Chromosomal karyotype is closely linked to species evolution, adaptability, and environmental responses. As global climate change intensifies, temperature fluctuations critically affect chromosomal behavior, consequently influencing plant growth and development. However, the patterns of karyotypic variation that underpin ploidy levels evolution in Cynodon dactylon (L.) Pers. remain poorly understood. In this study, we selected 42 individuals of C. dactylon from 13 regions and cultivated them under three temperature conditions (25℃, 30℃ and 35℃). Their ploidy levels encompassed diploid to hexaploid. This research investigated the effect of temperature changes on karyotypes of C. dactylon. We employed microscopic and karyotype analysis to examine populations at different ploidy levels along latitudinal gradients in China. Statistical methods comprised preliminary analyses (ANOVA with Games-Howell and Tukey HSD post-hoc, PCA, correlation) and advanced modeling (mixed-effects and logistic regression), all preceded by assumption checks. Karyotype asymmetry varied with ploidy level. Diploids possessed the most asymmetric karyotypes, characterized by a higher coefficient of variation for chromosome length (CVCL) compared to polyploids. Among polyploids, tetraploids exhibited the most symmetric karyotypes. Centromeric positions remained stable across all karyotypes. Inter-individual variation was primarily driven by both temperature and ploidy level. The temperature decreased from 30℃ to 25℃ triggered a karyotype shift (1A to 1B), primarily in diploids, by altering chromosome structure and meiosis. Diploids exhibiting chromosome length variation were mainly distributed in high-latitude regions, where their karyotypes exhibited heightened sensitivity to temperature fluctuations between 25℃ and 35℃. Diploids were more susceptible to temperature fluctuations due to their highly asymmetrical karyotypes. Conversely, tetraploids were less affected by temperature variation, which was associated with their symmetrical karyotypes. The karyotypic symmetry of higher ploidy levels underpinned the greater stability of polyploids under temperature variation. Temperature changes along latitudinal gradients influenced karyotype changes in C. dactylon, and karyotype evolution was pivotal in polyploid formation. These findings provide a theoretical basis for understanding the ploidy evolution of C. dactylon, screening wild resources in response to climate changes, and breeding new varieties.

Molecular dynamics simulations of whole cells and organelles aim to transform cell biology by providing a molecular view into the crowded cellular environment. However, constructing suitable starting configurations remains a major bottleneck due to their size and complexity. We present bentopy, a workflow for building cellular‐scale models ready for simulation. Bentopy uses a voxel‐based spatial representation to efficiently pack molecules into arbitrarily complex compartments. The modular design facilitates the assembly of molecular models containing millions of molecules in minutes on standard workstations. We demonstrate bentopy through three experimentally informed models spanning multiple biological scales. A JCVI‐Syn3A whole‐cell model combines existing membrane and chromosome structures with diverse cytosolic components. A mitochondrion model integrates cryo‐electron tomography maps with spatially resolved proteomics and metabolomics data. An atomistic SARS‐CoV‐2 virion inside a respiratory aerosol demonstrates bentopy's capability to pack at both atomistic and coarse‐grained resolution. Together, these applications establish bentopy as a workflow for constructing simulation‐ready models at the cellular scale.

In battlefield environments, enhancing situational awareness requires particular attention to two critical factors: coverage and detection. This study aims to optimize the coverage of a designated region and the detection of multiple targets using a limited set of available sensors. A Genetic Algorithm (GA)–based approach is employed to determine the optimal sensor deployment, maximizing both area coverage and target detection while minimizing the number of sensors used and ensuring a uniform spatial distribution. Uniformity is achieved by minimizing the repulsive forces between sensors, where these forces are modeled as functions of sensor strength and inter sensor distance. From this perspective, the fitness function consists of multiple objectives that are combined into a single scalar value by applying appropriate weighting factors. A compact chromosome structure is developed to support this multi-objective formulation. Each gene block encodes both the deployment coordinates and the type of sensor to be placed. Binary gene encoding is used to represent a wide range of continuous position values as well as sensor types. Targets are randomly distributed within a specified region, and it is assumed that they move collectively within a localized neighborhood. During the GA selection phase, the best chromosome is preserved in the chromosome pool. If the best solution remains unchanged for a predefined number of iterations, the algorithm terminates and the corresponding chromosome is taken as the optimal sensor deployment configuration.

