BMC Biology最新文献

{"title":"Design and development of a bispecific antibody targeting BAFF and IL-17 for systemic lupus erythematosus treatment.","authors":"Cheng Xin, Jingming Zhou, Yumei Chen, Yankai Liu, Hongliang Liu, Chao Liang, Xifang Zhu, Yanhua Qi, Gaiping Zhang, Aiping Wang","doi":"10.1186/s12915-025-02398-2","DOIUrl":"10.1186/s12915-025-02398-2","url":null,"abstract":"<p><strong>Background: </strong>This study aimed to develop and evaluate a bispecific single-chain variable fragment (bsscFv) targeting B-cell activating factor (BAFF) and interleukin-17 (IL-17) for the treatment of systemic lupus erythematosus (SLE).</p><p><strong>Methods: </strong>The bsscFv was engineered by linking single-chain variable fragments (scFvs) specific for BAFF and IL-17 with a flexible peptide linker. It was expressed in E. coli BL21 and purified using affinity chromatography. Binding affinities to BAFF and IL-17 were assessed by enzyme-linked immunosorbent assay (ELISA). In vitro neutralization assays were conducted using Raji and HT-29 cell cultures. In vivo therapeutic efficacy was evaluated in an MRL/lpr mouse model of SLE, with 10 mice per group. Statistical significance was determined using a Student's t-test for comparison of two groups.</p><p><strong>Results: </strong>The bsscFv demonstrated strong binding to both BAFF and IL-17 in ELISA. In vitro, it inhibited BAFF-induced B-cell survival, proliferation, and immunoglobulin production, as well as IL-17-induced inflammatory cytokine secretion in HT-29 cells. In the MRL/lpr mouse model, bsscFv treatment significantly reduced autoantibody levels (p < 0.05), proteinuria, renal pathology, and cytokine expression in a dose-dependent manner compared to controls.</p><p><strong>Conclusions: </strong>The bsscFv exhibited potent neutralizing activity in vitro and therapeutic efficacy in vivo, suggesting it as a promising bispecific therapeutic agent for the treatment of SLE. Further studies are warranted to explore its clinical potential.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"283"},"PeriodicalIF":4.5,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482122/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145191267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Machine learning combined with omics-based approaches reveals T-lymphocyte cellular fate imbalance in abdominal aortic aneurysm.","authors":"Demin Li, Ge Zhang, Pengchong Du, Chang Cao, Xuyu He, Yan Lv, Peiyu Yuan, Yujia Wang, Ruhao Wu, Yifan Cao, Yu Yang, Jiamin Gao, Bo Lan, Guo-Ping Shi, Xiaolin Cui, Jinying Zhang, Junnan Tang","doi":"10.1186/s12915-025-02400-x","DOIUrl":"10.1186/s12915-025-02400-x","url":null,"abstract":"<p><strong>Background: </strong>Abdominal aortic aneurysm (AAA) is typically an asymptomatic disease closely associated with immune mechanisms. A deep understanding of cellular responses within AAA tissues, particularly the molecular changes in T-cell populations, is critical for disease diagnosis and treatment. However, the specific mechanisms inducing T-lymphocyte fate imbalance in AAA remain to be elucidated.</p><p><strong>Results: </strong>The analysis revealed the core mechanisms driving T-lymphocyte fate imbalance in AAA. We successfully established a comprehensive regulatory map encompassing T-cell infiltration regulatory features, critical transcription factors, and dysregulated immune signaling pathways. Machine learning algorithms identified transcription factors FOSB and JUNB as key biomarkers. Validation across multiple independent datasets and clinical samples confirmed the feasibility and accuracy of FOSB and JUNB as clinical diagnostic biomarkers for AAA.</p><p><strong>Conclusions: </strong>Through the analysis of single-cell and bulk data, hallmarks of human AAA cellular landscape and T-cell comprehensive developmental relationships were recapitulated. This study identified important roles of T-cell and the molecular mechanisms for the dynamic T-cell infiltrating process, which could characterize disease status and landscape of human AAA microenvironment. Using the deep learning algorithms, FOSB and JUNB were demonstrated as pivotal biomarkers of AAA, together with screening the potential pharmacologic agents targeting T-cell polarization. Taken together, this expands the current understanding of AAA pathogenesis and may provide a feasible immune-targeted therapeutic strategy.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"280"},"PeriodicalIF":4.5,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465141/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145173666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High-throughput behavioural phenotyping of 25 C. elegans disease models including patient-specific mutations.","authors":"Thomas J O'Brien, Eneko P Navarro, Consuelo Barroso, Lara Menzies, Enrique Martinez-Perez, David Carling, André E X Brown","doi":"10.1186/s12915-025-02368-8","DOIUrl":"10.1186/s12915-025-02368-8","url":null,"abstract":"<p><strong>Background: </strong>Genetic diagnosis is fast and cheap, challenging our capacity to evaluate the functional impact of novel disease-causing variants or identify potential therapeutics. Model organisms including C. elegans present the possibility of systematically modelling genetic diseases, yet robust, high-throughput methods have been lacking.