Biology subjects

Li, P.

Publications and source records attributed to Li, P..

At least 19 recordsLinked to original sources

bioRxiv2026

Evasion of Hepatic ILC1 Immunosurveillance Drives Breast Cancer Liver Metastasis

Metastasis, the dissemination of cancer cells to distant organs, is an inefficient process1, yet remains the leading cause of cancer-related mortality2. The cellular barriers and evasion mechanisms governing organ-specific susceptibility remain incompletely understood3-5, hindering the development of effective anti-metastatic therapies6. Here, we show that liver-resident type 1 innate lymphoid cells (ILC1s) constitute an essential immunosurveillance barrier against breast cancer liver metastasis that can be bypassed through either cancer cell intrinsic or host-dependent mechanisms. In a multi-organ metastatic breast cancer patient cohort, liver metastasis occurred later and was associated with poorer survival than lung metastasis, with elevated body mass index emerging as a clinical risk factor. This metabolic vulnerability was recapitulated in mice, where a high-fat diet induced hepatosteatosis and selectively enhanced breast cancer colonization of the liver. Mechanistically, liver and lung colonization were restrained by ILC1s and circulating natural killer (NK) cells, respectively. Following cancer cell challenge, NK cells expanded and activated, employing lytic granule pathways and the death receptor DR5 for clearance, whereas activated ILC1s selectively required high DR5 expression on cancer cells, supported by AP-2a (TFAP2A) mediated transcriptional activation, for effective immunosurveillance. Heterozygous copy number deletion at TNFRSF10B (encoding DR5) in human tumours reduced DR5 expression and predisposed to liver metastasis. Hepatosteatosis further compromised this barrier by reducing IL-15 expression in macrophages, thereby depleting hepatic ILC1s effects reversible with glucagon-like peptide-1 (GLP-1) receptor agonists. Thus, hepatic ILC1s form a critical organ-specific barrier to breast cancer metastasis, vulnerable to both cancer cell-intrinsic DR5 downregulation and host metabolic dysfunction.

immunology↗

bioRxiv2026

Plantaricin JK from Lactiplantibacillus plantarum ZJ316 inhibits enterohemorrhagic Escherichia coli O104:H4 and alters fecal microbial communities in vitro

Enterohemorrhagic Escherichia coli (EHEC) O104:H4 is a highly virulent foodborne pathogen for which antibiotic therapy is contraindicated, severely restricting conventional treatment options; therefore, the development of novel antimicrobial strategies is essential. This study investigated the antibacterial activity and gut microbiota-modulating effects of plantaricin JK (PlnJK), a two-peptide bacteriocin from Lactiplantibacillus plantarum. Chemically synthesized PlnJK exhibited a minimum inhibitory concentration (MIC) of 32 M against E. coli O104:H4, disrupting membrane integrity as evidenced by increased extracellular conductivity, ATP depletion, and ultrastructural damage. In an in vitro fecal fermentation model, PlnJK reduced Escherichia-Shigella abundance from 36.70% to 30.60% which contains E. coli O104:H4-related taxa, enriched Clostridium (5.70% vs 2.40% in infection group), Rikenellaceae, and Lactobacillaceae, and significantly elevated short-chain fatty acid (SCFA) levels including butyrate (p < 0.01) and isovalerate (p < 0.05). To translate this into a deliverable format, CRISPR-Cas9-engineered L. plantarum strains with plnJK knockout, complementation, and overexpression were constructed. Compared with the chemically synthesized peptide, LAB-derived PlnJK--especially from the overexpression strain--showed superior efficacy in restoring microbial diversity and enhancing SCFA production, significantly increased Shannon index and reduced dominance (p < 0.01), while promoting butyrate (p < 0.01) and isovalerate (p < 0.01) production compared to the knockout control. The engineered strains further revealed a clear dose-dependent effect, as overexpression potentiated while knockout abolished the beneficial modulation. These findings demonstrate that PlnJK acts through membrane disruption and beneficially modulates gut microecology, with LAB-mediated in situ delivery offering a promising strategy for anti-EHEC live biotherapeutic development.