BackgroundProso millet (Panicum miliaceum L.) is a drought-tolerant cereal crop cultivated in arid and semi-arid regions. VQ proteins, a class of plant-specific proteins characterized by a conserved VQ motif (FxxxVQxxTG), are known to play critical roles in plant responses to abiotic stress. To elucidate the genetic basis of drought tolerance in proso millet, a genome-wide identification and characterization of the VQ gene family was undertaken.MethodsThis study involved the identification of all VQ family members from the proso millet genome, followed by comprehensive analyses including chromosomal localization, phylogenetic relationships, gene structure, conserved motifs, collinearity, and promoter cis-acting elements. Expression profiling was conducted using transcriptomics and Quantitative Real-Time Reverse Transcription Polymerase Chain Reaction (qRT-PCR) to investigate potential gene functions. Additionally, the drought tolerance of various germplasm materials was systematically assessed.ResultsA total of 70 VQ genes (PmVQ1–PmVQ70) were identified and classified into four distinct subfamilies. Based on the screening of root-preferential and drought-responsive candidate genes, combined with phenotypic and qRT-PCR analyses of drought-tolerant and drought-sensitive materials, four key candidate genes were identified. qRT-PCR analysis revealed that the four genes exhibited differential expression patterns between drought-tolerant and drought-sensitive materials, suggesting their potential roles as core regulators in proso millet’s drought response, particularly in root-specific regulatory pathways under drought stress. This study provides a systematic analysis of the VQ gene family in proso millet and offers valuable genetic resources for elucidating drought tolerance mechanisms and advancing molecular breeding.

Histone H1 and related linker histones play critical roles in chromosome organization in eukaryotic cells. Although histone H1 is essential for compacting nucleosomes into chromatin fibers and is a major structural component of chromosomes, its association with chromatin is highly dynamic. Histone H1 exchange modulates the accessibility of regulatory proteins to DNA and has been implicated in the regulation of gene expression and cellular pluripotency. Relatively little is known, however, about how histone H1 binding, exchange and function is regulated in vivo. In this study, we investigated the regulation of histone H1 function in Drosophila using live analysis and confocal microscopy. A gain-of-function genetic screen identified several factors that affect chromosome structure, histone H1 binding or histone H1 exchange, including the ATP-dependent chromatin-remodeling factor XNP, the hypoxia-induced factor Scylla, the winged helix transcription factor Jumeau and the microRNA bantam. Our findings show that altered expression of single factors can have surprisingly global effects on higher-order chromatin structure and histone H1 binding in vivo, with the potential to trigger large scale changes in genome organization and accessibility.

Structural-Maintenance-of-Chromosome (SMC) complexes, such as condensins, organise the folding of chromosomes. However, their role in modulating the entanglement of DNA and chromatin is not fully understood. To address this question, we perform single-molecule and bulk characterisation of yeast condensin in entangled DNA. First, we discover that yeast condensin can proficiently bind double-stranded DNA through its hinge domain, in addition to its heads. Through bulk microrheology assays, we then discover that physiological concentrations of yeast condensin increase both the viscosity and elasticity of dense solutions of lambda-DNA, suggesting that condensin acts as a crosslinker in entangled DNA, stabilising entanglements rather than resolving them and contrasting the popular theoretical picture where SMCs purely drive the formation of segregated, bottle-brush-like chromosome structures. We further discover that the presence of ATP fluidifies the solution–likely by activating loop extrusion–but does not recover the viscosity measured in the absence of protein. Finally, we show that the observed rheology can be understood by modelling SMCs as transient crosslinkers in bottle-brush-like entangled polymers. Our findings help us to understand how SMCs affect the dynamics and entanglement of genomes.

