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bioRxiv2026

Analysing antimicrobial resistance mobility patterns using a diverse dataset of over 8000 bacterial species

2.Advances in genomics have enhanced surveillance of antimicrobial resistance (AMR), yet the factors governing resistance gene mobility, and therefore their risk of spread, remain poorly characterized. Here, we analyzed AMR gene distributions across thousands of bacterial genomes from NCBI RefSeq, encompassing clinical, agricultural and environmental isolates, to quantify associations with plasmids and predicted mobile genomic islands. AMR genes were identified using the Resistance Gene Identifier, and in addition to plasmid identification, mobile chromosomal elements were predicted using IslandViewer 4. Analysing both the full dataset and subsets of data with corrections for sampling bias, we show that known AMR genes are significantly enriched in mobile regions overall. However, stratification by resistance mechanism supported marked heterogeneity: certain drug classes and mechanisms are strongly associated with mobile elements, whereas others are predominantly chromosomal and non-mobile. Notably, mechanisms with specialized functions showed higher mobility, consistent with their role as "ecological public goods" that need not be present in all cells to confer community-level benefit. Differences were also observed across bacteria with distinct cell envelope structures. Together, these findings lay the groundwork for predictive models of AMR gene mobility and provide a framework for incorporating gene-level mobility into AMR risk assessment and antimicrobial stewardship policy. 3. Impact statementUnderstanding which antimicrobial resistance (AMR) genes are most likely to spread is central to managing resistance in clinical, agricultural, and environmental settings. This study reports a large-scale, systematic analysis of antimicrobial resistance (AMR) gene mobility across >8000 bacterial species, spanning diverse clinical and other ecological sources. By linking resistance mechanisms to their genomic location (plasmids, genomic islands, or the rest of chromosomes), our study demonstrates that AMR genes are overall enriched in mobile elements, but that mobility varies substantially by mechanism and bacterial context. In particular, functionally specialized resistance mechanisms are more frequently associated with mobile elements, consistent with an "ecological public goods" model for AMR dissemination. These findings extend beyond gene-specific case studies to identify generalizable patterns that help explain why some resistance determinants spread more readily than others. The breadth of relevance spans clinical microbiology, evolutionary biology, environmental microbiology, agri-foods, and public health. The work provides evidence supporting an improved framework for AMR mobility risk assessment, and antimicrobial stewardship strategies, with direct implications for forecasting the durability of existing and future antibiotics. 4. Data summaryThe complete dataset and analysis code used to generate the results can be accessed via the Open Science Framework (OSF) repository under DOI:10.17605/OSF.IO/WE3TX

genomics↗
bioRxiv2026

Behavioral, Physiological, and Transcriptional Mechanisms of Memory in a Synthetic Living Construct

Synthetic living constructs, which lack the long histories of selection in ecological contexts that shape behaviors of conventional organisms, offer an important complement to traditional studies of learning. Could novel biobots exhibit sensing and memory of experiences? Here, we investigated the effects of chemical stimuli on basal Xenobots - autonomously motile entities derived from Xenopus embryonic ectodermal explants (with no additional sculpting or bioengineering). We quantified and characterized the coordinated ciliary activity that generates fluid flow fields guiding the trajectory of Xenobot motion. We also show distinct and specific changes in Xenobot behavior after brief exposure to Xenopus embryonic cell extract and to ATP. These two experiences produced distinct, long-term, stimulus-specific memories, detectable through both transcriptional and physiological signatures. Exposure to specific environmental stimuli induced alterations in the spatiotemporal patterns of calcium signaling across Xenobots. Together, these data lay a foundation for characterizing the capabilities of synthetic cellular collectives to sense and discriminate among stimuli, as well as store functional information in a non-neural context. Understanding behavioral competencies in novel, non-neural systems have broad implications across evolutionary biology, behavioral science, bioengineering, and bio/hybrid robotics.