microbiology↗

bioRxiv2026

FLASH X-rays preserve neutrophil chromatin to boost antitumor immunity

Ultrahigh dose-rate FLASH radiotherapy spares normal tissue while preserving antitumor activity, positioning it as a promising technology in radiation oncology, but its immunomodulatory mechanisms remain elusive. Here, using a bilateral subcutaneous tumor model in mice, we show that 8-Gy FLASH X-rays, versus an equal dose of conventional dose-rate (CONV) X-rays, elicit a robust abscopal antitumor effect with anti-PD-1 therapy. Single-cell transcriptome and T cell receptor (TCR) profiling reveal that FLASH X-rays plus anti-PD-1 enhance antitumor immune infiltration and TCR clonal expansion in both irradiated and abscopal tumor lesions. Mechanistically, the ultrashort temporal continuity of FLASH dose delivery conserves chromatin compaction in neutrophils during exposure and inhibits neutrophil extracellular trap (NET) formation, thereby dismantling NET-mediated CD8+ T-cell exclusion within primary tumors. Conversely, CONV or split-dose FLASH X-rays induce marked chromatin modifications prior to dose completion, leading to chromatin hyper-relaxation which promotes NETosis and consequently abrogates systemic antitumor immunity. Notably, this detrimental effect can be reversed by pharmacologically suppressing PARylation-mediated chromatin modification and decondensation in neutrophils. These findings identify radiation-induced aberrant chromatin relaxation in neutrophils as a critical determinant of radioimmunotherapy outcomes, providing a rationale for redefining the FLASH effect and advancing its clinical translation.

cancer biology↗

bioRxiv2026

Harnessing historical collections to reconstruct the invasion history of Microstegium vimineum (Poaceae)

The evolutionary processes underlying successful invasions are often difficult to disentangle. Historical collections provide a temporal perspective, offering great potential to reconstruct invasion histories and identify the processes driving invasions. Japanese stiltgrass (Microstegium vimineum) is an invasive C4 grass introduced to eastern North America over a century ago and now established in 31 USA states. To reconstruct its invasion history, we leveraged low-coverage whole-genome sequencing of 142 herbarium and 330 contemporary samples spanning the temporal and spatial extent of the North American invasion and the native range in Asia. We identified three independent introductions in the USA: an awnless form in the South and two independent introductions of awned forms in the North, with limited admixture among introductions across space and time. In both regions, we observed high genetic diversity in the earliest available collections despite demographic bottlenecks and identified several putative selective sweeps in or near flowering-time genes, suggesting rapid evolution in the introduced range. Our analyses support separate invasions in the USA, likely facilitated by standing genetic variation and selection, but provide little support for admixture playing a major role. Our study highlights the power of historical collections to uncover the processes and mechanisms underlying successful biological invasions.

evolutionary biology↗

bioRxiv2026

CRISPR mapping unveils global prevalence of viral predators of Myxobacteria

Myxobacteria are social Gram-negative bacteria that perform cooperative predation and form multicellular fruiting bodies, serving as promising biocontrol agents against drug-resistant pathogens. Their associated viruses are therefore important ecological regulators, yet remain largely unexplored. Here, we applied CRISPR spacer-based host-virus linkage analysis to 3,229 myxobacterial genomes and identified 790 nonredundant myxophages spanning diverse global ecosystems. Comparative genomic analyses revealed extensive diversity in the taxonomy, lifestyles, and functional potential of these myxophages. We found that myxophages encode auxiliary metabolic genes involved in carbon, sulfur, iron, and cell-envelope metabolism, which may modulate host physiological processes during infection. Gene-sharing networks, whole-proteome phylogenies, inter-genomic and proteome comparison further identified six previously undescribed myxoviral lineages (MV-1~MV-6), each represented by complete genomes. Detailed analyses revealed the mechanisms by which these viruses hijack host cellular machinery and reprogram host processes. Notably, MV-1 encodes immune modulators, including the anti-CRISPR protein AcrIIA15 and a Cas12m effector located adjacent to CRISPR arrays, empower myxophages with sophisticated immune evasion and host interference strategies. This study substantially expands the myxoviral diversity and provides insights into virus-host interactions and evolutionary adaptation of myxophages.