</p><p><strong>Results: </strong>Here we show that automated multi-dimensional behaviour tracking can detect phenotypes in 25 new C. elegans disease models spanning homozygous loss-of-function alleles and patient-specific single-amino-acid substitutions. We find that homozygous loss-of-function (LoF) mutants across diverse genetic pathways (including BORC, FLCN, and FNIP-2) exhibit strong, readily detectable abnormalities in posture, locomotion, and stimulus responses compared to wild-type animals. An smc-3 mutant strain-modelled by introducing a patient-identified missense change-exhibited developmental anomalies and distinct behavioural profiles even though complete loss of SMC-3 is lethal. In contrast, patient-derived missense mutations in another essential gene, tnpo-2, did not show a strong phenotype initially but it could be \"sensitized\" chemically (e.g., with aldicarb), potentially facilitating future drug screens.</p><p><strong>Conclusions: </strong>Our findings show that scalable behavioural phenotyping can capture a wide range of mutant effects-from strong to subtle-in patient-avatar worm lines. We anticipate that this standardized approach will enable systematic drug repurposing for rare genetic disorders as new disease variants are discovered.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"281"},"PeriodicalIF":4.5,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465487/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145173653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transposable elements create distinct genomic niches for effector evolution among Magnaporthe oryzae lineages.","authors":"Ana Margarida Sampaio, Daniel Croll","doi":"10.1186/s12915-025-02385-7","DOIUrl":"10.1186/s12915-025-02385-7","url":null,"abstract":"<p><strong>Background: </strong>Plant-pathogen interactions are characterized by evolutionary arms races. At the molecular level, fungal effectors can target important plant functions, while plants evolve to improve effector recognition. Rapid evolution in genes encoding effectors can be facilitated by transposable elements (TEs). In Magnaporthe oryzae, the causal agent of blast disease in several cereals and grasses, TEs play important roles in chromosomal evolution as well as the gain or loss of effector genes in host specialized lineages. However, a global understanding of TE dynamics driving effector evolution at population scale and across lineages is lacking.</p><p><strong>Results: </strong>Here, we focus on 16 AVR effector loci assessed across a global sampling of 11 reference genomes and 447 newly generated draft genome assemblies from publicly available short-read sequencing data across all major M. oryzae lineages and outgroups. We classified each effector based on evidence for duplication, deletion and translocation processes among lineages. Next, we determined AVR gain and loss dynamics across lineages allowing for a broad categorization of effector dynamics. Each AVR was integrated in a distinct genomic niche determined by the TE activity profile contributing to the diversification at the locus. We quantified TE contributions to effector niches and found that TE identity helped diversify AVR loci. We used the large genomic dataset to recapitulate the evolution of the rice blast AVR1-CO39 locus.</p><p><strong>Conclusions: </strong>Taken together, our work demonstrates how TE dynamics are an integral component of M. oryzae effector evolution, likely facilitating escape from host recognition. In-depth tracking of effector loci is a valuable tool to predict the durability of host resistance.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"282"},"PeriodicalIF":4.5,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465478/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145173591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MaskMol: knowledge-guided molecular image pre-training framework for activity cliffs with pixel masking.","authors":"Zhixiang Cheng, Hongxin Xiang, Pengsen Ma, Li Zeng, Xin Jin, Xixi Yang, Jianxin Lin, Xinxin Feng, Yang Deng, Changhui Deng, Bosheng Song, Xiangxiang Zeng","doi":"10.1186/s12915-025-02389-3","DOIUrl":"10.1186/s12915-025-02389-3","url":null,"abstract":"<p><strong>Background: </strong>Activity cliffs, which refer to pairs of molecules that are structurally similar but show significant differences in their potency, can lead to model representation collapse and make the model challenging to distinguish them.