Biology subjects

Ghosh, K.

Publications and source records attributed to Ghosh, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Can We Really See the World in Three Dimensions? An Exploratory Study with Finger Alignment Task and Ponzo Illusion

Stereopsis is the perception of depth when two 2-dimensional (2D) images of an object from slightly different angles align with corresponding retinal positions in both eyes. However, when we consider the blind spot (BS), a new set of challenges arises. In binocular vision, one eye's higher visual areas compensate for the other's non-receptive region. However, our brain only receives information from one image patch in the BS region, and another visual patch does not contribute to constructing a comprehensive 3-dimensional (3D) representation of the scene. This suggests that the brain adeptly manages this dimensional transition. We aimed to determine the extent to which we perceive 3D across our entire field of view (FoV). We employed the Ponzo illusion, a stimulus relying on visual depth cues (pictorial depth cues), and an eye-tracking technique to assess participants' accurate fixation and eye movement patterns. The participants attempted to align their index fingers before a chart paper to create a Horopter-like setup, supporting the hypothesis about our capacity for stereoscopic perception. The results of our exploratory pilot study with two specific tasks revealed that our ability to perceive depth diminishes beyond approximately 8$^{\circ}$ of retinal eccentricity (in the horizontal meridian) in both halves of the visual field centered around the fovea. This limitation is not apparent in our day-to-day experience.

neuroscience↗

bioRxiv2026

Mechanistic Insights into HIV-1 Capsid Interactions with CPSF6

A crucial stage of the HIV-1 life cycle is the docking of the viral capsid at, and its translocation through, the nuclear pore complex (NPC). During this process, the capsid interacts with a series of cellular host factors that regulate efficient nuclear entry. One such host factor is cleavage and polyadenylation specificity factor 6 (CPSF6), which plays a critical role in efficient HIV-1 nuclear entry and integration. Experimental evidence suggests that nucleoporins (NUPs), such as NUP153, initially engage the capsid, followed by CPSF6 binding and oligomerization during subsequent stages of nuclear import. However, the mechanistic basis by which CPSF6 binds to the capsid and subsequently oligomerizes remains poorly understood. To address this question, we have developed bottom-up coarse-grained (CG) models that explicitly simulate the process of CPSF6 binding and oligomerization on the HIV-1 capsid. Our simulations show that CPSF6 assembles into a mesh-like coating surrounding the capsid, consistent with experimental observations. Furthermore, we then demonstrate that CPSF6 binding is dependent on the intrinsic curvature of the capsid lattice. Finally, we investigate how perturbing CPSF6-CPSF6 interactions alters binding, oligomerization dynamics, and curvature dependence. Together, these findings provide new mechanistic insights into how CPSF6 regulates HIV-1 nuclear entry.

biophysics↗

bioRxiv2026

Who rests with whom? Sex composition and group demography shape resting associations in free-ranging dogs

Free-ranging dogs frequently rest near conspecifics, but the demographic factors structuring their resting associations remain poorly understood. We quantified dyadic resting associations in 26 free-ranging dog groups in West Bengal, India, observed between 2019 and 2023. Association strength was estimated from scan based resting co-occurrences using the Half-Weight Index. We tested whether dyadic association strength varied with dyad sex composition, dyad life stage composition, group size, and group sex ratio using a generalised additive model for location, scale and shape that accounted for group identity and repeated occurrence of individuals across dyads. Male-male dyads had lower association strengths than female-female dyads, whereas mixed-sex dyads did not differ from female-female dyads. Association strength decreased with increasing group size but increased as the male-to-female ratio within the group increased, while life-stage composition had no detectable effect. Individual level network metrics, including strength, reach, clustering coefficient, affinity, and eigenvector centrality, did not vary with sex or season. Mixed-sex pairs were also frequently represented among the strongest dyadic associations within groups. These findings indicate that resting associations in free-ranging dogs vary with dyad sex composition and group demography. Further opportunity-controlled analyses are required to determine whether the prominence of mixed-sex dyads reflects preferential association rather than group composition alone.

animal behavior and cognition↗

bioRxiv2026

Alcohol-Evoked Calcium Signaling Drives Distinct Responses in Zebrafish Hepatocytes and Pancreatic Acinar Cells