microbiology↗

bioRxiv2026

Chemistry and Structure of Birch Bark Support Passive Radiative Cooling

White-barked birches extend to the northern limit of tree growth, and their bark is known to reduce solar damage during winter and early-spring by limiting solar heating and the incidence of harmful freeze-thaw events. The physical basis for this protection, however, has remained unclear. Here, we show that extracted betulin, the dominant triterpenoid responsible for the bark's whiteness, and Himalayan birch bark, both exhibit passive radiative cooling. Under low solar irradiance, bark and betulin-pellets reach temperatures below that of a shaded reference, and pellets cool more than bark. The cooling arises from high solar reflectance, which suppresses solar heating, and substantial mid-infrared emission, which drives radiative heat loss toward outer space. These findings help explain how bark-whiteness may contribute to protecting birch trees from solar-induced thermal stress.

plant biology↗

bioRxiv2026

In Vivo Screening for a Promising Antiparasitic Agent Against Neobenedenia melleni in Epinephelus fuscoguttatusfemale x E. lanceolatusmale and Identification of Its Potential Target

Monogenean ectoparasites, particularly Neobenedenia species, cause severe economic losses in mariculture. Here, ectoparasites isolated from cultured hybrid groupers (Epinephelus fuscoguttatus[female] x E. lanceolatus[male]) were confirmed as Neobenedenia melleni based on ITS1 phylogeny. In vivo screening of six structurally diverse compounds identified compound D (CAS No. 206111-37-7), a 5,6-dihydropyridine derivative, as the most effective antiparasitic agent, achieving 76.54% efficacy at 0.5 mg/L in a 90 min bath treatment. Dose-response assays demonstrated that 0.7 mg/L compound D achieved 95.23% antiparasitic efficacy without causing evident tissue damage or cytotoxicity to GF-1 cells. Ultrastructural observation by scanning electron microscopy revealed marked tegumental alterations, including deep fissures and extensive surface folding, in treated parasites. Molecular docking against ten candidate proteins identified {beta}-tubulin as the most favorable docking target, with a binding energy of -6.53 kcal/mol and three hydrogen-bond interactions, suggesting that {beta}-tubulin may be involved in the antiparasitic activity of compound D. Overall, these findings highlight compound D as a promising lead candidate for short-bath therapy against N. melleni and suggest that cytoskeletal disruption through {beta}-tubulin interaction represents a plausible mechanism of action.

zoology↗

bioRxiv2026

Computer-aided drug screening of anti-Neobenedenia melleni drugs based on annexin B1 in farmed pearl grouper

Monogenean capsalids of the genus Neobenedenia are widespread parasites of wild and farmed marine fish, and represent a great threat to the mariculture of grouper in China. Fishery drug development to screen and find effective compounds to control and prevent the disease is urgent needed, considering the vast production of grouper in China (294 ktons in 2025). Annexins have been discovered in Neobenedenia and other parasites, and marked differences between the parasite annexins and those of the hosts make them potentially attractive drug targets for anti-parasite therapeutics. Herein, we utilized computer-based drug discovery screens using unique Neobenedenia melleni annexin B1 and a database of 1,456,161 small molecules. The 3D structure of annexin B1 was firstly modeled by three different protein prediction tools, namely AlphaFold 3, SWISS-MODEL, and I-TASSER, of which the most accurate protein structure was used as the drug target for the following structure-based virtual screening. In vivo experimental validation of 11 compounds after molecular docking shows that abamectin (Aba) has the most effective anti-Neobenedenia bioactivity at the concentration of 0.16 mg/L as the initial screening concentration. Given its low toxicity to host grouper (24 LC50=0.254 mg/L), abamectin was chose for further investigation. A 24 h bath exposure successfully lowered the parasitic load in infected grouper, yielding an 24 h EC50 of 0.033 mg. To elucidate the anti-parasite mechanism, long-timescale molecular dynamics simulations (1000 ns) of annexin B1 and Aba was conducted, which allowed for atomic and molecular-level analysis of the essential protein motions involved in the interaction of annexin B1 and its substrate. The interaction profile between annexin B1 and abamectin was dominated by hydrophobic contacts and water bridges, involving residues TYR-210, GLU-214, GLU-244, and SER-247, which path a way for further drug optimization.