</p><p><strong>Results: </strong>Our research indicates that as molecular similarity increases, graph-based methods struggle to capture these nuances, whereas image-based approaches effectively retain the distinctions. Thus, we developed MaskMol, a knowledge-guided molecular image self-supervised learning framework. MaskMol accurately learns the representation of molecular images by considering multiple levels of molecular knowledge, such as atoms, bonds, and substructures. By utilizing pixel masking tasks, MaskMol extracts fine-grained information from molecular images, overcoming the limitations of existing deep learning models in identifying subtle structural changes. Experimental results demonstrate MaskMol's high accuracy and transferability in activity cliff estimation and compound potency prediction across 20 different macromolecular targets, outperforming 25 state-of-the-art deep learning and machine learning approaches. Visualization analyses reveal MaskMol's high biological interpretability in identifying activity cliff-relevant molecular substructures. Notably, through MaskMol, we identified candidate EP4 inhibitors that could be used to treat tumors.</p><p><strong>Conclusions: </strong>This study raises awareness about activity cliffs and introduces a novel method for molecular image representation learning and virtual screening, advancing drug discovery and providing new insights into structure-activity relationships (SAR).</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"279"},"PeriodicalIF":4.5,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12462177/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145136539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Immune-mediated indirect interaction between gut microbiota and bacterial pathogens.","authors":"Maryam Keshavarz, Mathias Franz, Haicheng Xie, Caroline Zanchi, Susan Mbedi, Sarah Sparmann, Jens Rolff","doi":"10.1186/s12915-025-02399-1","DOIUrl":"10.1186/s12915-025-02399-1","url":null,"abstract":"<p><strong>Background: </strong>In many animals, survival during infection depends on the ability to coordinate interactions between the host immune system and gut microbiota. These tripartite interactions, in turn, potentially shape pathogen virulence evolution. A key regulator of the immune system and, hence, bipartite interactions in insects is the immune deficiency (Imd) pathway, which modulates gut microbiota and pathogens by synthesizing antimicrobial peptides (AMPs) through the NF-κB transcription factor Relish. However, whether Imd-dependent AMPs mediate indirect interactions between gut microbiota and pathogens in a tripartite context remains unclear. Using RNAi-mediated knockdown of Tenebrio molitor Relish (TmRelish), we hypothesized that Imd-dependent AMPs influence indirect interaction between Providencia burhodogranariea_B (P. b_B) infection and the gut microbiota.</p><p><strong>Results: </strong>TmRelish knockdown altered bipartite interactions by disrupting gut microbiota load and composition, increasing pathogen load, and ultimately leading to higher host mortality during infection. However, we did not find support for our tripartite hypothesis that Imd-dependent AMPs mediate indirect interactions between the gut microbiota and P. b_B infection, suggesting the involvement of alternative regulatory pathways or Imd-independent mechanisms. Nevertheless, our investigations of tripartite interactions showed a positive effect of P. b_B infection on gut microbiota load, which in turn stimulated the expression of a subset of AMPs. However, this upregulation of AMPs did not result in reduced P. b_B load. Notably, the gut microbiota did not affect pathogen load but promoted host survival during P. b_B infection, indicating a role in increasing host tolerance rather than resistance.</p><p><strong>Conclusions: </strong>These findings suggest that while Imd-dependent AMPs may not mediate tripartite interactions in our system, microbiota-host interactions, such as microbiota-mediated immune priming and changes in microbiota load, can shape infection outcomes. These effects on infection outcomes almost certainly exert important selective pressures on the evolution of bacterial virulence.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"278"},"PeriodicalIF":4.5,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442303/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145074454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A standing wave tube-like setup designed for tomographic imaging of the sound-induced motion patterns in fish hearing structures.","authors":"Isabelle P Maiditsch, Tanja Schulz-Mirbach, Martin Heß, Friedrich Ladich, Marco Stampanoni, Christian M Schlepütz","doi":"10.1186/s12915-025-02388-4","DOIUrl":"10.1186/s12915-025-02388-4","url":null,"abstract":"<p><strong>Background: </strong>Modern bony fishes exhibit a considerable variation in the morphology of their hearing structures, and the morphological composition of these has been studied for centuries. However, the precise interaction and contribution of individual structures to hearing remains unclear in many species. Measurements of their motion in situ are challenging and pose the risk of damage or altering results through invasive intervention. Recent developments in time-resolved synchrotron-radiation-based tomography have opened up possibilities for non-destructive quantification of the micron-level motion patterns of the auditory system. However, the strict requirements for miniaturised acoustic environments compatible with tomographic imaging hinder the production of ideal and well-characterised sound fields. To address this issue, we present the design of a miniature standing wave tube-like setup equipped with the necessary sensors to tune and monitor the sound field in situ, thereby generating and recording the desired acoustic conditions during experiments.