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Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns
IF 64.5 1区 生物学
Cell Pub Date : 2025-03-12 DOI: 10.1016/j.cell.2025.02.013
Rui Dai, Jingying Zhang, Fang Liu, Haoran Xu, Jing-Mei Qian, Shani Cheskis, Weidong Liu, Binglei Wang, Honghui Zhu, Lotte J.U. Pronk, Marnix H. Medema, Ronnie de Jonge, Corné M.J. Pieterse, Asaf Levy, Klaus Schlaeppi, Yang Bai
{"title":"Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns","authors":"Rui Dai, Jingying Zhang, Fang Liu, Haoran Xu, Jing-Mei Qian, Shani Cheskis, Weidong Liu, Binglei Wang, Honghui Zhu, Lotte J.U. Pronk, Marnix H. Medema, Ronnie de Jonge, Corné M.J. Pieterse, Asaf Levy, Klaus Schlaeppi, Yang Bai","doi":"10.1016/j.cell.2025.02.013","DOIUrl":"https://doi.org/10.1016/j.cell.2025.02.013","url":null,"abstract":"Reference genomes of root microbes are essential for metagenomic analyses and mechanistic studies of crop root microbiomes. By combining high-throughput bacterial cultivation with metagenomic sequencing, we constructed comprehensive bacterial and viral genome collections from the roots of wheat, rice, maize, and <em>Medicago</em>. The crop root bacterial genome collection (CRBC) significantly expands the quantity and phylogenetic diversity of publicly available crop root bacterial genomes, with 6,699 bacterial genomes (68.9% from isolates) and 1,817 undefined species, expanding crop root bacterial diversity by 290.6%. The crop root viral genome collection (CRVC) contains 9,736 non-redundant viral genomes, with 1,572 previously unreported genus-level clusters in crop root microbiomes. From these, we identified conserved bacterial functions enriched in root microbiomes across soils and host species and uncovered previously unexplored bacteria-virus connections in crop root ecosystems. Together, the CRBC and CRVC serve as valuable resources for investigating microbial mechanisms and applications, supporting sustainable agriculture.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"4 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143599380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional transcriptional circuits
IF 64.5 1区 生物学
Cell Pub Date : 2025-03-12 DOI: 10.1016/j.cell.2025.02.012
Loϊc Binan, Aiping Jiang, Serwah A. Danquah, Vera Valakh, Brooke Simonton, Jon Bezney, Robert T. Manguso, Kathleen B. Yates, Ralda Nehme, Brian Cleary, Samouil L. Farhi
{"title":"Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional transcriptional circuits","authors":"Loϊc Binan, Aiping Jiang, Serwah A. Danquah, Vera Valakh, Brooke Simonton, Jon Bezney, Robert T. Manguso, Kathleen B. Yates, Ralda Nehme, Brian Cleary, Samouil L. Farhi","doi":"10.1016/j.cell.2025.02.012","DOIUrl":"https://doi.org/10.1016/j.cell.2025.02.012","url":null,"abstract":"Pooled optical screens have enabled the study of cellular interactions, morphology, or dynamics at massive scale, but they have not yet leveraged the power of highly plexed single-cell resolved transcriptomic readouts to inform molecular pathways. Here, we present a combination of imaging spatial transcriptomics with parallel optical detection of <em>in situ</em> amplified guide RNAs (Perturb-FISH). Perturb-FISH recovers intracellular effects that are consistent with single-cell RNA-sequencing-based readouts of perturbation effects (Perturb-seq) in a screen of lipopolysaccharide response in cultured monocytes, and it uncovers intercellular and density-dependent regulation of the innate immune response. Similarly, in three-dimensional xenograft models, Perturb-FISH identifies tumor-immune interactions altered by genetic knockout. When paired with a functional readout in a separate screen of autism spectrum disorder risk genes in human-induced pluripotent stem cell (hIPSC) astrocytes, Perturb-FISH shows common calcium activity phenotypes and their associated genetic interactions and dysregulated molecular pathways. Perturb-FISH is thus a general method for studying the genetic and molecular associations of spatial and functional biology at single-cell resolution.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"5 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143599385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Engineering mtDNA deletions by reconstituting end joining in human mitochondria
