arXiv:2605.15558v1 Announce Type: cross Abstract: High-resolution remote sensing imagery is critical for environmental monitoring, urban mapping, and land cover analysis, but its transmission is often hindered by limited bandwidth and high communication costs. Conventional pipelines transmit full-resolution pixel data, resulting in redundant and inefficient delivery. This paper proposes a text-guided remote sensing image transmission system that replaces complete high-resolution data with low-resolution images accompanied by compact textual descriptions. An onboard text generator produces spatial and semantic summaries, reducing the transmitted data volume to approximately 2\% of the original size. For ground-based reconstruction, a text-conditioned image restoration model is introduced, which leverages cross-modal learning to recover fine spatial details and maintain semantic coherence. Experimental results on the Alsat-2B, UC Merced Land Use, and Aerial Image datasets demonstrate that the proposed framework achieves reconstruction PSNRs of 16.36 dB, 26.87 dB, and 27.41 dB, respectively, enabling efficient and information-preserving image transfer for remote sensing applications. The implementation will be made publicly available at \href{https://github.com/haoyangofficial/textrssr}{GitHub}.
Science Journals
arXiv:2412.03932v2 Announce Type: replace Abstract: This paper develops a physics-informed scenario approach for safety verification of nonlinear systems using barrier certificates (BCs) to ensure that system trajectories remain within safe regions over an infinite time horizon. Designing BCs often relies on an accurate dynamics model; however, such models are often imprecise due to the model complexity involved, particularly when dealing with highly nonlinear systems. In such cases, while scenario approaches effectively address the safety problem using collected data to construct a guaranteed BC for the unknown dynamical system, they often require solving an optimization problem with substantial amounts of data. To address this, we propose a physics-informed scenario approach that selects data samples such that the outputs of the physics-based model and the observed data are sufficiently close. This approach guides the scenario optimization process to eliminate redundant samples and potentially reduce the required dataset size. We validate our approach through three case studies, showcasing its practical application in reducing the required data.
arXiv:2605.15983v1 Announce Type: new Abstract: We formulate the Resource-Constrained Project Scheduling Problem (RCPSP) as optimal search over the reachability graph of a Timed Transition Petri Net with Resources, using relative-delay tokens so that scheduling decisions correspond to transition firings in the induced state space. We solve the resulting problem with $A^*$ guided by a heuristic that combines Critical Path and resource-based lower bounds, and prove that it is consistent under our token-based time semantics. Experiments on the PSPLIB benchmarks show that the approach outperforms strong exact Mixed-Integer Linear Programming (MIP) baselines (SCIP, CBC) in both success rate and solve time. Per-instance analysis shows that heuristic search and MIP degrade along independent axes, resource tightness for $A^*$ and formulation size for MIP, with resource strength mediating which solver benefits from scale.
arXiv:2605.13169v2 Announce Type: replace Abstract: Multimodal large laboratory models (MLLMs) still struggle with spatial understanding under the dominant perspective-image paradigm, which inherits the narrow field of view of human-like perception. For navigation, robotic search, and 3D scene understanding, 360-degree panoramic sensing offers a form of supersensing by capturing the entire surrounding environment at once. However, existing MLLM pipelines typically decompose panoramas into multiple perspective views, leaving the spherical structure of equirectangular projection (ERP) largely implicit. In this paper, we study pano-native understanding, which requires an MLLM to reason over an ERP panorama as a continuous, observer-centered space. To this end, we first define the key abilities for pano-native understanding, including semantic anchoring, spherical localization, reference-frame transformation, and depth-aware 3D spatial reasoning. We then build a large-scale metadata construction pipeline that converts mixed-source ERP panoramas into geometry-aware, language-grounded, and depth-aware supervision, and instantiate these signals as capability-aligned instruction tuning data. On the model side, we introduce PanoWorld with Spherical Spatial Cross-Attention, which injects spherical geometry into the visual stream. We further construct PanoSpace-Bench, a diagnostic benchmark for evaluating ERP-native spatial reasoning. Experiments show that PanoWorld substantially outperforms both proprietary and open-source baselines on PanoSpace-Bench, H* Bench, and R2R-CE Val-Unseen benchmarks. These results demonstrate that robust panoramic reasoning requires dedicated pano-native supervision and geometry-aware model adaptation. All source code and proposed data will be publicly released.