</p><p><strong>Results: </strong>By incorporating hydrophones into the tube of the standing-wave setup, we achieved a precise adjustment of the acoustic field within the tube at various frequencies. We generated and measured frequencies up to 2 kHz that fall within the relevant hearing spectrum of otophysan fish. The setup allows for the determination and adjustment of sound pressure levels during tomographic measurements, and phases can be regulated to achieve distinct differences between maximum (0° phase shift) and minimum (180° phase shift) sound pressure at the centre of the test tube.</p><p><strong>Conclusions: </strong>We are able to visualise the motion of the peripheral auditory structures from the swim bladder to the Weberian ossicles and the otoliths (sagittae) in terms of maximum and minimum (sound-induced particle motion) sound pressure, respectively. This methodology has been successfully applied to various otophysan fish species and is demonstrated in the example of a glass catfish (Kryptopterus vitreolus). Our setup not only enhances our understanding of basic principles in fish bioacoustics but also sets a new standard for non-invasive, high-resolution imaging techniques in the field of aquatic sensory biology.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"277"},"PeriodicalIF":4.5,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12439379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145069200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chromosome-level genome of the European hamster (Cricetus cricetus) and its genome-wide population structure across Western Europe.","authors":"Tobias Erik Reiners, David Prochotta, Tilman Schell, Carola Greve, Alexander Ben Hamadou, Charlotte Gerheim, Juan-Manuel Ortega, Carsten Nowak, Marcel Nebenführ, Axel Janke","doi":"10.1186/s12915-025-02384-8","DOIUrl":"10.1186/s12915-025-02384-8","url":null,"abstract":"<p><strong>Background: </strong>The European hamster (Cricetus cricetus) was once a pest on European farmland, but its numbers have declined dramatically in recent decades, making it a critically endangered species throughout Europe and beyond. While it is strictly protected by EU law and several conservations, breeding and release programs have been initiated, and little is known about the level of genetic erosion and inbreeding on a European scale.</p><p><strong>Results: </strong>Here, we present a chromosome-level de novo genome of a female hamster and a first population genomic analysis from the western range of the species' distribution, using Illumina short reads (10 × coverage) from 34 individuals. The genome is 2.89 Gbp long, with 11 chromosome-level scaffolds and around 600 unplaced scaffolds and scaffolds N50 of 267 Mbp. The genome is above the average length of a mammalian genome and longer than that of other studied hamster species. Four distinct hamster populations with no admixture can be identified, indicating highly isolated populations with limited connectivity. Heterozygosity (Ho) is generally low (< 0.05%, comparable to polar bears) with some exceptions of populations with Ho near zero and a few with Ho as high as 0.2%.</p><p><strong>Conclusions: </strong>Most dramatically, the genomes of individuals used as founders for conservation breeding programs show exceptionally long runs of homozygosity, questioning its long-term suitability. This study confirms earlier concerns about the dramatically decreasing genetic diversity of the European hamster and provides a basis for future conservation efforts, which require consideration of population genetic factors.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"276"},"PeriodicalIF":4.5,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12439417/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145069269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A single-cell transcriptome atlas of pig skin reveals cellular heterogeneity from embryonic development to postnatal aging.","authors":"Ting Zheng, Rong Yuan, Yu Zhang, Qin Zou, Yifei Wang, Yujing Li, Zhengyin Gong, Zhengli Chen, Yanzhi Jiang","doi":"10.1186/s12915-025-02390-w","DOIUrl":"10.1186/s12915-025-02390-w","url":null,"abstract":"<p><strong>Background: </strong>Mammalian skin exhibits profound cellular and molecular restructuring across lifespan, yet an integrated single-cell mapping from embryogenesis to senescence remains limited. The Chenghua (CH) pig, with exceptional skin thickness characteristics, provides a promising model for investigating human skin development and physiology.