Advanced genetics (Hoboken, N.J.)最新文献

{"title":"From Genes to Ecosystems: Marc Van Montagu on Science, Society, and the Future of Life","authors":"Marc Van Montagu","doi":"10.1002/ggn2.70047","DOIUrl":"10.1002/ggn2.70047","url":null,"abstract":"<p>Editor's Note: As part of the Advanced Dialogues series, the editor invites leading scientists and emerging voices to share their research journeys, experiences, and visions for the future of their fields. In this feature, Marc Van Montagu—Emeritus Professor at Ghent University, a founding father of plant genetic engineering, and Chairman of IPBO-VIB, shares his insights at 92, drawing on a personal conversation with the editor and a lecture he delivered at the ICG-20 conference, “From Feral to Fertile: Awakening Life in the Desert”, in Hangzhou.</p>","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13618600/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149076924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Foundation Models for Microbiome Research: From Sequence Semantics to Community Dynamics and Multimodal World Models","authors":"Haohong Zhang,&nbsp;Zixin Kang,&nbsp;Kang Ning","doi":"10.1002/ggn2.70046","DOIUrl":"https://doi.org/10.1002/ggn2.70046","url":null,"abstract":"<p>Microbiome sequencing has advanced faster than microbiome understanding. Although large-scale 16S, metagenomic, metatranscriptomic, and proteomic datasets have accumulated rapidly, most analyses remain cohort-specific and association-driven, limiting mechanistic insight, cross-study transferability, and robustness to technical confounding. Foundation models offer a new computational framework by learning reusable biological representations from large unlabeled datasets. In this Review, we present microbiome foundation models as a hierarchy spanning biological scales. Sequence-centric models capture the syntax and semantics of DNA and proteins for taxonomic inference, functional annotation, and generative design. Community-centric models learn ecological structure from abundance profiles, while addressing compositionality, sparsity, and the unordered nature of microbial communities. Emerging multimodal frameworks integrate sequence-derived functional potential with community-level ecological dynamics under host and environmental context. We discuss key design choices, including tokenization, representation granularity, self-supervised objectives, and evaluation strategies, and highlight challenges in interpretability, domain shift, causal reasoning, and biological validation. Finally, we propose a transition from static representation learning toward intervention-aware microbiome world models capable of simulation, digital twinning, and generative microbiome engineering.</p>","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ggn2.70046","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148942542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Rise of Plant Pan-Genomes: From Genome Variation to Predictive Breeding","authors":"Dan Peng,&nbsp;Xuezhu Liao,&nbsp;Liang Tang,&nbsp;Zhiqiang Wu","doi":"10.1002/ggn2.70044","DOIUrl":"https://doi.org/10.1002/ggn2.70044","url":null,"abstract":"<p>Plant pan-genomics is entering a new phase beyond genome variation discovery, requiring a shift from cataloguing genomic diversity toward understanding how variation generates biological function and breeding value. Here, we propose that the future of plant pan-genomics will be shaped by three conceptual transitions. First, structural variation (SV), presence–absence variation (PAV), and haplotype diversity should be interpreted not merely as genomic differences, but as regulatory components that influence gene networks, chromatin organization, and complex traits. Second, the expansion from species-level pan-genomes to genus-level super pan-genomes provides an evolutionary framework for uncovering adaptive genetic modules preserved in wild relatives and overlooked during domestication. Third, integrating pan-genomes with pan-omics, three-dimensional genome analyses, and artificial intelligence will enable the transformation of genomic variation into predictive models for crop improvement. We further propose that the ultimate value of pan-genomes lies not in generating increasingly complete genome collections, but in establishing a mechanistic bridge between genome diversity, biological function, and breeding decisions. This transition will move crop improvement from empirical selection toward rational genome design, where evolutionary diversity can be systematically interpreted, predicted, and engineered.</p>","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ggn2.70044","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148942251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From Cluster to Claim: Calibrating Interpretation in Single-Cell Transcriptomics","authors":"Shutong Lin,&nbsp;Guangchuang Yu","doi":"10.1002/ggn2.70045","DOIUrl":"https://doi.org/10.1002/ggn2.70045","url":null,"abstract":"<p>The widespread adoption of single-cell transcriptomics has expanded our ability to study cellular heterogeneity and molecular states. However, the high-resolution view it provides can also make it easier for descriptive data patterns to be translated into biological claims that go beyond the underlying evidence. We advocate a more calibrated approach to interpretation in single-cell transcriptomic studies. We focus on two common points of vulnerability: the direct equation of computational clusters with biological cell types and the treatment of pathway enrichment as sufficient evidence for mechanistic conclusions. These examples are offered as illustrations rather than as a systematic survey of the field. We therefore propose a three-tier logical framework—Observation, Inference, and Claim—to clarify the boundaries between statistical results, biological interpretation, and mechanistic claims. Single-cell transcriptomics is powerful for hypothesis generation, state discovery, and heterogeneity profiling, but strong mechanistic claims still require orthogonal validation. As large language models (LLMs) are increasingly used in cell-type annotation and biological narrative generation, explicit calibration between evidence strength and claim strength becomes even more important.