arXiv:2502.04871v2 Announce Type: replace Abstract: The Landau-Lifshitz equation describes the dynamics of magnetization in ferromagnetic materials. Due to the essential nonlinearity and nonconvex constraint, it is typically solved numerically. In this paper, we developed a finite volume element method (FVEM) with the Gauss-Seidel projection method (GSPM) for the micromagnetics simulations. We provide the approximation error in space and depict the energy law when the FVEM is adopted. Owing to the GSPM for time-marching, the discrete system is decoupled component by component, making the computational complexity comparable to that of solving the scalar heat equation implicitly. This significantly accelerates real simulations. We present several numerical experiments to validate the theoretical analysis and the efficiency gain. Additionally, we study the blow-up solution and efficiently simulate the 2D magnetic textures using the proposed method.
arXiv:2605.16116v1 Announce Type: new Abstract: Developing and evaluating e-commerce web agents requires environments that preserve meaningful task structure while enabling controllable, reproducible, and scalable scientific comparison. Existing methodologies force a tradeoff: live storefronts provide realism but are non-stationary, difficult to inspect, and irreproducible, while hand-built sandbox benchmarks provide control but cover only a narrow range of layouts, catalogs, policies, and interaction patterns. We argue that the core bottleneck is methodological: the field lacks a scalable way to construct evaluation settings that are simultaneously realistic, diverse, controllable, inspectable, and reproducible. We introduce ShopGym, an integrated framework for realistic simulation and scalable benchmarking of e-commerce web agents. ShopGym is a framework for constructing e-commerce simulation environments and grounded benchmark tasks. Its simulation layer, ShopArena, converts live seed storefronts into self-contained sandbox shops through anonymized shop specifications and a staged, validated generation process. On top of these simulated storefronts, ShopGuru synthesizes benchmark tasks across seven skill categories, grounding each task in the shop's catalog, navigation structure, policies, and interaction affordances. Together, ShopArena and ShopGuru produce self-contained, resettable, inspectable, and stable evaluation artifacts that preserve structural properties and agent-evaluation signals relevant to shopping tasks. We validate the framework through graph-based structural analysis and agent-based behavioral evaluation with 224 generated tasks across six sandbox shops: three constructed with synthetic data and three with real data. Our results show that the synthetic shops preserve key structural properties of live storefronts, with agent performance on synthetic shops positively correlated with performance on live storefronts.
arXiv:2605.16129v1 Announce Type: new Abstract: The IoT's explosive growth has led to a massive number of connected devices, which demand high-speed and pervasive connectivity, posing significant challenges for current-generation wireless communication infrastructures. Considering our evolution toward 5G and beyond 5G (B5G) and 6G networks, providing scalable, reliable, and low-latency communication for billions of devices is therefore essential. Massive Multi-Input Multi-Output (Massive MIMO) is a promising technology for fulfilling the requirements of 5G, as it can spatially multiplex a large number of users and increase the spectral efficiency per user. In this paper, we focus on optimizing the performance of Massive MIMO systems in IoT connectivity and low-latency use cases for 5G and B5G. It studies key issues, including pilot contamination, energy efficiency, and user scheduling, among dense IoT deployments. In addition, it surveys all recent progress in channel estimation, hybrid beamforming, and machine learning-based resource allocation technologies for enhancing IoT scenarios related to Massive MIMO. Simulation-based results reveal the trade-offs between capacity, latency, and energy utilization, indicating an optimal operating point that ensures optimal performance for diverse IoT applications. The work concludes with a discussion of future research avenues, such as integration with cell-free designs, intelligent reflecting surfaces, or AI-based network orchestration for enhanced IoT capabilities.