IF 64.5 1区 生物学
Cell Pub Date : 2025-03-10 DOI: 10.1016/j.cell.2025.02.009
Yi Fu, Max Land, Tamar Kavlashvili, Ruobing Cui, Minsoo Kim, Emily DeBitetto, Toby Lieber, Keun Woo Ryu, Elim Choi, Ignas Masilionis, Rahul Saha, Meril Takizawa, Daphne Baker, Marco Tigano, Caleb A. Lareau, Ed Reznik, Roshan Sharma, Ronan Chaligne, Craig B. Thompson, Dana Pe’er, Agnel Sfeir
{"title":"Engineering mtDNA deletions by reconstituting end joining in human mitochondria","authors":"Yi Fu, Max Land, Tamar Kavlashvili, Ruobing Cui, Minsoo Kim, Emily DeBitetto, Toby Lieber, Keun Woo Ryu, Elim Choi, Ignas Masilionis, Rahul Saha, Meril Takizawa, Daphne Baker, Marco Tigano, Caleb A. Lareau, Ed Reznik, Roshan Sharma, Ronan Chaligne, Craig B. Thompson, Dana Pe’er, Agnel Sfeir","doi":"10.1016/j.cell.2025.02.009","DOIUrl":"https://doi.org/10.1016/j.cell.2025.02.009","url":null,"abstract":"Recent breakthroughs in the genetic manipulation of mitochondrial DNA (mtDNA) have enabled precise base substitutions and the efficient elimination of genomes carrying pathogenic mutations. However, reconstituting mtDNA deletions linked to mitochondrial myopathies remains challenging. Here, we engineered mtDNA deletions in human cells by co-expressing end-joining (EJ) machinery and targeted endonucleases. Using mitochondrial EJ (mito-EJ) and mito-ScaI, we generated a panel of clonal cell lines harboring a ∼3.5 kb mtDNA deletion across the full spectrum of heteroplasmy. Investigating these cells revealed a critical threshold of ∼75% deleted genomes, beyond which oxidative phosphorylation (OXPHOS) protein depletion, metabolic disruption, and impaired growth in galactose-containing media were observed. Single-cell multiomic profiling identified two distinct nuclear gene deregulation responses: one triggered at the deletion threshold and another progressively responding to heteroplasmy. Ultimately, we show that our method enables the modeling of disease-associated mtDNA deletions across cell types and could inform the development of targeted therapies.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"91 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143582603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genome-scale resources in the infant gut symbiont Bifidobacterium breve reveal genetic determinants of colonization and host-microbe interactions
IF 64.5 1区 生物学
Cell Pub Date : 2025-03-10 DOI: 10.1016/j.cell.2025.02.010
Anthony L. Shiver, Jiawei Sun, Rebecca Culver, Arvie Violette, Char Wynter, Marta Nieckarz, Samara Paula Mattiello, Prabhjot Kaur Sekhon, Francesca Bottacini, Lisa Friess, Hans K. Carlson, Daniel P.G.H. Wong, Steven Higginbottom, Meredith Weglarz, Weigao Wang, Benjamin D. Knapp, Emma Guiberson, Juan Sanchez, Po-Hsun Huang, Paulo A. Garcia, Kerwyn Casey Huang
{"title":"Genome-scale resources in the infant gut symbiont Bifidobacterium breve reveal genetic determinants of colonization and host-microbe interactions","authors":"Anthony L. Shiver, Jiawei Sun, Rebecca Culver, Arvie Violette, Char Wynter, Marta Nieckarz, Samara Paula Mattiello, Prabhjot Kaur Sekhon, Francesca Bottacini, Lisa Friess, Hans K. Carlson, Daniel P.G.H. Wong, Steven Higginbottom, Meredith Weglarz, Weigao Wang, Benjamin D. Knapp, Emma Guiberson, Juan Sanchez, Po-Hsun Huang, Paulo A. Garcia, Kerwyn Casey Huang","doi":"10.1016/j.cell.2025.02.010","DOIUrl":"https://doi.org/10.1016/j.cell.2025.02.010","url":null,"abstract":"Bifidobacteria represent a dominant constituent of human gut microbiomes during infancy, influencing nutrition, immune development, and resistance to infection. Despite interest in bifidobacteria as a live biotic therapy, our understanding of colonization, host-microbe