</p><p><strong>Results: </strong>We constructed a comprehensive single-cell RNA atlas of 443,529 cells from CH pig skin spanning 10 developmental stages (embryonic day 56 to postnatally year 7). Our analysis identified eight major skin cell types and revealed stage-specific shifts in cellular composition. Fibroblasts (FBs) and mesenchymal stem cells (MSCs) dominated embryonic development while smooth muscle cells and endothelial cells increased postnatally, with aging marked by FB dysfunction and significant dermal thinning. Pseudotime trajectory analysis identified that FBs differentiated from a common progenitor with MSCs, diverging into five functionally distinct subpopulations including papillary, reticular, mesenchymal, pro-inflammatory, and a novel AUTS2⁺ subtype with neuromodulatory roles. Critically, FBs regulated postnatal skin aging via COL1A1-(ITGA1 + ITGB1) and MDK-SDC1 interaction signaling pathways, with the transcription factor EGR1 regulating collagen-related genes (DPT, COL12A1, COL5A2) during development; the age-dependent suppression of FBs coincided with collagen downregulation, reduced intercellular communication, and elevated transcriptional noise. Concurrently, immune cells including dendritic cells (DCs) and T cells (TCs) exhibited a marked decrease of cell numbers perinatally, with cytotoxic NKT cells reaching peak abundance at rapid growth stage; DCs and TCs primarily utilized SPP1 and TGF-β signaling pathways to regulate skin immunity during development and aging. Cross-species analysis confirmed the evolutionary conservation of skin cell types and FB functional gene profiles related to ECM deposition and inflammatory responses across pigs, humans, and mice during development and aging.</p><p><strong>Conclusions: </strong>This work delineates cellular dynamics underpinning skin homeostasis, uncovers the vital physiological functions of FBs and immune cells during skin development and aging, and validates the pig model for human cutaneous physiology research. The atlas serves as a pivotal resource for skin mechanistic and translational studies.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"275"},"PeriodicalIF":4.5,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12403584/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144943805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chromosome-scale genome assembly and gene annotation of the hydrothermal vent annelid Alvinella pompejana yield insight into animal evolution in extreme environments.","authors":"Sami El Hilali, Philippe Dru, Alan Le Moan, Yang I Li, Martijn A Huynen, André Hoelz, Robert C Robinson, José M Martín-Durán, Didier Jollivet, Adam Claridge-Chang, Richard R Copley","doi":"10.1186/s12915-025-02369-7","DOIUrl":"10.1186/s12915-025-02369-7","url":null,"abstract":"<p><strong>Background: </strong>The Pompeii worm Alvinella pompejana, a terebellid annelid, has long been an exemplar of a metazoan that lives in an extreme environment, on the chimney wall of deep-sea hydrothermal vents, but this very environment has made it difficult to study. Comprehensive assessment of Alvinella pompejana genome content, and the factors that could explain its ability to thrive in seemingly hostile conditions has been lacking.</p><p><strong>Results: </strong>We report the chromosome-level genome sequence of Alvinella pompejana and population-level sequence variants. We produced a set of gene models and analysed the predicted protein set in the light of past hypotheses about the thermotolerance of Alvinella, comparing it to other recently sequenced vent annelids. Despite its extreme environment, we find evidence for relatively conservative evolution of protein amino acid composition and genome evolution as measured by synteny. We suggest that prior hypotheses of loss of amino acid biosynthesis genes associated with obligate symbioses reported in siboglinid annelids are mistaken, and that Alvinella and siboglinids are typical metazoans in this regard. Alvinella encodes a number of respiratory enzymes unusual for bilaterian animals, suggesting an ability to better tolerate hypoxic environments. We find evidence of a parallel increase in the number of globin encoding genes and loss of light sensitive opsins and cryptochromes in deep-sea annelids.</p><p><strong>Conclusions: </strong>Our results provide a comprehensive Alvinella protein and genome resource and shed light on the adaptation of Alvinella to temperature, hypoxia and darkness, as well as cryptic speciation, giving a firm base from which future studies can be taken forward.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"274"},"PeriodicalIF":4.5,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12403961/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144943806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}