arXiv:2605.15456v1 Announce Type: cross Abstract: Solving imaging inverse problems has usually been addressed by designing proper prior models of the underlying signal. However, minimizing the data fidelity term poses significant challenges due to the ill-conditioned sensing matrix caused by physical constraints in the acquisition system. Thus, preconditioning techniques have been adopted in classical optimization theory to address ill-conditioned data-fidelity minimization by transforming the algorithm gradient step to achieve faster convergence and better numerical stability. We extend the preconditioning concept beyond convergence acceleration and use it to improve reconstruction quality. We introduce DIPA: Distilled Preconditioned Algorithms, where a preconditioning operator (PO) is optimized using teacher-guided distillation criteria. Unlike standard model-compression KD, the teacher and student differ by the sensing operators available during reconstruction: the teacher uses a simulated, better-conditioned, and more informative sensing matrix, whereas the student uses the physically feasible sensing matrix. We design different distillation loss functions to transfer different properties of the teacher algorithm to the preconditioned student. The PO can be linear (L-DIPA), allowing interpretability, or non-linear (N-DIPA), parametrized by a neural network, offering better scalability. We validate the proposed PO design across several imaging modalities, including magnetic resonance imaging, compressed sensing, and super-resolution imaging.
arXiv:2605.15912v1 Announce Type: cross Abstract: Subcellular protein complexes and organelles exhibit diverse dynamic behaviors that reflect the mechanical constraints and organization of the intracellular environment. Although some structures follow classical Brownian motion, many display anomalous dynamics. The transitions between these regimes are increasingly recognized as critical for subcellular organization, yet how they influence pattern formation remains unclear. Here, we investigate the spatial arrangement of cilia on the apical surface of multiciliated cells (MCCs) in developing Xenopus laevis embryos, where coordinated ciliary beating depends on the precise organization of hundreds of centriole-derived basal bodies (BBs). Using quantitative confocal, high-resolution and high-speed TIRF imaging together with theoretical modeling, we show that BB trajectories undergo time-resolved transitions between diffusive and anomalous motion, with distinct regimes that correlate with apical surface expansion. During the early stages, actin remodeling facilitates the dispersal of BBs by providing a permissive, low-confinement environment. As development progresses, the actin network becomes increasingly cross-linked that constrains BB movement and promotes uniform spacing across the apical domain. Disruption of $\alpha$-actinin-1, a major actin cross-linking protein, impairs the integrity of the apical actin meshwork, weakens BB confinement, and disrupts regular spatial patterning, ultimately compromising the arrangement of BBs required for proper cilia alignment. Together, we show that progressive apical actin cross-linking coordinates BB positioning and regulates their dynamic state, guiding the shift from diffusive to confined motion. This transition in dynamics enables the emergence of a uniform BB pattern, which in turn ensures the aligned deployment of motile cilia necessary for effective directional fluid flow.
arXiv:2603.25101v2 Announce Type: replace-cross Abstract: We present a formulation of the problem of finding the smallest T -Count circuit that implements a given unitary as a binary search over a sequence of continuous minimization problems, and demonstrate that these problems are numerically solvable in practice. We reproduce best-known results for synthesis of circuits with a small number of qubits, and push the bounds of the largest circuits that can be solved for in this way. Additionally, we show that circuit partitioning can be used to adapt this technique to be used to optimize the T -Count of circuits with large numbers of qubits by breaking the circuit into a series of smaller sub-circuits that can be optimized independently.
arXiv:2604.22393v2 Announce Type: replace-cross Abstract: Hexagonal diamond (HD), an exotic carbon allotrope recently synthesized in bulk form, exhibits superior mechanical properties compared to cubic diamond (CD) and holds promise for advanced industrial and quantum applications. Using first-principles calcu-lations, we systematically investigate intrinsic defects, extrinsic dopants, and defect complexes in HD. Our study shows that VC dominates intrinsic conductivity, while Ci is unstable. Among extrinsic dopants, boron acts as a benign acceptor enhancing p-type conductivity, whereas nitrogen and phosphorus serve as effective donors for n-type conductivity. Group II and Group IV dopants, however, introduce high formation energies or neutral charge states with limited impact. Furthermore, VC, MgC and XV defect com-plexes display multiple spin and charge states within the HD band gap, highlighting their potential as color centers for hosting qubits. These results not only clarify the defect physics of HD but also demonstrate its broader implications for conductivity engineering and quantum technologies.
