyploids. This allows a single miRNA locus to independently orchestrate both morphological patterning and metabolic programming, providing a fundamental framework for understanding complex trait evolution in polyploid crops.
Allopolyploidy fundamentally influences plant evolution, yet the genomic dynamics of allotetraploidization remain incompletely understood. We investigated Acanthus tetraploideus (2n = 4x = 96), an ecologically significant allotetraploid true mangrove from Indo-West Pacific intertidal zones. Our prior integrative investigations indicate that A. tetraploideus originated through hybridization of the diploid species A. ilicifolius and A. ebracteatus with subsequent chromosome doubling. Here, we present complete chromosome-scale genome assemblies for all three species, representing the first genomic resources for true mangrove polyploid research. Our analysis reveals that the three species have experienced at least four rounds of polyploidization events, with the most recent, approximately 53 mya, possibly an Acanthus-specific event. The allotetraploid A. tetraploideus, which emerged between 1.5 and 2.2 mya, has A. ebracteatus as its maternal progenitor and A. ilicifolius as its paternal one. Through a comprehensive genomic comparison and analysis of homoeologous gene expression, we propose a gradual evolutionary trajectory for allotetraploidy in A. tetraploideus. Despite the allotetraploidization event dating back to around 2 mya, A. tetraploideus retains a high degree of colinearity with its ancestral genomes, with the majority (76.2%) of duplicated genes retained and no significant sub-genome bias in gene expression. Furthermore, we have identified positive selection in specific genes that may facilitate the adaptation of Acanthus mangrove species to their intertidal habitats. These findings establish A. tetraploideus as a model for studying allopolyploid evolution while providing new insights into mangrove speciation processes.
Comparative cytogenetic and histologic studies on 18 mesothelial ovarian tumors revealed a normal chromosome complement in benign lesions, and the well-known cytogenetic pattern in cystadenocarcinomas. But all borderline tumors of the series evidenced an abnormal stem line and a more or less marked tendency to polyploidization. Serous papillary cystadenomas of this group showed in five out of six cases a stem line with the karyotype 47,XX+C10 (identified by Q-banding), present in both sides of bilateral lesions. It is evidenced that malignant change on the chromosomal level precedes histologically detectable features of malignancy. Histologic equivalents appeared, when the abnormal cell line was established. The initiation of malignant transformation therefore may be signalized by karyotype abnormalities before structural changes can be detected in the corresponding histologic specimens. The results discussed include the concepts of multicentric origin and clonal evolution of malignancy.
The relative biological effectiveness (RBE) has been considered for three kinds of cell radiation damages: subdamages (sublethals), one-track, and two-track lethal damages. In contrast to the "dual theory", which postulates the square relation between the lethal damage yield and the specific energy, it is assumed that the one-track lethal yield is linearly related to the specific energy per cell nucleus. As a result, the identical dependence has been obtained of both one-track lethals and subdamages on specific energy and absorbed dose. It is established that RBE for all three kinds of damages does not depend on the radiation dose. It is shown that RBE for subdamages and one-track lethals depends on LET of radiation only, and involves molecular parameters of sensitive cell structures. Within the limits of this assumption, the relations are general for all the types of eukaryotic cells. These can be used for a further development of the RBE theory, with spectra of LET, the track structure of charged particles, the contribution of delta-electrons etc being taken into consideration.
BACKGROUND: Cytokinins are key regulators of plant growth, reproductive development, and yield formation. In cereals, cytokinin biosynthesis is catalyzed by isopentenyltransferase (IPT) enzymes, yet the genomic organization and developmental regulation of IPT genes in polyploid wheat remain incompletely understood, especially at the cultivar level. RESULTS: Here, we present an integrated genomic, transcriptional, and hormonal analysis of the TaIPT gene family during vegetative and reproductive development in two wheat cultivars, awnless Kontesa and awned Ostka. Genome-wide analysis identified nine core TaIPT genes represented by 25 homoeologs distributed across the A, B, and D subgenomes, for which a unified nomenclature was established. Phylogenetic analysis resolved TaIPTs into conserved evolutionary clades corresponding to ATP/ADP-dependent and tRNA-dependent IPT groups. Expression profiling revealed distinct spatial and temporal patterns of TaIPT transcription across roots, leaves, inflorescences, and developing spikes. Several TaIPT genes showed enhanced expression during early reproductive stages, coinciding with dynamic changes in cytokinin concentrations. Comparative analyses revealed cultivar-specific expression and co-variation patterns, with Kontesa displaying more compartmentalized TaIPT expression and Ostka showing coordinated activation of multiple TaIPT genes during early grain development. Hormone profiling further indicated stage-dependent associations between TaIPT expression, cytokinin metabolism, and the balance between cytokinins and abscisic acid. These relationships are interpreted as correlative and provide a framework for future functional testing rather than direct evidence of causality. CONCLUSIONS: Together, these results provide a cultivar-focused framework for understanding the organization and regulation of cytokinin biosynthesis genes in wheat. The data highlight cultivar-dependent TaIPT expression patterns and their association with cytokinin dynamics during reproductive development, while also identifying the need for homoeolog-specific and functional validation. This study establishes a foundation for future research on cytokinin-mediated regulation of wheat growth and grain development.
The first T2T reference genome of Guazuma ulmifolia is reported, which serves as a core genomic resource for stress adaptation research and stress-tolerant breeding in cacao wild relatives. Climate change, particularly increased incidence of drought, poses a major threat to food security. Understanding the genomic basis of environmental adaptation in crop wild relatives can provide valuable resources for improving stress resilience. Guazuma ulmifolia, a wild relative of Theobroma cacao with important ecological and medicinal value, lacks high-quality reference genomic resources. Here, we report the first telomere-to-telomere (T2T) chromosome-level genome assembly of G. ulmifolia, with a genome size of 311.31 Mb, contig N50 of 35.19 Mb, and 98.70% BUSCO completeness. Repetitive sequences constitute 27.43% of the G. ulmifolia genome, with LTR retrotransposons as the predominant class. Comparative genomic analyses revealed that genome-size variation among Malvaceae species is associated with differences in polyploidization history and TE dynamics. Ancestral karyotype reconstruction identified five lineage-specific chromosome fusion events distinguishing G. ulmifolia from T. cacao. Comparative analyses further identified tandem duplication-associated expansion of stress-related LEA and GST gene families, suggesting potential genomic features associated with stress responses. Flavonoid biosynthesis genes were largely conserved in copy number but showed tissue-specific expression patterns, providing candidate genes for investigating secondary metabolism. Together, this study establishes a high-quality T2T genome resource for exploring genome evolution, chromosome organization, and stress-related genomic features in Malvaceae.