synthetic biology↗
bioRxiv2026

Protocol for genotyping cephalopod sex using a skin swab and quantitative PCR

The coleoid cephalopods (octopus, cuttlefish, and squid) are emerging model organisms for neuroscience, development, and evolutionary biology. Determining their sex early in life is critical for population management and controlled experiments. Here, we present a protocol to non-invasively determine the sex of multiple cephalopod species as young as 3 hours post-hatching using a skin swab and quantitative PCR (qPCR). We describe steps for designing qPCR primers, swabbing live animals, extracting DNA, running the qPCR, and analyzing the results. For complete details on the use and execution of this protocol, please refer to Rubino et al.1 HighlightsO_LISwab live cephalopods as early as 3 hours post-hatching C_LIO_LIExtract DNA from cephalopod skin swabs C_LIO_LIPerform qPCR-based sex determination C_LIO_LIDesign and validate qPCR primers for new species C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=190 SRC="FIGDIR/small/715692v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@10797f5org.highwire.dtl.DTLVardef@18961a2org.highwire.dtl.DTLVardef@690df0org.highwire.dtl.DTLVardef@1122899_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗
bioRxiv2026

Mount Fuji's stubby peak: the genotypic density of additive landscapes near maximal fitness

Additive fitness landscapes--also called Mount Fuji landscapes--are the simplest and most widely used models of sequence-function relationships. As such, they play essential roles across multiple areas of biology, including evolutionary theory, quantitative genetics, gene regulation, and protein science. One of the most basic properties of any fitness landscape is its genotypic density--the number of sequences near a given fitness value. Understanding this density is especially important near fitness peaks, as it quantifies the supply of high-fitness genotypes. Here I study the genotypic density of additive landscapes near fitness peaks. Although this density is well known to be approximately Gaussian near the middle of the fitness range, its behavior near maximal fitness has not been reported. I begin by deriving a saddle-point approximation that accurately describes the genotypic density of additive landscapes over virtually the entire fitness range. I then show that the log density follows a power law near maximal fitness, with the exponent determined by how much the best allele at each position outperforms its nearest competitor. This power-law behavior holds over a substantial fraction of fitness values, besting the Gaussian approximation on both simulated and empirical landscapes across roughly a quarter to a third of the fitness range. Under certain conditions this behavior also extends to globally epistatic landscapes (defined as nonlinear functions of one or more additive traits), though with a reduced range of validity. These findings advance our understanding of one of the most fundamental models of sequence-function relationships. In particular, they reveal that the uppermost reaches of Mount Fuji landscapes, rather than being sharply peaked, are actually quite stubby.

evolutionary biology↗
bioRxiv2026

Hybrid crosses reveal a cell-type-specific landscape of mouse regulatory variation

Understanding the genetic architecture of gene expression is fundamental to evolutionary biology and medicine. As part of the IGVF Consortium, we present a single-nucleus RNA-seq resource of 5.3 million nuclei across eight tissue groups, featuring seven F1 hybrids from C57BL/6J dams crossed with the other Collaborative Cross founder strains for comparison against parental strains. We identify 25,864 genes (91% of those detected) exhibiting non-conserved regulatory behavior in at least one of 92 cell types in one or more crosses. Our results show that while cis-acting variation primarily drives divergence, trans-acting effects are substantially more cell-type specific and sensitive to tissue environment. Notably, bulk tissue analyses frequently mask these signals, particularly in smaller populations such as astrocytes. Furthermore, increasing genetic divergence primarily expands the landscape of cis-acting variation, while trans-acting effects remain stable across genetic distances within species. This atlas establishes a foundational framework for decoding the complex interplay between genetic variation and cell-type-specific regulation across the mammalian body.

genomics↗
bioRxiv2026

Genomic insights into polyketide toxin synthesis and algal symbiosis using high-quality genome sequences of the early divergent hexacorallian genus Palythoa (Cnidaria, Zoantharia)