</p>","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ggn2.70045","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148849245","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mapping Meiotic Recombination DNA Double-Strand Breaks (DSBs) Hotspots —Methodological Advances and Challenges","authors":"Jianqiang Bao","doi":"10.1002/ggn2.202500019","DOIUrl":"10.1002/ggn2.202500019","url":null,"abstract":"<p>Programmed DNA double-strand breaks (DSBs) initiate meiotic recombination at discrete genomic hotspots, and their precise mapping is crucial for understanding the molecular regulation of genome stability and evolution. A variety of genome-wide methods have been developed, each leveraging different biochemical principles — from direct capture of Spo11-oligonucleotide covalent intermediates to sequencing protein-bound single-stranded DNA (ssDNA), in situ DNA end labeling, and chromatin immunoprecipitation (ChIP). Direct approaches such as Spo11-oligo mappin, CC-seq and in situ DNA end labeling (END-seq) achieve nucleotide-resolution detection of the initial cleavage site, but typically require large amounts of starting material. ChIP ssDNA-based methods (e.g., ChIP-SSDS) enrich for recombinase associated proteins- bound (DMC1, RAD51, RPA) intermediates, reflecting an indirect proxy of DSB sites, and are limited to early resection stages. Together, while these complementary methods comprise a toolbox for dissecting meiotic hotspot landscapes, a more robust and facile approach for routine detection of meiotic DSB hotspots across diverse species remains to be developed.</p>","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13365868/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148450785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Issue Information: (Advanced Genetics 3/07)","authors":"","doi":"10.1002/ggn2.70042","DOIUrl":"https://doi.org/10.1002/ggn2.70042","url":null,"abstract":"","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ggn2.70042","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148533475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic Bone Diseases: A Scoping Review of Pathology, Symptoms, Diagnosis, Treatment, and New Horizons","authors":"Colin Jones,&nbsp;Ambalangodage C. Jayasuriya","doi":"10.1002/ggn2.202500048","DOIUrl":"https://doi.org/10.1002/ggn2.202500048","url":null,"abstract":"<p>Genetic bone diseases are a rare group of afflictions suffered by the general population. However, their rarity should not diminish research efforts to help patients understand and treat their diseases. This review summarizes the pathology, symptoms, diagnosis, and treatment insight into six well-known genetic bone diseases. Only six bone diseases are included due to the relatively low prevalence of them as whole limiting our scope to ensure accurate information and attention is provided for each disease individually. A literature search of PubMed is conducted, including studies published within the past five years (January 2020–December 2025). Thirty-six studies met inclusion criteria, and no significant risk of bias is identified among the selected articles. Study findings are synthesized into disease overview, clinical and radiographic features, and diagnostic and treatment approaches. Actively developing or novel therapies relevant to each disease are also included. These treatments include: fresolimumab for osteogenesis imperfecta, small interfering ribonucleic acid (RNA) therapy for Osteopetrosis, denosumab for Paget's disease of bone, vosoritide/recifercept/infigratinib for achondroplasia, mesenchymal stem cell therapy for craniosynostosis, and combination losartan and atenolol therapy for Marfan syndrome. These treatments are generally more recently acknowledged in literature and are either actively undergoing research or require further research to determine their efficacy.</p>","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ggn2.202500048","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148324337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Compact Cas12 Systems for Multiplex Engineering of Plant Abiotic-Stress Networks","authors":"Samar G. Thabet,&nbsp;Khairiah Mubarak Alwutayd,&nbsp;Amr Elkelish,&nbsp;Fatmah Ahmed Safhi,&nbsp;Mona F.A. Dawood,&nbsp;Ahmad M. Alqudah","doi":"10.1002/ggn2.202500067","DOIUrl":"https://doi.org/10.1002/ggn2.202500067","url":null,"abstract":"<p>Compact CRISPR-Cas12 platforms, particularly miniature and hypercompact effectors such as Cas12f, Cas12j/CasPhi, and Cas12lambda, are emerging as delivery-efficient tools for plant genome engineering because their reduced coding size facilitates viral-replicon and other size-constrained delivery routes while supporting dense guide multiplexing. Here, we argue that their highest value for crop improvement lies not simply in additional nuclease choices, but in programmable, systems-level tuning of abiotic-stress defense layers, including ion homeostasis, redox buffering, osmotic adjustment, abscisic acid (ABA)-centered hormone signaling, and transcriptional control. We distinguish evidence already demonstrated in stable plants, transient plant assays, or protoplasts from approaches extrapolated from Cas9/Cas12a or non-plant systems, and emphasize that many compact Cas12 applications remain platform-building rather than field-ready technologies. Current plant evidence supports Cas12a as a mature multiplex-editing and transcriptional-repression platform, Cas12f as a rapidly improving mini-editor with stable and viral-delivery demonstrations, and Cas12j/CasPhi as a hypercompact system with recent crop-editing and base-editing potential. By contrast, Cas12g, Cas12h, Cas12lambda, and TnpB-like nucleases are best viewed as promising future modules until plant-active implementations are broadly validated. We offer a forward-looking roadmap in which compact Cas12 systems complement Cas9 and Cas12a by enabling rapid target triage, promoter and untranslated-region engineering, transient CRISPR activation/interference, and stepwise assembly of durable sentinel edits. Translation will depend on improving efficiency and fidelity across genotypes, reducing mosaicism, documenting off-target and structural variation in multiplex stacks, and aligning delivery strategies with regulatory expectations for transgene-free crops.</p>","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ggn2.202500067","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148281895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148122497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148091896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}