arXiv:2605.15350v1 Announce Type: cross Abstract: Stochastic compositional optimization minimizes objectives of the form $\min_{\bm{x} \in \mathcal{X}} F(\bm{f}(\bm{x}), \bm{x})$, where $\bm{f}$ is accessible only through noisy stochastic queries. Existing methods for this problem assume that the outer function $F$ is continuously differentiable, which excludes many practically important applications such as robust max-of-losses, Conditional Value-at-Risk, and norm regularizers. We propose the Hybrid Momentum Stochastic Frank--Wolfe algorithm, which drops the smoothness assumption on $F$. By combining a momentum-based Jacobian tracker with a Taylor-corrected function tracker, the algorithm feeds an entire stochastic linearization -- rather than a single gradient -- into a generalized linear minimization oracle. We establish an $\mathcal{O}(K^{-1/4})$ convergence rate in the generalized Frank--Wolfe gap for non-convex objectives with $L_F$-Lipschitz outer functions, matching the optimal complexity for projection-free single-sample stochastic methods under expected smoothness. The analysis extends to heavy-tailed noise oracles with bounded $r$-th moments for $r \in (1, 2]$ and recovers the deterministic rates of Vladarean et al (2023) as the noise vanishes.
Maximum utilization of existing genetic variability in a breeding program depends on the efficient classification of the inbred lines into heterotic groups, particularly under stress conditions. This study applied practical breeding approaches to determine the mode of genetic inheritance for Striga resistance and proposes a weighted heterotic grouping method based on the general combining ability of multiple traits (WHGCAMT) and compares its effectiveness with other existing methods in classifying the inbred lines into heterotic groups in Striga-infested and optimum environments. Using Diallel design IV, 300 crosses were generated from 21 inbred lines and 4 standard testers. The crosses, along with six checks, were evaluated in an 18 x 17 alpha lattice design with two replications at two locations, in both artificial Striga-infested and Striga-free environments. The inbred lines were genotyped using DArTtag SNP markers. Phenotypic and genotypic data were analyzed using R. Analysis of variance revealed significant mean squares for hybrid, general combining ability (GCA), specific combining ability (SCA) and their interactions with environment. Significant positive and negative GCA and SCA effects were detected for grain yield and other measured traits. However, a larger proportion of additive gene action than non-additive gene action was observed for grain yield and most measured traits. The analysis of molecular variance also showed substantial genetic differences within and between clusters. Except for HSCA, the mean grain yield between the inter-group and intra-group hybrids was significant for each method. Pairwise comparison of the inter- and intra-group hybrids of all the methods showed significant differences between the WHGCAMT and all other methods in most cases. WHGCAMT consistently produced higher-yielding inter-group hybrids and lower-yielding intra-group hybrids, achieving breeding efficiency improvements of 55.8%, 4.3%, 15.7%, and 11.4% over the HSCA…
Anxiety has been extensively studied in relation to memory, yet its dynamic association with spatial episodic memory in naturalistic clinical settings remains largely unexplored. We developed an anxiety-spatial-memory EMA protocol (asm-EMA) and deployed it in 30 epilepsy patients undergoing inpatient EEG monitoring, delivering combined momentary anxiety ratings and a validated spatial memory task pseudo-randomly every 90-150 minutes across multiple days. Subject-level asm-EMA means and session-to-session variability both correlated significantly with standard neuropsychological assessments, supporting the clinical validity of our design. Elevated within-person STAI-6 was selectively associated with faster retrieval responses, yet spatial memory accuracy was independent of all three anxiety measures, suggesting a shift in response strategy rather than memory impairment. Within-day anxiety showed short-term carryover between consecutive sessions, with little persistence beyond the next session. The asm-EMA protocol provides a feasible, autonomous framework for capturing moment-to-moment anxiety-memory dynamics in naturalistic settings.