Palytoxin, first isolated from Palythoa toxica, is among the most potent marine toxins known. Despite decades of biochemical investigation, genetic bases underlying its potential biosynthesis in Palythoa remain unresolved. Here we present four high-quality genome assemblies of Palythoa species, including Palythoa cf. toxica, and integrate these with a chromosome-scale genome assembly of P. caribaeorum. Performing comparative genomic analyses, we screened for candidate genes potentially involved in palytoxin biosynthesis and examined patterns of genome evolution. Unexpectedly, we identified only two classes of ketosynthase (KS) domain-containing genes in Palythoa: fatty acid synthases (FAS) and bacterial-like polyketide synthases (PKSs). Contrasting other anthozoans, animal FAS-like PKS (AFPK) genes common to all Palythoa species were not detected. We found no evidence for lineage-specific expansion of PKS genes unique to Palythoa, suggesting that if palytoxin/palytoxin-like molecule biosynthesis is host-encoded, it may involve functional modification or co-opting pre-existing FAS and/or bacterial-like PKS pathways. Comparative analyses revealed expansions of gene families associated with transport and binding functions in Palythoa, potentially reflecting molecular adaptations linked to their sand-incorporating body structure. We identified TPT1 and CLEC4A as rapidly evolving genes in multiple Palythoa species, consistent with possible roles in growth regulation and host-microbe interactions. Additionally, comparison between azooxanthellate and zooxanthellate species revealed mutations within conserved protein domains of LePin, which has been implicated in cnidarian endosymbiosis, suggesting lineage-specific modifications associated with symbiotic state. This study establishes a foundation for zoantharian genomic research, provides insights into lineage-specific genomic signatures, and advances molecular and evolutionary biological knowledge of this ecologically important group.

genomics↗
bioRxiv2026

A practical pipeline for volume rendering of trillion-voxel tomographic data

Recent advancements in tomography produce imaging data of geological materials (rocks and fossils) at trillion-voxel scales with multi-channels. Such high-resolution datasets are potentially keys to unveil evolutionary biological information with various shapes and sizes that have not been ever discovered. Volume rendering is an ideal visualization approach for them because it treats all voxels without relying on user-defined surface boundaries. However, these large-scale real-world tomographic data have rarely been volume-rendered at their native resolution, limiting the examination of rich morphological information. Here, we demonstrate a de facto standard volume-rendering pipeline running on a graphical processing unit (GPU)-equipped supercomputing system toward multi-channel, trillion-voxel tomographic data. Our workflow preserves original resolution, capturing detailed morphological information spanning microscopic to macroscopic scales. Systematic comparison of node types shows that GPU memory, rather than host memory, is the primary bottleneck. Our results establish a baseline for large-scale, multi-channel volume rendering of real tomographic data and demonstrate its applicability to geological samples. This work is presented as a practical demonstration of large-scale volume visualization.

paleontology↗
bioRxiv2026

Mechanical interaction enables a collective mode of protocell proliferation

The proliferation of primitive life-forms (known as protocells) without sophisticated cell-division molecular machineries has been an intriguing question in evolutionary biology, synthetic biology, and living matter physics. While various modes of protocell proliferation at the individual level have been proposed, the growth dynamics of protocell colonies (i.e., protocolonies) received less attention. Here we chose to study this question in protocolonies consisting of densely packed protocells derived from wall-deficient L-form bacteria. We discovered that protocolonies proliferated robustly under spatial confinement, while isolated protocells failed to divide and eventually experienced membrane rupture due to imbalance of surface and volume growth. Combining results from quantitative imaging and computational modeling, we attributed this unexpected finding to mechanical shearing between densely packed protocells driven by their growth activities; such mechanical shearing enhances cell deformation, thereby enabling cell division and sustaining population growth in a protocolony. Our study reveals a unique role of self-generated mechanical stresses in the lifestyle of primitive life-forms. The findings may help to understand and control the collective growth dynamics of synthetic protocells or active droplets.

biophysics↗
bioRxiv2026

Chromosome-scale genome assemblies of duckweeds provide insights into genomic plasticity, aquatic adaptation and morphological reduction

