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Functional Analysis of an FHOD3 Founder Variant Causing Hypertrophic Cardiomyopathy in the Balkans Population

Heart, Lung and Circulation 2024年 33卷 S97-S98页

作者： R. Bagnall S. Li G. Ranpura M. Holliday B. Hanna J. Ingles S. Kumar C. Semsarian S. Lim Bioinformatics and Molecular Genetics Centenary Institute Newtown NSW Australia The University of Sydney Sydney NSW Australia Agnes Ginges Centre for Molecular Cardiology Centenary Institute Newtown NSW Australia Department of Medical Genetics Westmead Hospital Sydney NSW Australia Genomics and Inherited Disease Program Garvan Institute of Medical Research Sydney NSW Australia Department of Cardiology Royal Prince Alfred Hospital Sydney NSW Australia Department of Cardiology Westmead Hospital Sydney NSW Australia

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Genome-wide analyses identify 30 loci associated with obsessive–compulsive disorder

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Nature Genetics 2025年 1-13页

作者： Strom, Nora I. Gerring, Zachary F. Galimberti, Marco Yu, Dongmei Halvorsen, Matthew W. Abdellaoui, Abdel Rodriguez-Fontenla, Cristina Sealock, Julia M. Bigdeli, Tim Coleman, Jonathan R. Mahjani, Behrang Thorp, Jackson G. Bey, Katharina Burton, Christie L. Luykx, Jurjen J. Zai, Gwyneth Alemany, Silvia Andre, Christine Askland, Kathleen D. Bäckman, Julia Banaj, Nerisa Barlassina, Cristina Nissen, Judith Becker Bienvenu, O. Joseph Black, Donald Bloch, Michael H. Børte, Sigrid Bosch, Rosa Breen, Michael Brennan, Brian P. Brentani, Helena Buxbaum, Joseph D. Bybjerg-Grauholm, Jonas Byrne, Enda M. Cabana-Dominguez, Judit Camarena, Beatriz Camarena, Adrian Cappi, Carolina Carracedo, Angel Casas, Miguel Cavallini, Maria Cristina Ciullo, Valentina Cook, Edwin H. Crosby, Jesse Cullen, Bernadette A. De Schipper, Elles J. Delorme, Richard Djurovic, Srdjan Elias, Jason A. Estivill, Xavier Falkenstein, Martha J. Fundin, Bengt T. Garner, Lauryn Gironda, Christina Goes, Fernando S. Grados, Marco A. Grove, Jakob Guo, Wei Haavik, Jan Hagen, Kristen Harrington, Kelly Havdahl, Alexandra Höffler, Kira D. Hounie, Ana G. Hucks, Donald Hultman, Christina Janecka, Magdalena Jenike, Eric Karlsson, Elinor K. Kelley, Kara Klawohn, Julia Krasnow, Janice E. Krebs, Kristi Lange, Christoph Lanzagorta, Nuria Levey, Daniel Lindblad-Toh, Kerstin Macciardi, Fabio Maher, Brion Mathes, Brittany McArthur, Evonne McGregor, Nathaniel McLaughlin, Nicole C. Meier, Sandra Miguel, Euripedes C. Mulhern, Maureen Nestadt, Paul S. Nurmi, Erika L. O’Connell, Kevin S. Osiecki, Lisa Ousdal, Olga Therese Palviainen, Teemu Pedersen, Nancy L. Piras, Federica Potluri, Sriramya Rabionet, Raquel Ramirez, Alfredo Rauch, Scott Reichenberg, Abraham Riddle, Mark A. Ripke, Stephan Rosário, Maria C. Sampaio, Aline S. Schiele, Miriam A. Skogholt, Anne Heidi Sloofman, Laura G. Smit, Jan Artigas, María Soler Thomas, Laurent F. Tifft, Eric Vallada, Homero van Kirk, Nathanial Veenstra-VanderWeele, Jeremy Vulink, Nienke N. Walker, Christopher P. Wang, Ying Wendland, Jens R. Winsvold Department of Psychology Humboldt-Universität zu Berlin Berlin Germany Department of Psychiatric Phenomics and Genomics (IPPG) Ludwig-Maximilians University Munich Munich Germany Centre for Psychiatry Research Department of Clinical Neuroscience Karolinska Institutet and Stockholm Health Services Region Stockholm Stockholm Sweden Department of Biomedicine Aarhus University Aarhus Denmark University Hospital of Psychiatry and Psychotherapy University of Bern Bern Switzerland Department of Mental Health and Neuroscience Translational Neurogenomics QIMR Berghofer Medical Research Institute Brisbane QLD Australia Department of Population Health and Immunity Healthy Development and Ageing Walter and Eliza Hall Institute of Medical Research Melbourne VIC Australia Department of Psychiatry Human Genetics Yale University New Haven CT United States VA Connecticut Healthcare System West Haven CT United States Department of Center for Genomic Medicine Psychiatric and Neurodevelopmental Genetics Unit Massachusetts General Hospital Boston MA United States Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA United States Department of Genetics University of North Carolina at Chapel Hill Chapel Hill NC United States Department of Psychiatry Amsterdam University Medical Centers University of Amsterdam Amsterdam Netherlands Center for Research in Molecular Medicine and Chronic Diseases (CiMUS) Genomics and Bioinformatics University of Santiago de Compostela Santiago de Compostela Spain Grupo de Medicina Xenómica Genetics Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS) Santiago de Compostela Spain Vanderbilt Genetics Institute Vanderbilt University Nashville TN United States Department of Psychiatry and Behavioral Sciences SUNY Downstate Health Sciences University Brooklyn NY United States VA NY Harbor Healthcare System Brooklyn NY United States Social Genetic and Developmental Psychiatry Centre Insti