Meiotic homolog pairing relies on programmed DNA recombination and large-scale chromosome movements, yet, how these genetic and mechanical events are coordinated remains unclear. ZCWPW1 is a histone reader that recognizes PRDM9-deposited chromatin marks. We identify an unexpected role for ZCWPW1 as a regulator of rapid prophase movements (RPMs). Using super-resolution imaging, we show that ZCWPW1 is strongly enriched at subtelomeric regions of mouse spermatocytes, where it stabilizes TRF1, LINC complex components, dynein, and meiosis-specific cohesin (STAG3). Loss of ZCWPW1 disrupts telomere architecture, weakens telomere–LINC– motor coupling, and abolishes chromosome movement, leading to defective synapsis and pairing, and persistence of DSBs. These defects are more severe than, and mechanistically independent of, those observed inPrdm9−/−spermatocytes. Together, our findings reveal that ZCWPW1 acts independently of PRDM9 as a chromatin-based intranuclear regulator of telomere architecture and telomere-led chromosome movements, thereby linking telomeric chromatin state to nuclear force transmission required for faithful meiotic progression.Significance StatementMeiotic pairing requires recombination and telomere-led chromosome movements, yet no chromatin factor has been shown to regulate both. We identify ZCWPW1 as the first chromatin-based regulator of rapid prophase movements. ZCWPW1 organizes telomeric chromatin and promotes cohesin and motor assembly at telomeres that for force transmission across the nuclear envelope. Loss of ZCWPW1 disrupts the telomere-nuclear envelope mechanical coupling, impairing motion and altering recombination. This function doesn’t rely on PRDM9 despite their co-evolution and co-expression, challenging the prevailing view that ZCWPW1 only acts downstream of PRDM9 in DNA repair. Our findings show that chromatin readers can function as structural regulators of genome organization, revealing a conserved mechanism integrating chromosome structure, motion, and repair to ensure proper pairing and fertility.

Genome-wide characterization and evolutionary insights into Auxin Response Factor (ARF) genes in sesame (Sesamum indicum L.) reveal their potential roles in waterlogging response.

A novel method for mapping the interphase genome architecture in Drosophila polytene chromosomes is proposed. The method is based on physical mapping of the boundaries between interbands, gray bands, and black bands. Mapping relies on three criteria: the 4HMM bioinformatic model that considers the associations between each of the four chromatin states and polytene chromosome structures and the findings of ChIP-seq analysis in salivary glands for two critical markers: the CHRIZ/CHRO protein localized in housekeeping gene promoters and H3K36me3 histone modification, a marker of transcriptional elongation. For mapping the 1AF region of the X chromosome, FISH probes were selected from AQUAMARINE chromatin (interbands) at the boundary with black bands, which provided precise coordinates of the edges of black bands (localization of the developmental genes). The localization of promoters and housekeeping gene bodies was then identified by ChIP-seq analysis for CHIRIZ and H3K36me3 in salivary glands (the interbands and gray bands, respectively). These maps will allow one to better understand the architecture of an actively functioning genome.

ABSTRACT Taphrinomycotina, a subphylum of the phylum Ascomycota, comprises fungi with diverse morphologies and ecologies. Saitoella and Savitreella are genera of red-colored yeasts within Taphrinomycotina, but their precise phylogenetic positions have remained controversial. In this study, we sequenced the whole genomes of Saitoella coloradoensis and Savitreella phatthalungensis in order to elucidate their phylogenetic relationships using a phylogenomic approach based on chromosome-level genome assemblies generated by long-read sequencing technologies. Our phylogenetic analyses suggest that Saitoella is distinct from all currently described classes within Taphrinomycotina, whereas Savitreella seems to belong to the class Taphrinomycetes. Furthermore, Saitoella shares high average amino acid identity with all other classes in Taphrinomycotina, suggesting that it retains ancient gene sequences. Our findings enable us to propose a new class, order, and family—namely, Saitoellomycetes, Saitoellales, and Saitoellaceae—automatically typified by the genus Saitoella. Our chromosome-level assembly reveals that Saitoella coloradoensis possesses 38 chromosomes, the highest number of chromosomes among fungi reported to date. We also identify structural differences between two Saitoella species and a chromosome structure lacking the canonical palindromic centromeric repeat sequence.