Accurate and reproducible assessment of foliar disease severity is essential for evaluating the performance of heterogeneous plant communities and understanding host-pathogen interactions. However, traditional visual scoring methods remain subjective, with limited precision, and difficult to scale in large phenotyping experiments. Here, we present a semi-automated image analysis workflow designed to quantify multiple foliar disease symptoms simultaneously on wheat flag leaves sampled from varietal mixtures. The workflow combines three methodological components: (i) a standardized protocol for leaf sampling and imaging, (ii) supervised machine learning segmentation using Random Forest implemented in Ilastik to classify multiple symptoms (powdery mildew and yellow rust), and (iii) a graphical user interface facilitating pipeline deployment by non-specialist operators. To evaluate the influence of image representation on classification performance, four color spaces (RGB, HSV, HLS, LAB) were systematically compared. The approach was validated using images of durum wheat flag leaves collected from a field experiment assessing eight-way varietal mixtures under natural fungal pressure. Cross-validation against manually annotated images demonstrated high segmentation accuracy across all symptom. Comparison among color spaces revealed only minor differences in performance. Overall, this workflow offers a cost-effective, annotation-efficient and reproducible alternative to deep learning approaches, leveraging open-source and actively maintained tools while requiring limited training data and enabling objective, reproducible and scalable disease phenotyping.
RNA-seq experiments routinely identify thousands of differentially expressed genes, but translating these into biological insights and therapeutic hypotheses often requires integrating multiple tools. Existing web platforms such as iDEP, NetworkAnalyst, and GEPIA2 address individual steps, differential expression, network visualization, or TCGA queries, but lack a unified environment spanning raw data processing to clinical and pharmacological interpretation. TransXplorer (https://www.transxplorer.org) is a freely available web platform that addresses this limitation by integrating the complete RNA-seq analytical workflow. It supports processing from raw FASTQ files using HISAT2 or Salmon, as well as direct GEO dataset import with automated metadata handling. Differential expression analysis is implemented via DESeq2, edgeR, and limma-voom, followed by functional enrichment across more than 1,800 species using Bioconductor resources. Batch effects are automatically detected and corrected using a composite of PVCA, kBET, and Silhouette metrics without requiring predefined batch annotations. Downstream analyses include co-expression network construction (WGCNA), protein-protein interaction mapping (STRING), cell-type deconvolution, and transcription factor inference using integrated DoRothEA and TFLink resources. The platform further links gene signatures to drug candidates through DGIdb and OpenTargets and enables survival and tumour-normal comparisons across TCGA cohorts. Application to cardiac endothelial differentiation (GSE151427) and kidney renal papillary cell carcinoma (TCGA-KIRP) datasets demonstrates accurate batch correction, biologically consistent pathway enrichment, recovery of expected cell-type proportions, and identification of clinically relevant genes and drug candidates. TransXplorer is freely available without a login.
Chromosome-scale assemblies are increasingly available for non-model organisms, but functional annotation remains limited when deep evolutionary divergence erodes primary amino-acid sequence identity even though protein structural similarity can remain conserved. We present a hybrid annotation framework that decouples gene-model discovery from cross-species similarity assignment by combining Evo2-based ab initio prediction of exon-intron structures with ESM-2 protein-embedding-based structural similarity mapping. Applied to the sea lamprey, the framework derives high- or medium-confidence cross-species similarity assignments for 73,485 Evo2-derived translated protein models, including 35,395 high-confidence calls, and expands the deduplicated structural catalog to 31,286 loci, including 20,871 additions absent from the Ensembl baseline. A joint alignment-structure classification identifies 21,391 structurally supported catalog loci that a fixed human DIAMOND protein search does not confidently assign on its own, including 21,184 loci with no detectable human protein-sequence match and 207 loci with only low-confidence matches in the classical 20-30% amino-acid-identity twilight zone. These rescue-space totals describe catalog loci rather than validated one-to-one human-absent genes. In a single-cell RNA sequencing application, a stricter UTR-aware Ensembl+Evo2 reference improves gene recovery and expands the interpretable feature space of the lamprey immune compartment relative to the Ensembl baseline. This enables more resolved annotation of four transcriptionally defined immune cell states, including VLRA+-associated T-like and VLRB+-associated B-like programs together with oxidative iron-handling and iron-associated VLR-linked states. Together, these results show that structural protein signal often persists beyond the limits of pairwise sequence alignment and that an embedding-based annotation layer can extend that signal to improve downstream comparative and…
Terpenes constitute the largest and most structurally diverse class of plant secondary metabolites, with critical roles in plant-environment interactions and broad industrial applications. Although nuclear genome engineering of terpene pathways has been extensively explored, chloroplast genome engineering remains largely undeveloped, with all reported studies restricted to the model plant Nicotiana. Here we report successful chloroplast genome engineering for diterpene production in the crop plant potato (Solanum tuberosum). First, we identified the trnT/trnL plastomic locus as optimal for minimizing integration-associated growth penalties. Insertion of a bifunctional diterpene synthase gene into this plastomic site yielded transplastomic plants with successful diterpene production, but with reduced growth. The co-expression of a geranylgeranyl diphosphate synthase gene to enhance precursor supply restored normal growth while elevating diterpene accumulation. Transplastomic plants were otherwise agronomically comparable to wild-type. This work expands chloroplast engineering as a viable strategy for terpene pathway engineering in crop improvement and high-value terpene production.