Alcohol exposure perturbs intracellular calcium (Ca2+) homeostasis in digestive organs, yet whether common or organ-specific mechanisms coordinate this response remains unclear. Using an acute ethanol paradigm in zebrafish, single-cell transcriptomics revealed broad up-regulation of Ca2+-signaling genes in hepatocytes and pancreatic acinar cells. In vivo Ca2+ buffering with SpiCee, a genetically encoded chelator, demonstrated a shared requirement for Ca2+ flux: in hepatocytes, lineage-restricted buffering was associated with pronounced cytoplasmic vacuolation composed of lipid-negative vesicles, consistent with stalled lysosomes or autophagosomes; in pancreatic acinar cells, it was associated with accumulation of aggregated/misfolded protein. Mechanistic experiments using pharmacological inhibitors implicated distinct molecular contributors in each tissue. In hepatocytes, inhibition of Pikfyve or its downstream effector, the lysosomal Ca2+ channel TRPML1, phenocopied Ca2+ buffering. While, in acinar cells, Pick1 inhibition produced analogous associations. These data position Pikfyve and Pick1 as organ-specific components linked to the Ca2+-coupled alcohol response. Notably, pharmacologic activation of TRPML1 in hepatocytes recapitulated alcohol-like Ca2+ dynamics but increased macrophage recruitment and cell death, indicating that Ca2+ signaling is required for the alcohol response yet can be detrimental when amplified. Together, our results support a model in which alcohol elicits a shared Ca2+ dynamics across liver and pancreas, modulated by tissue-specific molecular nodes.

cell biology↗

bioRxiv2026

Sequence-Dependent DNA Base Selection Fidelity: A Kinetics-based Model and its validation

DNA replication achieves error rates as low as 10-9-10-11 per base pair through the combined contribution of base selection, exonuclease proofreading, and mismatch repair. Among those processes, base selection determines the initial level of accuracy and is strongly modulated by local sequence context. Existing models address this dependence either by fitting individual rate constants for each sequence context or by invoking the global template properties, neither of which derives sequence dependence from the underlying thermodynamics and kinetics of base pair formation. Here we present a mechanism for sequence-dependent base selection fidelity, built from two physical properties: nearest-neighbor stacking thermodynamics and directional kinetic asymmetry. The model fits the experimentally observed mutation spectra from three mismatch repair-deficient organisms well (r=0.74, 0.70, and 0.63), and predicts that base-selection accuracy varies non-monotonically with temperature in a sequence-dependent manner. Our model, therefore, provides a framework that connects sequence-dependent thermodynamic and kinetic effects during nucleotide incorporation to experimentally observed mutation rates.

biochemistry↗

bioRxiv2026

Directional purine pyrimidine asymmetry in CRISPR repeats facilitates spacer acquisition

Spacer acquisition is the primary and essential step of CRISPR-Cas adaptive immunity in most prokaryotes and occurs preferentially at the leader-repeat junction of the CRISPR array. Despite the conservation of the adaptation machinery, spacer acquisition efficiencies and site-specificity vary markedly across CRISPR-Cas systems, suggesting that the local sequence architecture of the repeat and leader-repeat junction may contribute to the variation in the adaptation efficiency. To investigate this possibility, we systematically analyzed the direct repeat sequences and the terminal base pairs at the 3' end of leader regions adjacent to the integration site. We identify a conserved asymmetric purine-pyrimidine (RY) distribution within direct repeats, characterized by a 5' pyrimidine-rich half and a 3' purine-rich half, together with purine enrichment at the 3' end of leader sequences. Building on these observations, we develop a mechanistic model for spacer acquisition by demonstrating the importance of the sequence motif of the first direct repeat and the leader-repeat junction, using the sequence-dependent asymmetric cooperativity model that captures DNA unzipping kinetics. According to our model, sequences with such directional RY-asymmetric nucleotide distribution as direct repeats have high unzipping propensity and thus can promote efficient spacer integration. Consistent with this mechanism, experimental data from previous studies show that repeats with stronger asymmetry and appropriately positioned pyrimidine-to-purine transition sites are associated with larger spacer counts within CRISPR arrays. These findings reveal a conserved architectural feature of CRISPR repeats and provide a mechanistic model connecting DNA sequence organization to efficiency.

genomics↗

bioRxiv2026

Highly diverged non-vertebrate Ki-67 proteins with conserved biophysical and functional properties