Obsessive–compulsive disorder (OCD) affects ~1% of children and adults and is partly caused by genetic factors. We conducted a genome-wide association study (GWAS) meta-analysis combining 53,660 OCD cases and 2,044,417 controls and identified 30 independent genome-wide significant loci. Gene-based approaches identified 249 potential effector genes for OCD, with 25 of these classified as the most likely causal candidates, including WDR6, DALRD3 and CTNND1 and multiple genes in the major histocompatibility complex (MHC) region. We estimated that ~11,500 genetic variants explained 90% of OCD genetic heritability. OCD genetic risk was associated with excitatory neurons in the hippocampus and the cortex, along with D₁ and D₂ type dopamine receptor-containing medium spiny neurons. OCD genetic risk was shared with 65 of 112 additional phenotypes, including all the psychiatric disorders we examined. In particular, OCD shared genetic risk with anxiety, depression, anorexia nervosa and Tourette syndrome and was negatively associated with inflammatory bowel diseases, educational attainment and body mass index. © The Author(s) 2025.

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17P Assessment of the Intratumoral Heterogeneity in Metastatic Breast Cancer (Mbc) Through the Analysis of the Frequency of Pik3Ca Mutant Alleles

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Annals of Oncology 2012年 23卷 ii19-ii20页

作者： L. De Mattos-Arruda J. Cortes A. Sánchez-Pla C. Aura V. Ortega J. Jimenez C. Saura J. Tabernero J. Seoane A. Vivancos Medical Oncology Vall d'Hebron University Hospital Barcelona SPAIN Breast Cancer Program Vall d'Hebron University Hospital Barcelona SPAIN Statistics and Bioinformatics Unit Institut de Recerca of Vall d'Hebron University Hospital Barcelona SPAIN Pathology Department Vall d'Hebron University Hospital. Barcelona SPAIN Gene Expression and Cancer Laboratory Vall d'Hebron Institute of Oncology Barcelona SPAIN Cancer Genomics Laboratory Vall d'Hebron Institute of Oncology Barcelona SPAIN

Introduction The phosphatidylinositol-3-kinase (PI3K) pathway has an important prognostic and predictive significance in MBC. Mutations of PI3KCA could be heterogeneously distributed within the tumor and this could have clinical implications. In this study, we sought to assess the frequency of PIK3CA mutant alleles in different MBC phenotypes taking into account that formalin-fixed paraffin-embedded (FFPE) samples contain non-tumor and tumor areas (TA). Methods The OncoCarta Panel v1.0 (Sequenom) was used to profile 67 consecutive MBC FFPE tumor samples. The relative ratio between the mutant and wild-type alleles (% mutant allele, mA) of PIK3CA mutations was quantified by the MassARRAY® System. The viable tumor zone was scored to determine the TA. Patients (pts) were stratified (luminal, LUM; HER2-positive, HER2; triple negative, TN). Results 26.8% of MBC pts had PIK3CA mutation. PIK3CA mutation in LUM tumors was more frequent than non-LUM (40% vs.15 %, p = 0.047) ( table 1 ). The mean PIK3CA mA (p = 0.029) and the mean TA (p = 0.014) differed among MBC phenotypes. There was a linear relation between mA and TA for the LUM tumors (r =0.71), but when HER2 and TN tumors were also considered, this relation was less substantial (r = 0.53). Conclusion We could assess the intratumoral heterogeneity through the PIK3CA mA/TA ratio in the analyzed tumor samples. In the case of a homogeneous cellular distribution of heterozygous PIK3CA mutations within the tumor mass, the mA/TA ratio should be around 0.5. Interestingly, the mA/TA ratio of PIK3CA in LUM tumors was close to 0.5 while in the HER2 and TN tumors the ratio was lower. This suggests that LUM tumors might be more homogeneous regarding PIK3CA mutation than HER2 and TN. Therefore, PIK3CA oncogenic activation could be an early hit for tumor initiation or progression in LUM tumors and the use of PI3K inhibitors with endocrine therapy could have a greater clinical impact. Table 1 . PIK3CA mutant frequencies in MBC pts. Empt