Phyllanthus niruri (Phyllanthaceae) is a medicinally important herb known for producing phyllanthin, a bioactive dibenzylbutane lignan with reported hepatoprotective and antioxidant properties. However, the biosynthetic basis of phyllanthin production remains unresolved, largely due to the absence of a reference genome for the species. We report a chromosome-scale assembly of P. niruri generated by integrating PacBio HiFi long reads and Illumina short reads, followed by reference-guided scaffolding against Phyllanthus cochinchinensis. The assembly has an L50 of 7 and 97.6% BUSCO completeness. Annotation predicted 19,254 protein-coding genes, of which 91.1% were functionally annotated, with phenylpropanoid biosynthesis emerging as the most enriched specialized-metabolism pathway in the genome. Using pathway-guided genome mining, structural similarity analysis, and comparative metabolic reconstruction, we propose a putative biosynthetic pathway for phyllanthin originating from the phenylpropanoid-lignan branch through secoisolariciresinol-like intermediates followed by terminal O-methylation reactions. A total of 305 unique candidate genes associated with the proposed pathway were identified, including expanded families of dirigent proteins, peroxidases, secoisolariciresinol dehydrogenases, and O-methyltransferases. Comparative transcriptomic analyses across related Phyllanthus species further supported the proposed pathway through coordinated expression of lignan-associated genes and tissue-specific enrichment of O-methyltransferases. This work provides the first reference genome for P. niruri and a prioritized candidate gene set for functional characterization of phyllanthin biosynthesis.
Holcosus orcesi, the Orces Blue Whiptail, is a Critically Endangered lizard endemic to the upper Jubones River basin in southern Ecuador. Restricted to a narrow elevational range within semi-arid Andean shrublands, it represents one of the few montane members of a predominantly lowland lineage. Here we present the first high-quality reference genome for H. orcesi, generated using Oxford Nanopore Technologies long-read sequencing. The assembly spans 1.68 Gb across only 91 contigs, with an N50 of 76.2 Mb and a BUSCO completeness of 96.8%, making it among the most contiguous and complete squamate genomes to date. Structural annotation predicted 25,682 genes, of which 85% showed homology to known proteins and 45% were assigned Gene Ontology terms. Repetitive elements accounted for 46.3% of the genome, with LINEs representing the predominant class. This genome provides a foundational resource for future evolutionary, comparative and conservation-genomic research of H. orcesi and other mountain reptiles, enabling studies of population genomics, local adaptation, and genomic erosion in isolated populations. By expanding the genomic representation of tropical montane reptiles, this work helps address longstanding phylogenetic and geographic gaps in global biodiversity genomics and provides a foundation for evidence-based conservation of H. orcesi and related taxa.
Measles virus remains a significant global health threat, and despite the availability of an effective vaccine, measles cases continue to increase worldwide in recent years. Genomic surveillance has become an essential tool for monitoring virus circulation and investigating outbreaks. Here, we describe a wet laboratory method for whole genome sequencing of measles virus using a tiled amplicon approach and Illumina sequencing technology. A previously published Oxford Nanopore based tiled primer scheme was adapted to include both circulating measles genotypes and for use on the Illumina platform. Two Illumina library preparation kits, Illumina DNA Prep (IDP) and Nextera XT (XT), were evaluated for performance. The IDP kit demonstrated more complete genomes and consistent genome coverage compared with XT. Using quantified reference genomes, the limit of detection was determined to be 10,000 genome copies for genotype B3 and D8. Sequence accuracy was evaluated using previously characterized clinical samples and showed high concordance. This method provides a reliable and sensitive approach for measles virus whole-genome sequencing using Illumina platforms and is suitable for genomic surveillance applications.