The Ki-67 protein is a widely used marker of mammalian cell proliferation that plays critical roles in heterochromatin organisation and mitotic perichromosomal layer formation. Thus, its apparent restriction to vertebrates is puzzling. However, sequences with limited homology to subdomains of Ki-67 are present in genomes from some non-vertebrate species. Here, using structural modelling, biophysical and functional analysis, we identify Ki-67-like proteins across diverse non-vertebrate eukaryotes, including tunicates, sponges, molluscs, insects and fungi. Despite extremely low sequence homology, the disordered domains of Ki-67 homologues have generally conserved biophysical and molecular properties. This is further reflected by comparison of cellular localisation, dynamics and effects on chromatin organisation of human, Ciona and Drosophila Ki-67 homologues. These results reinforce the emerging paradigm that functions may be encoded by general biophysical features in highly diverged intrinsically disordered domains. Our approach provides a blueprint for comparative biology of disordered proteins and a foundation for future studies exploring functions of Ki-67 homologues across eukaryotes.

Cell Biology↗

bioRxiv2026

Mechanism of HIV-1 Capsid Rupture and Uncoating by Reverse Transcription

One of the key events in the HIV-1 life cycle is reverse transcription, during which single-stranded viral RNA (ssRNA) is converted into double-stranded DNA (dsDNA). This process occurs inside the mature virus capsid and, once it reaches a critical threshold, drives capsid rupture. This uncoating is essential for infection because it releases viral genetic material into the host cell nucleus. Despite its importance, many mechanistic details of this process remain to be fully understood. To address this gap, we develop a multiscale computational method for simulating reverse transcription inside the capsid, termed Coarse-Grained Kinetic Monte Carlo (CG-KMC). CG-KMC stochastically adds deoxynucleotide triphosphates (dNTPs) to the coarse-grained RNA model, enabling stepwise growth of DNA inside the HIV-1 capsid. We implement this method within an integrative coarse-grained framework that combines a "bottom-up" capsid model with a "top-down" representation of the viral RNA/DNA genome. Our simulations phenomenologically capture and predict diverse capsid rupture pathways during reverse transcription. The resulting ruptured structures closely match previously identified cryo-ET images. We further perform an extensive analysis of the rupture process, examining its mechanistic and kinetic aspects as well as the role of capsid-DNA interactions. Our findings illuminate how different capsid-DNA conditions give rise to distinct rupture pathways, which differ from ruptures due to simple outward pressure expansion models from within the capsid. Significance StatementReverse transcription (RT) is a critical step in the life cycle of HIV-1, the causative agent of the AIDS pandemic. During RT, single-stranded RNA (ssRNA), encapsulated inside a mature capsid, is converted into double-stranded DNA (dsDNA). The rigidity of dsDNA generates increased internal pressure inside the capsid which, beyond a critical threshold, drives capsid uncoating, releasing the viral genome into the infected host cell. However, key mechanistic and kinetic aspects of this process remain unresolved. Here, using coarse-grained simulations, we elucidate the mechanistic basis of RT-induced capsid uncoating and quantify the role of capsid-genome interactions. Our results demonstrate that tuning these interactions may provide a potential antiviral strategy to inhibit infectivity by targeting RT.

biophysics↗

bioRxiv2026

Ineffectual Genomic Error Correction Under Environmental Perturbation Dynamically Regulates Mutational Supply and Robustness

Adaptive evolution depends on the supply of heritable variation, yet excessive mutation threatens viability by degrading essential molecular functions. Here, we show that this trade-off emerges naturally from the kinetic proofreading mechanism that controls replication fidelity. In our model, environmental shifts alter the optimal driving rate constant of proofreading enzymes, transiently elevating replication error rates and triggering rapid evolutionary change until a new fidelity optimum is reached. This produces alternating periods of stasis and rapid adaptation, consistent with punctuated equilibrium. We further show that coding-region length and population size jointly determine whether adaptation succeeds or mutational collapse occurs, reflecting the balance between mutation supply and error tolerance predicted by the drift-barrier principle. These results provide a molecular mechanistic basis for nearly neutral evolutionary dynamics and illustrate how genomic organization constrains long-term evolutionary resilience.

evolutionary biology↗

bioRxiv2026

Morphological parameters can capture emergent properties of dynamic disordered cytoskeletal networks