Compacting chromatin within the cellular nucleus presents a significant challenge for biology. Chromosomes must be both condensed and spatially organized to enable essential processes such as transcription and replication. Chromosome conformation capture experiments (e.g., Hi-C) provide valuable information about the spatial organization and, therefore, the connectivity between different genomic regions. These experiments inspired polymer models that describe the physical mechanism of the chromosomal energy landscape. The Full-Inversion Chromatin model (FI-Chrom), a data-driven approach for modeling genome organization, uses Hi-C contact maps to infer pairwise interaction potentials between all chromosomal loci. It combines Graphics Processing Unit (GPU)-accelerated simulations with efficient training of tens of millions of parameters derived from the maximum-entropy principle to determine 3D structures of chromosomes that accurately reproduce Hi-C-like data. FI-Chrom does not make any a priori assumptions regarding chromosome architecture, making it applicable to any chromosome conformation capture experiment. Its derived structural ensembles capture all essential features from the short- and long-range interactions of typical chromosome organization, such as segregated compartments, chromosome territories, and fully or partially formed loops. Although Hi-C contains only structural information, FI-Chrom extends these data by revealing an emergent dynamical mechanism encoded in the inferred energy landscape. For example, simulations show that chromatin loops are not static architectural features but rather transient structural elements. Statistical analyses further indicate that loops confined within a single compartment occur more frequently than those spanning multiple compartments, highlighting the dynamic and compartment-dependent nature of chromatin organization.

Tetraploid non-apomictic citrus genotypes are key female parents for 4x × 2x hybridizations aimed at producing seedless triploid hybrids. However, the extent to which different tetraploidization methods affect genome integrity remains insufficiently characterized at a genome-wide scale. In this study, genotyping-by-sequencing (GBS) was used to evaluate marker-based genomic stability in ten tetraploid plants of 'Clemenules', 'Fina', and 'Marisol' clementines obtained via colchicine treatment, in vitro adventitious organogenesis, or somatic cybridization. Diploid parental plants, two haploid plants of 'Clemenules' and 'Fina' clementines, and one doubled haploid plant of 'Clemenules' clementine were included, being the haploid and double haploid essential to resolve allelic phases. After quality filtering, 3333 SNP (Single Nucleotide Polymorphism) markers distributed across the nine citrus chromosomes were identified and used to compare allele dosage patterns along the genome. Across all GBS-covered regions, no major marker-based genomic gains or losses were detected in any tetraploid plant. These results indicate that, at the resolution provided by GBS, all three tetraploidization methods largely preserve chromosome structure, supporting their suitability for citrus triploid breeding programs based on 4x × 2x sexual hybridizations.