interactions, and the health-promoting effects of bifidobacteria is limited. To address these major knowledge gaps, we used a large-scale genetic approach to create a mutant fitness compendium in <em>Bifidobacterium breve</em>. First, we generated a high-density randomly barcoded transposon insertion pool and used it to determine fitness requirements during colonization of germ-free mice and chickens with multiple diets and in response to hundreds of <em>in vitro</em> perturbations. Second, to enable mechanistic investigation, we constructed an ordered collection of insertion strains covering 1,462 genes. We leveraged these tools to reveal community- and diet-specific requirements for colonization and to connect the production of immunomodulatory molecules to growth benefits. These resources will catalyze future investigations of this important beneficial microbe.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"86 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143582600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Polarity-guided uneven mitotic divisions control brassinosteroid activity in proliferating plant root cells 极性引导的不均匀有丝分裂控制增殖植物根细胞中的黄铜素活性
IF 64.5 1区 生物学
Cell Pub Date : 2025-03-10 DOI: 10.1016/j.cell.2025.02.011
Nemanja Vukašinović, Che-Wei Hsu, Marco Marconi, Shaopeng Li, Christopher Zachary, Rachel Shahan, Pablo Szekley, Ziv Aardening, Isabelle Vanhoutte, Qian Ma, Lucrezia Pinto, Pavel Krupař, Nathan German, Jingyuan Zhang, Claire Simon--Vezo, Jessica Perez-Sancho, Pepe Cana Quijada, Qianzi Zhou, Laura R. Lee, Jianghua Cai, Eugenia Russinova
{"title":"Polarity-guided uneven mitotic divisions control brassinosteroid activity in proliferating plant root cells","authors":"Nemanja Vukašinović, Che-Wei Hsu, Marco Marconi, Shaopeng Li, Christopher Zachary, Rachel Shahan, Pablo Szekley, Ziv Aardening, Isabelle Vanhoutte, Qian Ma, Lucrezia Pinto, Pavel Krupař, Nathan German, Jingyuan Zhang, Claire Simon--Vezo, Jessica Perez-Sancho, Pepe Cana Quijada, Qianzi Zhou, Laura R. Lee, Jianghua Cai, Eugenia Russinova","doi":"10.1016/j.cell.2025.02.011","DOIUrl":"https://doi.org/10.1016/j.cell.2025.02.011","url":null,"abstract":"Brassinosteroid hormones are positive regulators of plant organ growth, yet their function in proliferating tissues remains unclear. Here, through integrating single-cell RNA sequencing with long-term live-cell imaging of the <em>Arabidopsis</em> root, we reveal that brassinosteroid activity fluctuates throughout the cell cycle, decreasing during mitotic divisions and increasing during the G1 phase. The post-mitotic recovery of brassinosteroid activity is driven by the intrinsic polarity of the mother cell, resulting in one daughter cell with enhanced brassinosteroid signaling, while the other supports brassinosteroid biosynthesis. The coexistence of these distinct daughter cell states during the G1 phase circumvents a negative feedback loop to facilitate brassinosteroid production while signaling increases. Our findings uncover polarity-guided, uneven mitotic divisions in the meristem, which control brassinosteroid hormone activity to ensure optimal root growth.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"38 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143582602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Evolution of KoRV-A transcriptional silencing in wild koalas
IF 64.5 1区 生物学
Cell Pub Date : 2025-03-07 DOI: 10.1016/j.cell.2025.02.006
Tianxiong Yu, Michaela B.J. Blyton, Milky Abajorga, Birgit S. Koppetsch, Samantha Ho, Bo Xu, Zhongren Hu, Jeremy Luban, Keith Chappell, Zhiping Weng, William E. Theurkauf