The actin cytoskeleton is an inherently disordered active system. the actomyosin cortex and reconstituted actomyosin systems are globally disordered, yet undergo transitions between distinct disordered states as parameters like motor and crosslinker concentration and filament length and rigidity change. In cells these changes are related to genetic mutations or differences in cell state and dictate fundamental biological processes. However, we dont have well established methods to detect and classify differences in disordered polymer networks. Image-based morphology techniques provide a non-invasive, high-throughput method of extracting information about a system. In this work we simulate biopolymer networks under varying conditions and develop and use morphological descriptors to construct trajectories in morphospace. Using statistical analysis we find that morphological descriptors are able to distinguish between different trajectories of the system, including differences not apparent to the eye. However, no single descriptor alone is able to capture all the differences in the simulated trajectories. Nematic order parameters typically perform the worst for our simulations while curvature and texture descriptors can collectively distinguish between dynamic trajectories. This work helps develop quantification of cytoskeleton dynamics for classification and data-driven modeling.

biophysics↗

bioRxiv2026

TRACKING EVOLUTIONARY COSTS OF IMMUNE ADAPTATION AGAINST SINGLE VERSUS COINFECTING PATHOGENS

Immunity against pathogens is costly and can adversely affect fitness through resource allocation or physiological trade-offs. Infection by multiple pathogens may further worsen the effects if hosts require the activation of multiple immune responses, which in turn can elevate the overall immunological costs. Poor body condition and stressful environments can also exacerbate these trade-offs. In this study, we experimentally tested these possibilities using Tribolium castaneum populations that were evolving against either a single or a set of coinfecting bacterial pathogens. Contrary to our expectations, none of these evolved beetles showed any measurable trade-offs between pathogen resistance vs major fitness traits, such as reproduction or lifespan. Instead, they appeared to increase reproductive success and resistance to starvation, suggesting improved body condition that could mask underlying fitness costs. However, evolved beetles showed reduced quinone production, an externally secreted antimicrobial defence, indicating trade-offs between internal vs external immunity. Finally, we identified reproductive costs only under limited resource availability, but not under suboptimal resource quality, suggesting that trade-offs can be highly condition-dependent. Overall, this study provides a unique comparison across pathogens and infection types, highlighting the importance of analysing variation in life-history traits within relevant ecological contexts to understand fitness costs of evolving immunity.

evolutionary biology↗

bioRxiv2026

HDAC5-encoded Microprotein NISM Mediates Nucleolar Formation and Ribosomal RNA Synthesis

Ribosome biogenesis is the process by which ribosomal RNA (rRNA) and ribosomal proteins are synthesized, processed, and assembled into functional ribosomes. This process begins in the nucleolus, a multiphase liquid condensate. Here, we discover an arginine-rich disordered nucleolar microprotein encoded within the HDAC5 5'-UTR that we termed Nucleolar Integrity and Stress Microprotein (NISM). NISM overexpression leads to impaired rDNA transcription, triggering nucleolar stress, p53 activation, and suppressed proliferation. NISM knockout causes disruption of nucleolar structure and also induces p53 activation. Mechanistically, NISM interacts with the DExH-box RNA helicase DHX9 and regulates its activities related to pre-rRNA synthesis. Computational analyses and polymer physics-based mathematical modeling revealed that NISM coordinates nucleolar formation and pre-rRNA synthesis by enhancing the liquid-liquid phase separation of DHX9. This study establishes NISM as a regulator of nucleolar biology and deepens our understanding of how disordered microproteins can facilitate the formation of membraneless organelles.

molecular biology↗

bioRxiv2026

Cryptic Sex in Leishmania Depends on SPO11 Paralogs

Genetic exchange in Leishmania is established, yet the molecular mechanisms enabling hybrid formation in sand flies remain poorly defined. In Leishmania, as in plants and several protists, two paralogs of the conserved meiotic endonuclease SPO11 are present, but their contribution to hybridization is unknown. Here, we dissect the roles of SPO11-1 and SPO11-2 during in vivo sand fly infections using targeted gene deletions, catalytically-dead mutants, expression analyses, and genome-wide characterization of hybrid progeny. We show that both SPO11 paralogs are essential for efficient hybridization: deletion of either paralog in both parents abolishes hybrid recovery, and catalytic inactivation fails to rescue mating. When only one parent lacks SPO11-1 or SPO11-2, hybrid formation is reduced in a strain-dependent manner, revealing asymmetric requirements for each paralog. Genomic analysis of hybrids from SPO11-deficient crosses reveals polyploidy and altered parental genome contributions, including unbalanced and near-balanced triploid configurations, indicating disrupted reductional processes. Together, these results establish SPO11-dependent DNA break formation as a core requirement for Leishmania hybridization and define distinct, strain-specific roles for the two SPO11 paralogs. Highlights{square} Leishmania encodes two non-redundant SPO11 paralogs that are differentially required in each mating partner for efficient hybridization. {square}The catalytic activity of SPO11 is essential, indicating conservation of its ancestral mode of action. {square}Loss of either paralog disrupts reductional division and prevents balanced genome segregation. {square}Cell fusion proceeds without SPO11, revealing a separation between fusion and meiosis-like functions. {square}SPO11-deficient hybrids show widespread aneuploidy and highly distorted parental genome contributions.