BackgroundDuckweeds (Lemnaceae) present a striking example of convergent genome evolution following the return from land to water. As the smallest and fastest-growing angiosperms, they exhibit extreme morphological reduction yet retain remarkable genomic plasticity through recurrent interspecific hybridisation, chromosomal rearrangements, and selective gene-family remodelling. The genomic mechanisms that distinguish this secondarily aquatic lifestyle from terrestrial ancestors, and whether these changes are convergent with other aquatic lineages such as seagrasses, have remained incompletely resolved. ResultsHere we report chromosome-scale genome assemblies for four duckweed species, Spirodela polyrhiza, Lemna minuta, Lemna japonica, and Lemna aequinoctialis, generated with PacBio HiFi long reads and Omni-C chromatin conformation capture. These assemblies include the first genomic characterisation of an unresolved hybrid lineage (L. aequinoctialis x) that harbours a previously uncharacterised 3.5 Mb reciprocal translocation between subgenomes, as well as confirmation of the allodiploid origin of L. japonica. Comparative phylogenomics with land plants and the seagrass Zostera marina reveals a coherent, non-random programme of gene loss: effector-triggered immunity (ETI) components (EDS1 and PAD4) and the high-affinity nitrate transporter NRT2 are convergently absent across duckweeds and Zostera marina, consistent with relaxed pathogen pressure and abundant dissolved nutrients in aquatic habitats. In contrast, secondary-metabolite biosynthesis pathways for flavonoids, anthocyanins, flavones and flavonols are retained or expanded despite overall genome compaction. ConclusionThese findings illustrate how the return to aquatic environments following terrestrialisation shaped duckweed genome evolution through convergent gene loss and selective pathway retention, and provide high-quality genomic resources to support future research in plant evolutionary biology and biotechnology.

genomics↗
bioRxiv2026

MUSE enables cross-species multi-omics integration that incorporates transcriptional regulatory modules

Recent advances in evolutionary biology and biomedical research have promoted comparative analyses of cellular states and developmental processes across species, leading to the development of numerous cross-species alignment methods based on scRNA-seq data. However, alignments relying solely on RNA expression are strongly driven by lineage signals and cell typespecific transcriptional programs. As a result, they are limited in their ability to identify conserved regulatory modules across species and to compare regulatory logic beyond developmental lineages, thereby constraining biological interpretability. Meanwhile, recent technological developments have enabled the acquisition of multi-omics data, including chromatin accessibility, making it increasingly feasible to analyze and interpret conservation at the level of regulatory modules across species. Nevertheless, computational methods that can integratively handle such heterogeneous omics data and enable cross-species comparative analysis in a unified framework remain insufficiently established. To address this challenge, we propose Multi-omics Unified embedding across Species (MUSE), a novel framework for integrating multi-omics data across species. MUSE constructs a graph that captures relationships among features both within and across species, and learns a shared latent space based on this graph structure. By leveraging this integrated graph-based representation, MUSE enables cross-species alignment that preserves species-specific characteristics while reflecting similarities not only at the level of gene expression and chromatin states but also at the level of regulatory modules.

bioinformatics↗
bioRxiv2026

The impact of long-read sequencing on fungal genome assemblies: progress and disparity

Fungal genomics has expanded rapidly over the past 30 years, and recently the pace and breath has further quickened for many taxa, although many taxonomic gaps persist. With three decades of rapid growth, fungal genomics now merits a re-examination of its history, progress, and unresolved taxonomic gaps. Here, we review the development of fungal genomics from early efforts such as the Fungal Genome Initiative to current progress driven by third-generation long-read sequencing. We have compiled and summarised publicly available fungal genomes to highlight trends in assembly quality, adoption of long-read technologies, and taxonomic representation. Notably, substantial phylogenetic gaps remain, particularly outside Dikarya, and significant challenges persist for unculturable taxa. This review identifies priorities for the fungal community, including: (1) coordinated efforts to close major taxonomic gaps across the fungal tree of life; (2) improved repository metrics to facilitate identification of high-quality assemblies; and (3) improved and standardised genome annotation which is lacking for most assemblies. Together, these steps will support the development of reliable genomic resources that capture the full breadth of diversity across the fungal kingdom, generating foundational data for comparative genomics, evolutionary biology, functional studies, genetic studies and applied research.