zoology↗

bioRxiv2026

Pretraining Enhances Megabase-Scale Gene Expression Prediction with GeneUnet

Predicting gene expression from DNA sequence across diverse genomic tracks is essential for understanding gene regulation and interpreting non-coding variants. Existing supervised methods are limited to few species and fail to exploit conserved regulatory mechanisms, while DNA foundation models capture cross-species information but remain constrained to kilobase-scale contexts insufficient for this task. Here we introduce GB.GeneUnet, an 837M-parameter transformer-based U-Net pretrained on 6 trillion tokens from multi-species genomes in OpenGenome2, extending genomic context to 1 Mb with up to 100x inference speedup over GeneMoE, a preliminary MoE transformer baseline of similar model size pretrained on the same data. Fine-tuned for gene expression prediction, GB.GeneUnet achieves state-of-the-art performance on the Borzoi benchmark at 524 kb context, and attains performance comparable to AlphaGenome at 1 Mb context while requiring a lighter fine-tuning procedure. Together, these results establish a scalable framework linking multi-species pretraining to ultra-long-context gene expression modeling.

genomics↗

bioRxiv2026

Precise Functional Localization of the Foveolar Representation in Anesthetized Macaque Visual Cortex

The foveola-the central ~1{degrees} of the visual field-supports the highest-acuity spatial vision, yet localizing its cortical representation is technically demanding, particularly under anesthesia where gaze cannot be behaviorally controlled. Here we describe a hierarchical, meridian-based 7T BOLD fMRI strategy for sub-degree localization of the foveolar representation in anesthetized macaques. Drifting grating bars presented at three successively finer scales (4.5{degrees}, 1.5{degrees}, 0.5{degrees}) independently refined the vertical and horizontal meridian representations, each identified by a characteristic activation signature: bilateral convergence at the V1/V2 border for the vertical meridian, and simultaneous dorsal and ventral V2/V3 activation at the fundus of the calcarine sulcus for the horizontal. Their functional intersection defined candidate foveolar coordinates, which were refined using 0.2{degrees} spot stimuli. Surface-based rendering resolved discrete foveolar loci at the lateral end of the V1/V2, V2/V3, V3/V4 and V4/TEO borders, together delimiting the previously described 'foveolar core'. Pooling these with awake data, we place the loci in a common stereotaxic frame, yielding a first anatomical atlas of the core. Intrinsic-signal optical imaging further shows that this territory lacks the ocular-dominance and orientation columns of surrounding cortex. The approach provides a reproducible framework for locating and targeting foveolar cortex in anesthetized primates.

neuroscience↗

bioRxiv2026

ETAP-CLF: an ESM3-based transformer attention framework for binary protein classification

Binary protein classification supports diverse tasks in computational biology, including pathway-membership inference and sequence-based candidate prioritization. Protein language models generate information-rich residue-level representations, but downstream classifiers commonly compress them using fixed pooling operations that may discard task-relevant sequence context. We present ETAP-CLF, a compact framework that combines pretrained per-residue ESM3 embeddings with lightweight transformer contextualization and learned attention pooling to classify variable-length proteins and generate residue-level attention scores. The ESM3 parameters remained frozen, and the same ETAP-CLF architecture and hyperparameter configuration were used across ferroptosis-, senescence-, and pyroptosis-associated protein prediction. ETAP-CLF achieved AUROCs of 0.98, 0.95 and 0.91 for these tasks, respectively. In the ferroptosis benchmark, ETAP-CLF outperformed the evaluated published models. These results demonstrate that a common downstream design can adapt to multiple process-associated classification tasks without fine-tuning the task-specific model architecture. ETAP-CLF provides a generalizable approach for sequence-based protein prioritization and a basis for broader evaluation across binary protein-classification problems.