evolutionary biology↗

bioRxiv2025

An ancestral transmembrane transcription factor couples cell envelope regulation and the SOS response in Caulobacter crescentus

The DNA damage (SOS) response in bacteria involves derepression of a set of genes in order to activate mechanisms to tolerate stress, repair DNA and slow down cell division. While some of these genes are well characterized, many genes exist which are clearly induced by DNA damage but for which the function is unclear. In Caulobacter crescentus, the toxin-antitoxin (TA) system higBA and a closely associated downstream transcription factor (higX) are strongly induced as part of the SOS response, but the role of higX is unknown. We show that, unexpectedly, HigX functions independently of HigBA as a cell membrane-associated regulator and is toxic when overexpressed in filamentous cells. ChIP-Seq indicated that it binds to several promoters associated with cell envelope regulation. In cells with the SOS response constitutively activated, HigX was overproduced, but at the same time was unable to bind the majority of its target promoters. higX was highly conserved in genomic context among many alpha-proteobacteria, while higBA was only found upstream of it in a small number of Caulobacter genomes, including the universal laboratory strain C. crescentus NA1000. Compositional analysis suggested that higBA originated from a foreign source, while higX is likely ancestral to the alpha-proteobacteria. Our data support a model where dysregulation of HigX production and activity in filamentous {Delta}lexA cells contributes to cell envelope instability and antibiotic sensitivity. Thus, the protective effect of inhibiting cell division during the SOS response in order to repair the DNA, carries the hidden cost of interference with HigX-mediated cell envelope maintenance. Author summaryThe DNA damage (SOS) response in bacteria is key for their survival in harsh conditions, but the genes which are induced by this response and the molecular mechanisms involved are variable between different bacteria. We investigated the function of an uncharacterized SOS-induced gene in Caulobacter crescentus (higX) and found that it is a membrane-localized DNA binding protein, but that it did not help survival in DNA damage. Instead, it negatively affected cell viability when induced, unlike other SOS response genes. Genomic analysis showed that higX is highly conserved among alphaproteobacteria, but it is only under SOS control in a small number of genomes (including Caulobacter crescentus) where a toxin-antitoxin system and its SOS-regulatory promoter have been inserted upstream. This work uncovers HigX as a novel factor in cell envelope regulation, and shows that loss of cell shape regulation, eg. in filamentous {Delta}lexA cells, can influence the ability of transmembrane transcription factors to bind to their target genes.

microbiology↗

bioRxiv2025

The transcriptome of highly aneuploid senescent cells reveals interaction with the tumour microenvironment and a pro-survival role of Yorkie

Chromosomal instability (CIN), characterized by frequent changes in chromosome number and structure, is common in human carcinomas and often leads to aneuploidy. Drosophila has been instrumental in demonstrating that CIN can promote tumour growth and malignancy through aneuploidy-induced senescence, a state marked by cell-cycle arrest and high secretory activity. Despite extensive chromosomal heterogeneity, we show that these cells share a distinct transcriptional program, with most responses to aneuploidy and senescence regulated at the transcriptional level. Nearly 10% of the most upregulated genes encode secreted proteins of the senescence-associated secretory phenotype. Five of these proteins act additively, locally or systemically, to block proliferation and induce cell death in neighbouring tissues. This non-autonomo*us cell death feeds back to the tumour to enhance its growth, resembling super-competition and providing insight into tumour-host interactions relevant to human cancer. Teaser: Aneuploidy-induced senescent cells activate the pro-survival Hippo-Yorkie pathway and the SASP drives tumour host interactions