genomics↗
bioRxiv2026

A horizontally transferred fungal deubiquitinase facilitates insecticides resistance in whitefly

Horizontal gene transfer (HGT) has enabled insects to acquire novel genetic material that can fuel adaptation to environmental change. However, the role of HGT in the evolution of insecticide resistance remains poorly characterised. Here, we identify BtUCH19, a fungal gene that has integrated into the genome of the global pest Bemisia tabaci and functions as a deubiquitinating enzyme (DUB). We show that compared to endogenous DUB, BtUCH19 specifically removes K63-linked ubiquitin chains from a cytochrome P450, CYP4C64, thereby stabilizing this key detoxification enzyme in vivo. Sustained CYP4C64 abundance enhances metabolic detoxification of two commonly used insecticides thiamethoxam (TMX) and clothianidin (CLO) to their low-toxicity products TMX-Urea and CLO-Urea. Consequently, BtUCH19 drives insecticide resistance through a novel "HGT-PTM-Metab" axis. Our work reveals the instrumental role of a HGT in orchestrating ubiquitin-proteasome system (UPS)-mediated protein level regulation of a key detoxification pathway. These findings offer new insights into the intricate mechanisms underlying co-evolutionary biology, and provide a new molecular target for Integrated Pest Management (IPM).

zoology↗
bioRxiv2026

Snake Venom Fluidic Properties and Design of Venom Mimics as Rheological Surrogates

Snake venom composition and its contribution to toxic effects has been heavily researched, but there is a comparative lack of information on venoms fluidic properties and their relationship with fang morphology during the envenomation process. Understanding how venom flows through a fang can shed light on bite site dynamics and potentially explain bite symptoms. In this article we first conduct a broad comparative test of the rheological properties of venom from thirteen snake species, including multiple viperid and elapid snake species, revealing a shear-thinning non-Newtonian flow behavior in all studied species. However, we have not observed strong phylogenetic signal in venom fluidic properties, suggesting that flow properties may vary independently of evolutionary relationships between snake species. Second, we demonstrate that snake venoms fluidic properties can be modeled by other inexpensive, safe, and abundant shear-thinning surrogate fluids. We found that aqueous solutions of bovine serum albumin protein and xanthan gum are useful venom mimics, matching the rheological behavior of venoms from the studied snake species across a range of relevant shear rates. We further evaluated the performance of these snake venom mimics in a simulated venom delivery system, showing good and robust mimetic control of the flow properties as a function of applied pressure. By elucidating the fluidic properties of snake venom and providing a non-toxic, scalable surrogate fluid model to be used in further studies, we provide the biomedical, toxicology, evolutionary biology communities with a tool to study envenomation physics in an inexpensive and safe fashion. We suggest it is possible to design species-specific venom mimics that facilitate research on the biomechanics and fluid dynamics of venom delivery via snake bites, and inform the design of bioinspired puncture and injection devices.

bioengineering↗
bioRxiv2026

Ecological drivers of social complexity: the role of predation risk and nesting resource in group-living cichlid

Understanding how social complexity responds to environmental variation remains a longstanding challenge in evolutionary biology. Here, we investigated the drivers of social complexity using intraspecific social variation across seven locations of the obligatory shell-brooding cichlid Neolamprologus meeli in Lake Tanganyika. We quantified the number of subordinate individuals per female territory and examined the effects of predation risk, shell availability, and their interaction. Social complexity increased with shell availability under high predation risk but showed little association under low predation risk. A field manipulative-experiment further demonstrated that increasing shell availability led to higher juvenile retention, indicating a causal effect of territory quality. In addition, removal of subordinates reduced shell availability, suggesting the feedback between group size and territory maintenance. We also assessed genetic population structure based on nuclear SNPs obtained by MIG-seq and found only weak genetic differentiation among localities, suggesting that the observed social variation is unlikely to simply reflect strong genetic subdivision. Together, these results show that predation risk promotes group living, whereas nesting resource availability constrains its extent. Our study highlights that social complexity emerges from the interaction between macro- and micro-ecological factors, providing a mechanistic understanding of the evolution of social complexity and philopatry.