bioinformatics↗

bioRxiv2026

Functional profiling of ESKAPE viromes uncovers resistance-limiting phage-host dynamics

ESKAPE pathogens drive clinical antibiotic resistance and intractable infections, severely compromising antimicrobial therapies. Bacteriophages are promising alternatives to antibiotics, yet their diversity, function and ecological impacts in ESKAPE pathogens remain poorly defined, hindering phage therapy translation. Here, we integrated 11,947 high-quality ESKAPE genomes with global metagenomic viral data to construct a comprehensive non-redundant virome of 14,496 ESKAPE-associated viruses, including four unreported viral clades. We found pervasive competition among mobile genetic elements (MGEs) in the ESKAPE mobilome, where nested MGE architectures empower low-mobility antibiotic resistance genes (ARGs) with horizontal transfer ability to fuel resistance dissemination. Unlike ARG-rich MGEs, ESKAPE phages carry minimal ARGs and antagonize plasmids to constrain ARG propagation, confirming their biosafety for therapy. We further revealed distinct phage-host arms races, typically virulent phages enrich anti-defense genes to evade bacterial immunity, and novel viruses hijack host methyltransferases targeted by CRISPR-Cas systems. This study establishes a systematic ESKAPE virome resource, demonstrates phages dual roles in targeting resistant pathogens and curbing resistance spread, and provides mechanistic support for phage therapy clinical application.

microbiology↗

bioRxiv2026

Single-cell profiling reveals MMP7-associated epithelial transition and immune-stromal remodeling in esophageal carcinogenesis

The progression from reflux esophagitis (RE) to Barretts esophagus (BE) and esophageal adenocarcinoma (EAC) is a major route of inflammation-associated esophageal tumorigenesis, but the cellular transitions involved remain incompletely understood. We performed single-cell transcriptomic profiling of RE, BE, and EAC tissues and integrated public EAC datasets, yielding 51,283 cells across the RE-BE-EAC continuum. The analysis identified stage-associated epithelial and microenvironmental differences. Pseudotime analysis placed Basal epithelial cells along two differentiation branches, one toward mature epithelial states and the other through proliferative and gastric-type metaplastic states toward copy number alteration-bearing malignant epithelial cells. MMP7 increased along this malignant branch, was enriched in cancer-associated epithelial cells. Its knockdown reduced the proliferation and migration of OE19 and OE33 cells, supporting an association with proliferative and migratory phenotypes. In parallel, the microenvironment shifted toward immune suppression and stromal remodeling, with increased T-cell exhaustion, macrophage polarization toward tumor-associated states, and enrichment of CAF-like myofibroblasts. Ligand-receptor analysis further suggested an epithelial-centered communication network involving MDK-SDC2/LRP1/NCL interactions between malignant epithelial cells and fibroblast, T-cell, and myeloid compartments. These results identify MMP7-associated epithelial states and candidate MDK-related communication pathways for further longitudinal and functional validation.

cancer biology↗

bioRxiv2026

Imaging-Based Age- and Sex-specific Cardiovascular and Skeletal Phenotypes in Fbn1C1041G/+ Mice