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Identification of rare coding variants associated with Alzheimer’s disease.

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Alzheimer's & Dementia 2023年第S12期19卷

作者： Zainab Khurshid Lindsay A. Farrer Xiaoling Zhang Eden R. Martin Amanda B Kuzma John Farrell Tong Tong Congcong Zhu Adam C. Naj Laura B Cantwell Otto Valladares Li-San Wang Kathryn L. Lunetta Gerald D. Schellenberg Jonathan L. Haines Yuk Yee Leung Margaret A. Pericak-Vance Boston University Chobanian & Avedisian School of Medicine Boston MA USA Boston University Bioinformatics Program Boston MA USA John P. Hussman Institute for Human Genomics Miller School of Medicine Miami FL USA Penn Neurodegeneration Genomics Center Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Medicine (Biomedical Genetics) Boston University Chobanian & Avedisian School of Medicine Boston MA USA Penn Neurodegeneration Genomics Center Department of Pathology and Laboratory Medicine University of Pennsylvania Perelman School of Medicine Philadelphia PA USA University of Pennsylvania Perelman School of Medicine Philadelphia PA USA Penn Neurodegeneration Genomics Center University of Pennsylvania Perelman School of Medicine Philadelphia PA USA Department of Biostatistics Boston University School of Public Health Boston MA USA Department of Genetics and Genome Sciences Case Western Reserve University School of Medicine Cleveland OH USA University of Miami Miller School of Medicine Miami FL USA

Background Previous whole exome sequencing (WES) studies of Alzheimer’s disease (AD) have identified genome-wide significant associations with rare variants in several novel genes and highlighted the need for investigations in larger samples. We combined WES and whole genome sequencing (WGS) data assembled by the Alzheimer Disease Sequencing Project (ADSP) to increase the power for detecting associations of AD with rare variants in gene coding regions. Method We developed an efficient computational pipeline to perform both pre-merging and post-merging genotype, variant and sample-level quality control (QC) on WGS data containing 16,905 individuals and WES data for 20,504 individuals. The resultant sample included participants from European (EA, 11,279 AD cases, 8,924 controls), African American (AA, 2,757 AD cases, 4,336 controls), and Caribbean Hispanic (CH 1,438 AD cases, 3,256 controls) ancestries. We employed GENESIS to test association of AD with 250,465 bi-allelic QC’d variants using a logistic model including covariates for age, sex, exome capture kit, read length, and ancestry principal components (PCs). Result In the total sample, variants from APOE and other known AD genes including SORL1 (P = 5.30×10-7), NECTIN2 (P = 6.94×10-7), and TREM2 R47H (P = 2.34×10-13) crossed or neared the study-wide significance (SWS) threshold of P = 2.00×10-7 (0.05/250,465). SWS or borderline significant associations were also found with variants in several novel loci including TKTL2 (P = 2.35×10-8), D2HGDH , (P = 1.09×10-7) , CECR1 (P = 4.02×10-7), PDHA2 (P = 2.76×10-7), GOLGA1 (P = 1.72×10-7), CYLD (P = 1.84×10-7), and RP11-243M5.4 (P = 1.37×10-7). PSEN1 missense mutation G206A (rs63750082) previously associated with early onset AD in the CH group, was significantly associated with late onset AD in the same population (P = 1.58×10-13). SWS association of AD with APOE was observed in all groups. Significant associations were also observed with variants in SERPINB8 (P = 3.77×1

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Uncovering the conformational dynamics of dengue virus and its virus-like particles as novel vaccine candidates

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Biophysical Journal 2023年第3期122卷 508a-509a页