ecology↗
bioRxiv2026

Near-Gapless and Haplotype-Resolved Capsella Genomes Enable Investigation into Genomic Consequences of Mating System Shifts

The shift from outcrossing to self-fertilization is a common evolutionary transition in flowering plants. The genus Capsella, comprising the obligate outcrosser C. grandiflora and two self-fertile species, C. rubella and C. orientalis, provides a powerful system to explore genomic consequences of mating system shifts. Despite its utility, existing genomic resources in Capsella are fragmented, incomplete, and particularly deficient in repetitive genomic regions, hindering the study of transposable element (TE) dynamics and gene annotation. Here, we present high-quality, chromosome-scale, near-gapless genome assemblies for C. grandiflora, C. rubella, and C. orientalis. Leveraging these improved genomes, we created high-quality genomic resources for the Capsella genus by performing comprehensive, de novo annotations of protein-coding genes and TEs. Comparative genomic analysis among these species reveals differences in TE abundance, position, and production of small RNAs. These resources provide an unprecedented opportunity to explore how mating system transitions influence genome architecture, TE behavior, and gene evolution. This research also developed a static online platform for Capsella genomic resources, Capsella Database (CapBase, www.capsella.uk), to support community use of these resources. Our findings advance understanding of the genomic impacts of selfing and establish a robust foundation for future research into genomics, epigenomics, and evolutionary biology within Capsella and related plant systems. Significance statementThe Capsella species are model plants for investigating the genomic impacts of the shift from outcrossing to self-fertilization. However, genomic resources for these species remain poor. In this study, we created high-quality genome assemblies and annotations for three Capsella species, performed comparative genomic analysis among these genomes, and constructed the first Capsella online genomic database, CapBase (www.capsella.uk). These outputs provide a valuable foundation for studying plant genome dynamics following the evolution of self-fertilization.

plant biology↗
bioRxiv2026

Long-read sequencing based genomic data of a dipluran species, Occasjapyx japonicus

We present the genome dataset of a dipluran species, Occasjapyx japonicus, representing the first dipluran genome assembled using HiFi long-read sequencing technology. The assembled genome is approximately 439.3 Mbp in size, comparable to those of other dipluran species available in public databases. The N50 value of 15.5 Mbp exceeds that reported for other dipluran species. The assembled gene set contains 19,635 genes, a number not significantly different from those estimated in previous analyses of two other dipluran species. Functional gene annotation was conducted using predicted amino acid sequences derived from the gene set. BUSCO analysis indicated that the assembled genome contains the majority of conserved core genes. These findings suggest that the O. japonicus genome and associated data are of sufficient quality to serve as a reference genome. The dataset will be valuable for studies in comparative or evolutionary biology, particularly in understanding hexapod evolution and the emergence of insects.

genomics↗
bioRxiv2026

Comparative genomic and transcriptomic analyses of Strongylus vulgaris reveal developmental and evolutionary deployment of parasitism in a migratory equine nematode