Abstract Clinical genomic sequencing has revealed that prostate cancer (PCa) progression is associated with changes to chromosome number and structure, termed chromosomal instability (or CIN). While mutations in common driver genes are rare in primary PCa, CIN is detected in >90% of cases, suggesting that CIN may be a driver of the disease. However, the underlying mechanisms that cause CIN in PCa are poorly understood. Cells are susceptible to CIN during mitosis, when the duplicated genome must be equally segregated into two daughter cells. Normally, two centrosomes (cytoplasmic, non-membranous organelles) nucleate and organize microtubules to guide assembly of the mitotic spindle, thus ensuring the fidelity of cell division. However, we recently discovered that cells within primary PCa lack centrosomes, the first cancer type to show this phenomenon. Furthermore, we showed that centrosome elimination in non-tumorigenic cells generates CIN which can transform these cells, causing them to form xenograft tumors in mice. Therefore, we sought to understand the underlying mechanisms that drive the centrosome loss observed in PCa. The prostate is a naturally hypoxic organ, averaging around 4% oxygen tension in the healthy organ which declines as men age. Additionally, tumor hypoxia is strongly correlated with high CIN, particularly in prostate cancers. However, there are few mechanistic links between hypoxia and CIN. Therefore, we hypothesized that hypoxia could cause centrosome loss and, thus, predispose cells to CIN. Indeed, we found that immortalized prostate RWPE-1 cells progressively lost centrosomes when exposed to 1% O2 for as short as 6 hours in vitro. Using ultrastructure expansion microscopy (U-ExM), we find centrosomes are replaced by non-functional microtubule husks devoid of centrosome proteins which we call ‘remnants’. These phenomena also occur in PC-3 and LNCaP prostate cancer lines. Furthermore, we observe centrosome loss specifically in the hypoxic regions of xenograft tumors. Using a combination of RNAseq and chemical inhibitors, we determined that centrosome elimination sits at the crossroads of 3 transcriptional programs: (1) centrosome elimination occurs in basal cells and basal-like cancers that express p63; (2) cells must be confluent with active Hippo pathway; and (3) hypoxia induces a HIF-independent transcriptional response. When these conditions are met, cells transcriptionally downregulate 4 key centrosome proteins (Cep63, Cep152, Cep192, and Cep215), resulting in the depletion of a protective shell of pericentriolar material (PCM) and subsequent centrosome elimination. By overexpressing the mitotic kinase Polo-like kinase 1 (PLK1), we can strengthen the PCM and prevent elimination. Finally, we identify PCa cells containing remnants within prostatectomy tissue samples. This work is significant as it identifies the first examples and mechanisms of centrosome elimination in human somatic and cancer cells, provides a mechanistic link between hypoxia and CIN, and identifies remnants as a cellular indicator for CIN predisposition. Citation Format: John M. Ryniawec, Natalya K. Seppanen, Gregory C. Rogers, Anne E. Cress. Hypoxia-induced centrosome elimination as a driver of chromosomal instability in prostate cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Innovations in Prostate Cancer Research and Treatment; 2026 Jan 20-22; Philadelphia PA. Philadelphia (PA): AACR; Cancer Res 2026;86(2_Suppl):Abstract nr B065.

The Fantastic Four gene family encodes small, plant-specific regulatory proteins involved in developmental control; however, their roles in wheat remain poorly understood. In this study, we conducted a comprehensive genome-wide analysis of the Fantastic Four gene family in wheat. A total of 42 TaFAF genes were identified and systematically characterized in terms of their chromosomal distribution, phylogenetic relationships, gene structures, conserved motifs, and promoter cis-regulatory elements. Phylogenetic analysis classified TaFAF genes into four distinct clades, which exhibit high structural conservation but show divergent motif compositions. Expression profiling revealed tissue-specific expression patterns and suggested that a subset of TaFAF genes responded transcriptionally to heat stress in a genotype-dependent manner. Subcellular localization assays showed that representative Fantastic Four proteins were localized in the cytoplasm. Protein–protein interaction analyses indicated that TaFAF-1A.1 and TaFAF-5D.5 physically interact with the key flowering regulator TaFT1. Furthermore, haplotype analysis of TaFAF-5D.5 across 145 wheat accessions revealed a significant association with wheat growth habit, with a favorable haplotype preferentially enriched in winter wheat. Together, these results provide insights into the evolutionary diversification and functional relevance of the Fantastic Four genes and identify TaFAF-5D.5 as a candidate gene potentially associated with developmental adaptation and heat stress responses in wheat.

As a class of glutathione-dependent oxidoreductases, glutaredoxins (GRXs) play a central role in maintaining cellular redox homeostasis, thereby influencing diverse biological processes including growth, development, and stress adaptation in plants. This study identified 36 GRX genes in Litsea cubeba through whole-genome analysis. Phylogenetic classification placed them into four subfamilies (CC-, CGFS-, CPYC-type, and a species-specific SS branch), consistent with patterns in model plants like Arabidopsis thaliana and Oryza sativa, indicating evolutionary conservation of GRX core motifs. Genomic analyses including chromosomal location, collinearity, and gene structure revealed family evolution features. Expression profiling showed 11 LcGRX genes were flower-specific, with marked differential expression during stamen (M2) and pistil (F2) degeneration, supporting their roles in sexual dimorphism. Functional assays confirmed that floral highly expressed LcGRX12 directly interacts with TGA transcription factor LcTGA10, similar to its Arabidopsis homolog ROXY1. This study reveals the GRX-TGA module’s role in floral organ development in L. cubeba, offering insights into redox-mediated sex differentiation in Lauraceae and providing candidate genes for molecular breeding.