作者： Jan K. Marzinek Venkata Raghuvamsi Palur Gielenny Salem Fan-Chi Chen Shang-Rung Wu Peter J. Bond Day-Yu Chao Bioinformatics Institute Agency for Science Technology and Research Singapore Republic of Singapore Graduate Institute of Microbiology and Public Health College of Veterinary Medicine National Chung Hsing University Taichung City Taiwan Microbial Genomics Ph.D. Program National Chung Hsing University Taichung City Taiwan Academia Sinica Taipei Taiwan Department of Dentistry Institute of Oral Medicine National Cheng Kung University Tainan Taiwan Department of Biological Sciences National University of Singapore Singapore Republic of Singapore

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Single‐cell eQTLGen Consortium: A personalized understanding of disease

arXiv

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arXiv 2019年

作者： van der Wijst, M.G. de Vries, D.H. Groot, H.E. Trynka, G. Hon, C.C. Nawijn, M.C. Idaghdour, Y. van der Harst, P. Ye, C.J. Powell, J. Theis, F.J. Mahfouz, A. Heinig, M. Franke, L. Department of Genetics Oncode Institute University of Groningen University Medical Center Groningen Groningen Netherlands Department of Cardiology University of Groningen University Medical Center Groningen Groningen Netherlands Wellcome Trust Sanger Institute Open Targets Wellcome Genome Campus Hinxton Cambridge United Kingdom RIKEN Center for Integrative Medical Sciences Yokohama Japan Department of Pathology and Medical Biology GRIAC Research institute University of Groningen University Medical Center Groningen Netherlands Program in Biology Public Health Research Center New York University Abu Dhabi United Arab Emirates Institute for Human Genetics Bakar Computational Health Sciences Institute Bakar ImmunoX Initiative Division of Rheumatology Department of Medicine Department of Bioengineering and Therapeutic Sciences Department of Epidemiology and Biostatistics Chan Zuckerberg Biohub University of California San Francisco San Francisco United States Garvan‐Weizmann Centre for Cellular Genomics Garvan Institute Sydney Australia UNSW Cellular Genomics Futures Institute University of New South Wales Sydney Australia Institute of Computational Biology Helmholtz Zentrum München Neuherberg Germany Department of Mathematics Technical University of Munich Garching bei München Germany Leiden Computational Biology Center Leiden University Medical Center Leiden Netherlands Delft Bioinformatics Lab Delft University of Technology Delft Netherlands Institute of Computational Biology Helmholtz Zentrum München Neuherberg Germany Department of Informatics Technical University of Munich Garching bei München Germany

In recent years, functional genomics approaches combining genetic information with bulk RNA-sequencing data have identified the downstream expression effects of disease‐associated genetic risk factors through so‐called expression quantitative trait locus (eQTL) analysis. Single‐cell RNA-sequencing creates enormous opportunities for mapping eQTLs across different cell types and in dynamic processes, many of which are obscured when using bulk methods. The enormous increase in throughput and reduction in cost per cell now allow this technology to be applied to large‐scale population genetics studies. Therefore, we have founded the single‐cell eQTLGen consortium (sc-eQTLGen), aimed at pinpointing disease‐causing genetic variants and identifying the cellular contexts in which they affect gene expression. Ultimately, this information can enable development of personalized medicine. Here, we outline the goals, approach, potential utility and early proofs‐of-concept of the sc‐eQTLGen consortium. We also provide a set of study design considerations for future single‐cell eQTL studies. Copyright © 2019, The Authors. All rights reserved.

关键词： RNA

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Genome-wide association studies identify susceptibility loci for epithelial ovarian cancer in east Asian women

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Gynecologic oncology 2019年第2期153卷 343-355页