BackgroundStrongylus vulgaris is a highly pathogenic equine strongyle whose larval stages migrate through the mesenteric arterial system, yet the molecular basis of its development, host association, and evolutionary biology remains poorly resolved. We generated an integrated genomic and transcriptomic resource to characterize genome structure, gene annotation, stage-associated expression, candidate secreted proteins, isoform diversity, gene-family evolution, putative horizontal gene transfer, and drug resistance-associated homologs in S. vulgaris. ResultsPacBio HiFi sequencing produced a 329.0 Mb genome assembly comprising 3,913 contigs, with a contig N50 of 147 kb and 94.8% BUSCO completeness, substantially improving the prior fragmented draft. Repeat annotation identified 127.5 Mb of repetitive sequence, representing 38.72% of the genome and dominated by unclassified repeats. Integration of RNA-seq-guided annotation with PacBio Iso-Seq evidence refined 16,387 loci and 24,546 transcripts, generating an isoform-retaining discovery proteome of 23,363 predicted proteins. Functional annotation supported 93.5% of predicted proteins and identified 1,530 unknown or weakly annotated candidates. Consensus secretome prediction identified 2,210 high-confidence putative secreted proteins. Stage-associated transcriptomics showed that development was the dominant axis of expression variation, with 5,299 genes differentially expressed between larvae and adults and strong adult sex-associated divergence. Isoform analysis identified 490 high-confidence isoform switches, concentrated primarily in the ML5 female-to-adult female transition. Comparative genomics identified 27,641 orthogroups, 201 S. vulgaris-specific orthogroups, and, after repeat-aware filtering, 48 expanded and 250 contracted gene families. Structure-guided annotation prioritized migratory-stage-enriched secreted candidates, including Cysteine-rich secretory proteins, Antigen 5, and Pathogenesis-related 1 (CAP), Sperm-coating protein (SCP) Tpx-1/Ag5/PR-1/Sc7 protein superfamily (TAPS) -like, von Willebrand factor type A (VWA) - domain, lipid-binding-like, DNase II-like, and peptidase-like proteins. Conservative screening retained 17 putative horizontal gene transfer (HGT) candidates, and drug resistance-homolog analysis recovered 18 nonredundant S. vulgaris homologs without canonical {beta}-tubulin benzimidazole-resistance substitutions. ConclusionsThese results establish the first integrated, high-quality molecular framework for S. vulgaris and show that its parasitic biology is developmentally structured, isoform-rich, and shaped by both conserved strongylid features and lineage-specific gene-family change. This resource provides a foundation for future studies of interhost migration, host interaction, parasite evolution, and genomic surveillance.

genomics↗
bioRxiv2026

A Telomere-to-telomere genome of the hibernating fat-tailed dwarf lemur (Cheirogaleus medius)

Madagascars dwarf lemurs (genus Cheirogaleus) are the only obligate-hibernating primates and closest relative to humans capable of hibernation. Endemic to the increasingly fragmented dry forests of Madagascar, the fat tailed dwarf lemur (Cheirogaleus medius) represents a unique model for understanding primate physiology and tropical hibernation. Here we present FatTail1, a highly contiguous diploid genome assembly generated from a male C. medius at the Duke Lemur Center using Oxford Nanopore Technologies PromethION sequencing. The assembly spans 2.3 Gb, with an N50 of 103Mb, L50 of 10, and a BUSCO completeness score of over 99%. In addition to a complete mitogenome, we generated allele-specific DNA methylation profiles and annotated 23,925 genes using NCBIs EGAPX. FatTail1 exceeds the gap-free contiguity of previously published strepsirrhine genomes, representing the first telomere-to-telomere genome of a Strepsirrhine primate, and providing a foundation for future studies of primate hibernation, epigenetic regulation, and conservation genomics. ARTICLE SUMMARYDwarf lemurs are the only primates and closest relative to humans capable of months-long hibernation, making them an important model for understanding metabolic adaptations with relevance to human physiology. Here we present FatTail1, the first telomere-to-telomere genome assembly of a strepsirrhine primate, generated from a fat-tailed dwarf lemur (Cheirogaleus medius) using Oxford Nanopore Technologies PromethION sequencing. In addition to a highly complete nuclear genome, we assembled the mitogenome, identified allele-specific DNA methylation profiles and annotated 23,925 genes. FatTail1 exceeds the gap-free contiguity of previously published strepsirrhine genomes and provides an improved genomic resource for studies of hibernation, comparative genomics, epigenetic regulation, evolutionary biology, and conservation of this threatened primate.

genomics↗