Marfan syndrome is a multisystem connective tissue disorder with age-dependent and sex-dependent phenotypic variability. This study characterized early cardiovascular, valvular, transmitral flow, and skeletal changes in Fbn1C1041G/+ mice. Male and female wild-type and Fbn1C1041G/+ mice were examined from 4 to 20 weeks of age. Transthoracic echocardiography was used to measure aortic root and ascending aortic diameters, anterior mitral leaflet length, and mitral inflow Doppler parameters. Lateral X-ray imaging was used to quantify kyphosis angle. Fbn1C1041G/+ mice of both sexes developed progressive aortic dilation, with earlier and broader aortic root involvement in males and delayed annular dilation in females. Anterior mitral leaflet elongation was detected from 8 weeks in males and at 20 weeks in females. In contrast, reduced E-wave velocity and E/A ratio were present from 4 weeks in both sexes, without changes in A-wave velocity. Kyphosis was detectable earlier in females than in males. These findings show that early Fbn1-related phenotypes follow organ-specific and sex-dependent temporal patterns, supporting age-resolved and sex-stratified assessment in preclinical Marfan syndrome studies.

pathology↗

bioRxiv2026

Peroxiredoxin 6 limits mitochondrial peroxidation to prevent mitochondrial ER contact site assembly and inflammatory signalling following adaptive stress

Peroxiredoxin 6 (PRDX6) is a multifunctional enzyme with peroxidase, calcium independent phospholipase A2 (aiPLA2) and lysophospatidylcholine acyltransterase (LPCAT) activities. Although PRDX6 can repair peroxidised phospholipids and help prevent ferroptosis, its role in the adaptive response to physiological oxidative stress remains unclear. In this study PRDX6 function was investigated using myoblasts exposed to an acute low concentration of H2O2 and Caenorhabditis elegans subjected to a swimming intervention. Mild oxidative stress promoted myogenesis and mitochondrial turnover in myoblasts, while exercise enhanced activity and longevity in C. elegans. The adaptive responses were associated with increased mitochondrial localisation of PRDX6. In contrast, loss of PRDX6 under mild stress conditions resulted in increased mitochondrial lipid peroxidation, enhanced mitochondrial ER contact sites (MERCS), mitochondrial calcium accumulation, release of mitochondrial DNA and activation of innate immune signalling pathways. Similar phenotypes were induced by the ferroptosis activator erastin and rescued by the lipid peroxyl scavenger Ferrostatin-1, indicating lipid peroxidation was the key triggering event. Furthermore, inhibition of mitochondrial calcium uptake in C. elegans prevented calcium overload and attenuated inflammatory signalling. Together, the results identify PRDX6 as a conserved regulator of mitochondrial adaptation to physiological oxidative stress, functioning to limit mitochondrial lipid peroxidation and prevent excessive MERCS assembly, mitochondrial calcium dysregulation and inflammatory activation.

cell biology↗

bioRxiv2026

Evaluation of gaseous ozone technology for decontaminating porcine reproductive and respiratory syndrome virus (PRRSV) and porcine epidemic diarrhea virus (PEDV) from non-porous surface in truck cabins

Porcine reproductive and respiratory syndrome virus (PRRSV) and porcine epidemic diarrhea virus (PEDV), both economically detrimental to the swine industry, can be spread through contaminated truck cabins, posing significant transport biosecurity risks. This study evaluated the effectiveness of gaseous ozone technology in decontaminating PRRSV and PEDV on non-porous surfaces in truck cabins. An incomplete factorial study comprising 26 treatment groups, including controls, and ozone treatments at three capacities (30, 38, and 68 g/h) was conducted over varied exposure times (0.5, 1, or 2 hours) in a climate-controlled truck cabin, where PRRSV or PEDV contaminated rubber coupons were subjected to treatments under continuous environmental monitoring, followed by virus elution and titration in cell cultures. Statistical analyses included regression models and ANOVA with Tukey's comparisons, standard deviations for ozone machines, and Pearson correlations between ozone concentration and environmental factors. Ozone treatments showed variable results with less than two-log viral titer reduction. Ozone concentrations varied across identical setups (SD: 4.75 ppm for 30 g/h, 5.43 ppm for 38 g/h machines) during the first 30 minutes, while across the entire study period, ozone concentration showed weak negative correlation with virus titer (p > 0.05), moderate positive correlation with temperature (r = 0.5, p < 0.0001), and moderate negative correlation with humidity (r = -0.56, p < 0.0001). In conclusion, ozone treatments showed inconsistent and limited effectiveness in PRRSV and PEDV decontamination, influenced by temperature and humidity under the tested conditions.