{"title":"Evolution of KoRV-A transcriptional silencing in wild koalas","authors":"Tianxiong Yu, Michaela B.J. Blyton, Milky Abajorga, Birgit S. Koppetsch, Samantha Ho, Bo Xu, Zhongren Hu, Jeremy Luban, Keith Chappell, Zhiping Weng, William E. Theurkauf","doi":"10.1016/j.cell.2025.02.006","DOIUrl":"https://doi.org/10.1016/j.cell.2025.02.006","url":null,"abstract":"Koala retrovirus-A (KoRV-A) is spreading through wild koalas in a north-to-south wave while transducing the germ line, modifying the inherited genome as it transitions to an endogenous retrovirus. Previously, we found that KoRV-A is expressed in the germ line, but unspliced genomic transcripts are processed into sense-strand PIWI-interacting RNAs (piRNAs), which may provide an initial “innate” form of post-transcriptional silencing. Here, we show that this initial post-transcriptional response is prevalent south of the Brisbane River, whereas KoRV-A expression is suppressed, promoters are methylated, and sense and antisense piRNAs are equally abundant in a subpopulation of animals north of the river. These animals share a KoRV-A provirus in the <em>MAP4K4</em> gene’s 3′ UTR that is spreading through northern koalas and produces hybrid transcripts that are processed into antisense piRNAs, which guide transcriptional silencing. We speculate that this provirus triggers adaptive transcriptional silencing of KoRV-A and is sweeping to fixation.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"2 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143569641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Functional diversification of dietary plant small molecules by the gut microbiome
IF 64.5 1区 生物学
Cell Pub Date : 2025-03-07 DOI: 10.1016/j.cell.2025.01.045
Gavin A. Kuziel, Gabriel L. Lozano, Corina Simian, Long Li, John Manion, Emmanuel Stephen-Victor, Talal Chatila, Min Dong, Jing-Ke Weng, Seth Rakoff-Nahoum
{"title":"Functional diversification of dietary plant small molecules by the gut microbiome","authors":"Gavin A. Kuziel, Gabriel L. Lozano, Corina Simian, Long Li, John Manion, Emmanuel Stephen-Victor, Talal Chatila, Min Dong, Jing-Ke Weng, Seth Rakoff-Nahoum","doi":"10.1016/j.cell.2025.01.045","DOIUrl":"https://doi.org/10.1016/j.cell.2025.01.045","url":null,"abstract":"Plants are composed of diverse secondary metabolites (PSMs), which are widely associated with human health. Whether and how the gut microbiome mediates such impacts of PSMs is poorly understood. Here, we show that discrete dietary and medicinal phenolic glycosides, abundant health-associated PSMs, are utilized by distinct members of the human gut microbiome. Within the <em>Bacteroides</em>, the predominant gram-negative bacteria of the Western human gut, we reveal a specialized multi-enzyme system dedicated to the processing of distinct glycosides based on structural differences in phenolic moieties. This <em>Bacteroides</em> metabolic system liberates chemically distinct aglycones with diverse biological functions, such as colonization resistance against the gut pathogen <em>Clostridioides difficile</em> via anti-microbial activation of polydatin to the stilbene resveratrol and intestinal homeostasis via activation of salicin to the immunoregulatory aglycone saligenin. Together, our results demonstrate generation of biological diversity of phenolic aglycone “effector” functions by a distinct gut-microbiome-encoded PSM-processing system.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"17 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143569642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Sampling representational plasticity of simple imagined movements across days enables long-term neuroprosthetic control
IF 64.5 1区 生物学
Cell Pub Date : 2025-03-06 DOI: 10.1016/j.cell.2025.02.001
Nikhilesh Natraj, Sarah Seko, Reza Abiri, Runfeng Miao, Hongyi Yan, Yasmin Graham, Adelyn Tu-Chan, Edward F. Chang, Karunesh Ganguly