Tartary buckwheat has increasingly become the focus of people’s attention due to its powerful health benefits. Golden buckwheat is a traditional Chinese medicine. People have begun to utilize it through wide hybridization to further enhance the health benefits of Tartary buckwheat. To study the genetic stability of the interspecific hybrids of Tartary buckwheat with golden buckwheat, and to provide scientific basis for the interspecific cross breeding of buckwheat, the mitotic chromosomes of two buckwheat double lines and their interspecific hybrids with golden buckwheat were subjected to observe the karyotypes. The results showed as follows: (1) The two autotetraploid Tartary buckwheat lines (Long Black-4T and Daku-1) have chromosome number 2n = 32. The karyotype formula of 2n = 4x = 32 consisted of 16 pairs of metacentric chromosomes for Long Black-4T (TTTT) while Daku-1 (TTTT) has 1sm + 7m Gui Jinqiao 4 with 2n = 32 has a karyotype formula of 2n = 4x = 32 that consisted 1sm + 6m + 1M (genome M) and 2sm + 5m + 1M (genome M’). The normal fertile tetraploid hybrid F1 plants between Long Black-4T and Gui Jinqiao 4 has 2n = 4x = [1sm + 7m (M), 1sm + 7m (M’), 14m + 2M (TT)]. The normal fertile variety Gui Jinku 1 from the above hybrid progenies shows 2n = 4x = [3sm + 5m (M), 2sm + 6m (M’), 16m (TT)], indicating an increment of sm chromosomes by rearrangements of chromosome structure in the M and M’ genomes. The above parents and their hybrids with the MM’TT genome show fertility. A plant from F2 of the above cross, showing highly infertility, has 2n = 3x= [1sm + 7m (M), 1sm + 7m (M’), 8m (T)]; and back cross progeny plant from Daku 1/Gui Jinqiao 4 F2//Gui Jinqiao 2 golden buckwheat has 2n = 4x = [16m (MM), 5sm + 3m (M’), 1sm + 7m (T)], showed high infertility, which is caused by genome aneuploidy and non-even ploidy. The above shows that there are obvious variations of genome karyotypes from the same parent, indicated by certain chromosome structural rearrangements in genomes T, M, and M’.

Transcription factors (TFs) control the rate of transcription of genetic information by binding to specific DNA sequences. The time needed for a TF to find its specific target sites is a bottleneck to the genetic response mechanism. While TF target site search is a well studied problem, the effect of genome 3D architecture on the TF target search times is poorly understood. Here, we use accurate and cell-specific 3D structural ensembles of human chromosomes to investigate how the spatial organization of binding sites on chromosomes influences the dynamics of TFs. We use Chromatin Immuno-Precipitation data to map the position of binding sites for several TFs on chromosomal structures and simulate the dynamics of individual TF within chromosomal territories. We find that the distribution of binding sites along chromosomes cooperates with the 3D folding of the chromatin fiber to induce dynamics in which TFs tend to visit sites distributed sequentially along the genome. In this way, genome 3D architecture appears to reduce the time each TF spends in the unbound state while commuting from one target site to the other. At the same time, genome 3D architecture further reduces the flux of TFs between binding sites already well separated along the genome, effectively isolating distant clusters of binding sites. We compare the TF traffic patterns generated by the 3D structures of human chromosomes with those generated by several alternative structural models characterized by increasing randomness. Finally, we study the effect of lengthwise compaction and phase separation, known architectural features of the human genome, in TFs target search. In short, our analysis demonstrates that genome architecture regulates the traffic of TFs within chromosomal territories and reduces the time each TF spends commuting between binding sites.

Genome-wide identification of the HMG family in cucumber and regulatory analysis of CsHMG9 in spine density.

Genome-wide identification of TGA transcription factors in wheat and the TaTGA13 negatively modulates stripe rust resistance.

Genome-wide identification of NF-Y genes in kiwifruit genome and the role of AcNF-YC22 in response to heat stress.