microbiology↗

bioRxiv2026

Integrated pangenome and population genomics reveal selection on standing genetic variation driving fiber flax-linseed divergence

Flax (Linum usitatissimum L.) has been domesticated for dual end uses as linseed and fiber flax, yet the genomic basis of morphotype divergence remains unclear. Here, we constructed a morphotype-resolved pangenome by integrating three newly generated near telomere-to-telomere genome assemblies with 14 previously published ones. Despite substantial variation in assembly size, driven primarily by DNA transposons, gene content was highly conserved, with little evidence for significant morphotype-specific gene presence-absence variation. Population genomic analyses of 407 accessions revealed that fiber flax had reduced nucleotide diversity, extended linkage disequilibrium, and a more compact population structure relative to linseed, consistent with stronger selection and a narrower genetic base. Genome-wide differentiation was heterogeneous and concentrated in discrete regions. Integration of FST, nucleotide diversity ratios, Tajimas D, and genome-wide association signals identified morphotype-enriched genomic blocks distributed across the genome. Many candidate regions are primarily supported by directional shifts in nucleotide diversity rather than extreme differentiation, indicating selection on standing genetic variation. Genome-wide association analyses identified 1,712 unique quantitative trait nucleotides (QTNs), with predominantly small effect sizes and strong enrichment in gene-proximal regions, consistent with a polygenic architecture. Overall, fiber flax traits tend to be controlled by fewer loci with moderate-to-large effects, whereas linseed traits exhibit a more diffuse genetic architecture. Patterns of Tajimas D further support non-classical selection dynamics, with predominantly positive values in linseed and localized negative values in fiber flax, consistent with selection on standing genetic variation. Together, our results suggest that flax morphotype divergence is driven primarily by selection on pre-existing allelic variation within a conserved gene repertoire. This study provides a comprehensive framework linking genome structure, population genomics, and trait architecture, and highlights the importance of standing genetic variation as a key resource for flax breeding and improvement.

genomics↗

bioRxiv2026

The contribution of recent and historical demographic histories to genomic diversity and conservation status in plant species

Demographic factors are intrinsically crucial to evaluate species extinction risk. However, measuring them remains difficult and time-consuming and the use of genomic summary statistics has been advocated to assess the conservation status of a species. In the present study, we estimated (i) the census number (Nc), (ii) effective population size (Ne) over three different time periods, recent, historical and ancient, (iii) neutral genetic diversity ({pi}4), and (iv) a measure of the efficacy of purifying selection ({pi}0/{pi}4) for 101 plant species using population genomic sequencing data. Twenty-one species are from the Plant Species with Extremely Small Populations (PSESP) program of SW China. Threatened species exhibited significantly lower Ne, Nc,{pi} 4, and weaker purifying selection, but had a higher Ne/Nc ratio than non-threatened ones. Nc was the main determinant in identifying conservation status, and contemporary neutral genetic diversity was predominantly influenced by historical Ne. In the absence of demographic information, genetic parameters are a good proxy of conservation status, likely because currently threatened species also had a low historical population size. In summary, our findings suggest that direct estimates of Nc are more useful than{pi} 4, although the latter remains a valuable conservation indicator. Hence, efforts such as the PSESP should be extended. Significance StatementExtinction is essentially a demographic process. However, evaluating the risk of extinction of species based only on demographic parameters remains a difficult task, and today only 18% of plant species are included in the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. Here, we use demographic data and whole genomic data from 101 plant species to show that while census number remains the best predictor of extinction risk, genomic based parameters provide good alternatives. More specifically, current neutral nucleotide diversity and historical effective population size are good predictors of the extinction risk of plant species.

evolutionary biology↗