cancer biology↗

bioRxiv2025

Genome size and nucleotide skews as predictors of bacterial growth rate

Bacterial growth rates are constrained by genome replication, yet the role of replication kinetics in bacterial growth rates remains incompletely understood. Here, we examine if genome size, replichore organization, and nucleotide compositional asymmetry are reasonable predictors of bacterial doubling times. In free-living bacteria, both genome size and the length of the longest replichore are found to correlate positively with doubling time, pointing to an influence of replication dynamics on bacterial growth rates. Moreover, fast-growing bacteria are shown to exhibit stronger nucleotide compositional skew. Incorporating skew into the model substantially improves predictive accuracy, suggesting that compositional asymmetry in genomes may facilitate replication fork progression and thereby enhance growth rates. Based on these observations, we speculate that nucleotide skew may play a potential adaptive role in bacterial genome replication. To assess whether the observed association between genome architecture and growth rate reflects an evolutionary signature or a mechanistic link, we reconstructed ancestral states and found that the model fits ancestral traits more strongly, with predictive strength (R2) decreasing progressively along the evolutionary tree as successive speciations occur. We speculate that this association has been stronger early in bacterial evolution and became subsequently screened as organisms diversified and increased in ecological and physiological complexity.

genomics↗

bioRxiv2025

Lysyl oxidase-dependent bone marrow stiffening promotes neutrophil activation in diabetes

Persistent neutrophil activation contributes to the development of diabetic vascular complications in many organs including the retina. Past studies have implicated abnormal molecular or biochemical cues in neutrophil activation. Here we show that neutrophils can also be mechanically activated through an increase in bone marrow (BM) stiffness that results from diabetes-induced overexpression of matrix collagens and their crosslinker lysyl oxidase (LOX). Administration of LOX inhibitor {beta}-aminopropionitrile (BAPN) in diabetic mice concomitantly blocked BM matrix stiffening and neutrophil activation (superoxide generation and gp91phox upregulation), which predictably inhibited neutrophil cytotoxicity towards co-cultured retinal endothelial cells. Further, culturing neutrophils within BM-mimicking hydrogels of tunable stiffness indicate that matrix-localized and soluble LOX act synergistically to mechanochemically activate neutrophils in the BM. Thus, LOX-dependent changes in the BM physical environment offer a new mechanistic basis and therapeutic target for diabetic complications marked by neutrophil activation.

pathology↗

bioRxiv2025

Replication rate-information storage trade-off shapes genome architecture across domains

Genome size varies widely among organisms, from compact genomes of bacteria to vast and complex genomes of eukaryotes. In this study, we theoretically identify the evolutionary pressures that may have driven this divergence in genome size. We use a parameter-free model to study genome size evolution under selection pressure to minimize replication time and maximize information storage capacity. We substantiate this choice by demonstrating a correlation between replication time and genome size using literature data. We show that bacteria tend to reduce genome size, constrained by a single replication origin, while eukaryotes expand their genomes by incorporating multiple replication origins. We propose a connection between genome size and cellular energetics, suggesting that endosymbiotic organelles, mitochondria and chloroplasts, evolutionarily regulate the number of replication origins, thereby influencing genome size in eukaryotes. We substantiate this claim by showing a correlation between organelle count and genome size data. We argue that nucleotide skews, present in nearly all genomes studied, and are used to identify replication origins, directly influence DNA unzipping kinetics, and hence its replication time. This connection enables us to derive nearly universal observations, such as Chargaffs second parity rule and replichore symmetrization, as adaptive consequences. We argue that high skews lead to faster replication, and substantiate it by showing a correlation between skews and replication speed in bacteria. The model reproduces more evolutionary genomic observations, such as a general preference for deletions over insertions across domains, and elongation and high variance of genome size under reduced selection pressure for replication rate, an integral component of C-value paradox. We highlight the possibility of regulation of the firing of latent replication origins in response to cues from the extracellular environment, leading to the regulation of cell cycle rates in multicellular eukaryotes. Significance StatementUnderstanding the forces shaping genome architecture is a long-standing challenge in evolutionary biology. Our study demonstrates that the balance between replication speed, influenced by nucleotide skews, and information storage, constrained by cellular energetics, drives the divergence in genome size between bacteria and eukaryotes. By quantifying selection pressure as the ratio of replication time to genomic information storage capacity, we show that this pressure enforces adaptive constraints, giving rise to observed features such as symmetric replichores and Chargaffs second parity rule. These insights not only help us resolve an enduring evolutionary puzzle, but also offer a unified framework linking genome organization, cellular specialization, and even potential mechanisms underlying carcinogenesis.

genomics↗