{"title":"Sampling representational plasticity of simple imagined movements across days enables long-term neuroprosthetic control","authors":"Nikhilesh Natraj, Sarah Seko, Reza Abiri, Runfeng Miao, Hongyi Yan, Yasmin Graham, Adelyn Tu-Chan, Edward F. Chang, Karunesh Ganguly","doi":"10.1016/j.cell.2025.02.001","DOIUrl":"https://doi.org/10.1016/j.cell.2025.02.001","url":null,"abstract":"The nervous system needs to balance the stability of neural representations with plasticity. It is unclear what the representational stability of simple well-rehearsed actions is, particularly in humans, and their adaptability to new contexts. Using an electrocorticography brain-computer interface (BCI) in tetraplegic participants, we found that the low-dimensional manifold and relative representational distances for a repertoire of simple imagined movements were remarkably stable. The manifold’s absolute location, however, demonstrated constrained day-to-day drift. Strikingly, neural statistics, especially variance, could be flexibly regulated to increase representational distances during BCI control without somatotopic changes. Discernability strengthened with practice and was BCI-specific, demonstrating contextual specificity. Sampling representational plasticity and drift across days subsequently uncovered a meta-representational structure with generalizable decision boundaries for the repertoire; this allowed long-term neuroprosthetic control of a robotic arm and hand for reaching and grasping. Our study offers insights into mesoscale representational statistics that also enable long-term complex neuroprosthetic control.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"16 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
MEER: Extraordinary flourishing ecosystem in the deepest ocean
IF 64.5 1区 生物学
Cell Pub Date : 2025-03-06 DOI: 10.1016/j.cell.2024.12.037
Xiang Xiao, Jian Wang, Kang Ding
{"title":"MEER: Extraordinary flourishing ecosystem in the deepest ocean","authors":"Xiang Xiao, Jian Wang, Kang Ding","doi":"10.1016/j.cell.2024.12.037","DOIUrl":"https://doi.org/10.1016/j.cell.2024.12.037","url":null,"abstract":"Here, we introduce the Mariana Trench Environment and Ecology Research (MEER) project, which provides the first systematic view of the ecosystem in the hadal zone.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"31 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Evolution and genetic adaptation of fishes to the deep sea
IF 64.5 1区 生物学
Cell Pub Date : 2025-03-06 DOI: 10.1016/j.cell.2025.01.002
Han Xu, Chengchi Fang, Wenjie Xu, Cheng Wang, Yue Song, Chenglong Zhu, Wenyu Fang, Guangyi Fan, Wenqi Lv, Jing Bo, Honghui Zeng, Zhongli Sha, Helu Liu, Hongmei Jing, Hao Liu, Taoshu Wei, Jiwei Li, Lisheng He, Shanya Cai, Xiaoni Gan, Shunping He
{"title":"Evolution and genetic adaptation of fishes to the deep sea","authors":"Han Xu, Chengchi Fang, Wenjie Xu, Cheng Wang, Yue Song, Chenglong Zhu, Wenyu Fang, Guangyi Fan, Wenqi Lv, Jing Bo, Honghui Zeng, Zhongli Sha, Helu Liu, Hongmei Jing, Hao Liu, Taoshu Wei, Jiwei Li, Lisheng He, Shanya Cai, Xiaoni Gan, Shunping He","doi":"10.1016/j.cell.2025.01.002","DOIUrl":"https://doi.org/10.1016/j.cell.2025.01.002","url":null,"abstract":"The deep sea, especially hadal zones, characterized by high-hydrostatic pressure, low temperatures, and near-total darkness, present some of the most challenging environments for life on Earth. However, teleost fish have successfully colonized these extreme habitats through complex adaptations. We generated genome assemblies of 12 species, including 11 deep-sea fishes. Our findings reconstructed the teleost deep-sea colonization history and revealed the overall impact of the deep-sea environment on fishes. Interestingly, our results question the previously assumed linear correlation between trimethylamine oxide (TMAO) content and depth. By contrast, we observed a convergent aa replacement in the <em>rtf1</em> gene in most deep-sea fishes under 3,000 m, and <em>in vitro</em> experiments suggest that this mutation can influence transcriptional efficiency, which is likely to be advantageous in the deep-sea environment. Moreover, our study underlines the pervasive impact of human activities, as we detected the presence of persistent organic pollutants in species from the Mariana Trench.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"4 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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