Abstract As part of preparedness activities supporting pathogens classified under the UK High Consequence Infectious Diseases (HCID) framework, we previously evaluated both a whole-genome tiling amplicon sequencing scheme and a pan-viral hybridisation capture approach (TWIST-CVRP) for sequencing Andes virus (ANDV). In light of the recent outbreak, we make available viral sequencing datasets generated using a historical ANDV isolate (Chile, 1997). In addition, we provide an evaluation of tiling amplicon scheme performance and present recommended primer updates informed by in silico comparison with the recently released outbreak genome. These datasets are intended to support benchmarking, validation, and optimisation of bioinformatic pipelines across the community.
Biological sequences are known to be not random. Thus, the comparison of in silico restriction fragment distributions of random and biological sequences may be an indicator of this non-randomness. Our analyses show that for most of the tested combinations of restriction enzyme and genome sequence the fragments per Megabase of the biological sequence deviate at least more then 10% from the corresponding random sequence. This deviation goes into both directions, i.e. clearly increased values are as common as clearly decreased values. Although there is no species- or restriction-enzyme-specific effect, a clear impact of the GC content both of the restriction site and of the genome sequence can be seen. In contrast to the random sequences, the genome sequences show distinct peaks in their fragment length distributions, hinting to repetitive elements such as transposons.
As one of the earliest-diverging multicellular eukaryotic lineages, the bladed Bangiales (Rhodophyta) possess a deep evolutionary history with a central role in the multi-billion-dollar global seaweed aquaculture industry. Although North Atlantic representatives are emerging candidates for regional mariculture, the scarcity of high-quality genomic resources for these taxa hinders both fundamental research and commercial optimization. To address this, we present the first chromosome-level genome assemblies for two native European species: Porphyra dioica (150.44 Mbp) and Porphyra linearis (95.22 Mbp). By integrating Oxford Nanopore Technologies (ONT) long-read sequencing with Hi-C proximity ligation, we generated highly contiguous nuclear genomes resolved into five chromosomes. Structural gene models were predicted through the BRAKER3 pipeline, identifying 12,548 and 10,382 protein-coding genes for P. dioica and P. linearis, respectively. Subsequent homology-based functional annotation characterized 57.4% and 59.8% of these predicted proteins. Supplemented by circularized organellar genomes, these reference genomes provide a critical framework for future research, enabling comparative studies of Atlantic-Pacific divergence and facilitating the development of selective breeding programs for sustainable European aquaculture.
LINE-1 retrotransposons are the only autonomous mobile elements still active in human genomes and remain a potent source of mutation, genome remodeling, and disease risk. However, young, full-length, potentially active copies (the elements most likely to shape present-day genomes) have been largely inaccessible to population-scale analysis because they are long, repetitive, and poorly resolved by short-read sequencing. Here, we use 47 phased long-read assemblies from the Human Pangenome Reference Consortium, representing 94 haplotypes, to build an allele-resolved view of recent human LINE-1 evolution. We identify 13,617 LINE-1 alleles with intact ORF1 and ORF2 across 683 unique insertion sites, revealing that every genome carries a distinct repertoire of potentially active source elements. These intact LINE-1 profiles recapitulate broad human population structure while exposing a large, rare, and population-enriched reservoir of mobile-element diversity missed by single-reference approaches. We also resolve a structurally variable chromosome 11 LINE-1 array, demonstrating that local duplication and rearrangement can amplify LINE-1 sequence independently of canonical retrotransposition. By comparing full-length LINE-1 sequences, we define activity signatures that separate ancient remnants from recently expanding lineages and uncover young LINE-1 groups whose activity is not fully explained by canonical subfamily labels. Sequence-network analyses further reveal a dynamic history of lineage turnover, in which successful source elements rise, seed new insertions, and are replaced by descendants marked by specific nucleotide changes. Together, these data transform human LINE-1s from a repetitive background into a resolved evolutionary system, linking insertion polymorphism, coding potential, population history, and recent retrotransposon adaptation. Our findings establish the human pangenome as a framework for discovering active source elements and for testing how mob…