作者： Kate Lawrenson Fengju Song Dennis J Hazelett Siddhartha P Kar Jonathan Tyrer Catherine M Phelan Rosario I Corona Norma I Rodríguez-Malavé Ji-Hei Seo Emily Adler Simon G Coetzee Felipe Segato Marcos A S Fonseca Christopher I Amos Michael E Carney Georgia Chenevix-Trench Jiyeob Choi Jennifer A Doherty Weihua Jia Gang J Jin Byoung-Gie Kim Nhu D Le Juyeon Lee Lian Li Boon K Lim Noor A Adenan Mika Mizuno Boyoung Park Celeste L Pearce Kang Shan Yongyong Shi Xiao-Ou Shu Weiva Sieh Pamela J Thompson Lynne R Wilkens Qingyi Wei Yin L Woo Li Yan Beth Y Karlan Matthew L Freedman Houtan Noushmehr Ellen L Goode Andrew Berchuck Thomas A Sellers Soo-Hwang Teo Wei Zheng Keitaro Matsuo Sue Park Kexin Chen Paul D P Pharoah Simon A Gayther Marc T Goodman Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute Cedars-Sinai Medical Center 8700 Beverly Boulevard Suite 290W Los Angeles CA USA Center for Bioinformatics and Functional Genomics Cedars Sinai Genomics Core Cedars-Sinai Medical Center Los Angeles CA USA. Electronic address: kate.lawrenson@***. National Clinical Research Center for Cancer Tianjin Medical University Cancer Institute and Hospital Tianjin China Department of Epidemiology and Biostatistics Key Laboratory of Cancer Prevention and Therapy Tianjin China. Center for Bioinformatics and Functional Genomics Cedars Sinai Genomics Core Cedars-Sinai Medical Center Los Angeles CA USA. Department of Oncology Centre for Cancer Genetic Epidemiology University of Cambridge Strangeways Research Laboratory Cambridge UK. Department of Gynecologic Oncology Moffitt Cancer Center Tampa FL USA Department of Cancer Epidemiology Moffitt Cancer Center Tampa FL USA. Center for Bioinformatics and Functional Genomics Cedars Sinai Genomics Core Cedars-Sinai Medical Center Los Angeles CA USA. Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA. Department of Preventive Medicine University of Southern California Keck School of Medicine 1450 Biggy Street Los Angeles CA USA. Department of Genetics Ribeirão Preto Medical School University of São Paulo 14049-900 Brazil. Institute for Clinical and Translational Research Department of Medicine Baylor School of Medicine HoustonTX USA. Department of Obstetrics and Gynecology John A. Burns School of Medicine University of Hawaii Honolulu HI USA. Genetics and Computational Biology Department QIMR Berghofer Medical Research Institute 300 Herston Road Herston QLD 4006 Australia. Department of Preventive Medicine Seoul National University College of Medicine Seoul Republic of Korea Cancer Research Institute Seoul National University Seoul Republic of Korea Department of Biomedical Science Graduate School Seoul National Un

OBJECTIVE:Genome-wide association studies (GWASs) for epithelial ovarian cancer (EOC) have focused largely on populations of European ancestry. We aimed to identify common germline variants associated with EOC risk in Asian women. METHODS:Genotyping was performed as part of the OncoArray project. Samples with >60% Asian ancestry were included in the analysis. Genotyping was performed on 533,631 SNPs in 3238 Asian subjects diagnosed with invasive or borderline EOC and 4083 unaffected controls. After imputation, genotypes were available for 11,595,112 SNPs to identify associations. RESULTS:At chromosome 6p25.2, SNP rs7748275 was associated with risk of serous EOC (odds ratio [OR] = 1.34, P = 8.7 × 10) and high-grade serous EOC (HGSOC) (OR = 1.34, P = 4.3 × 10). SNP rs6902488 at 6p25.2 (r = 0.97 with rs7748275) lies in an active enhancer and is predicted to impact binding of STAT3, P300 and ELF1. We identified additional risk loci with low Bayesian false discovery probability (BFDP) scores, indicating they are likely to be true risk associations (BFDP <10%). At chromosome 20q11.22, rs74272064 was associated with HGSOC risk (OR = 1.27, P = 9.0 × 10). Overall EOC risk was associated with rs10260419 at chromosome 7p21.3 (OR = 1.33, P = 1.2 × 10) and rs74917072 at chromosome 2q37.3 (OR = 1.25, P = 4.7 × 10). At 2q37.3, expression quantitative trait locus analysis in 404 HGSOC tissues identified ESPNL as a putative candidate susceptibility gene (P = 1.2 × 10). CONCLUSION:While some risk loci were shared between East Asian and European populations, others were population-specific, indicating that the landscape of EOC risk in Asian women has both shared and unique features compared to women of European ancestry.

关键词： Asian ancestry Enhancer Epithelial ovarian cancer Gene regulation Genome-wide association study eQTL

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Author Correction: Genotypic characterization of multiple drug resistant Escherichia coli isolates from a pediatric cancer hospital in Egypt

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Scientific reports 2020年第1期10卷 7415页

作者： Reem Hassan Marwa Tantawy Nouran A Gouda Mariam G Elzayat Sara Gabra Amena Nabih Aya A Diab Mohamed El-Hadidi Usama Bakry Mohamed R Shoeb Mervat Elanany Lobna Shalaby Ahmed A Sayed Molecular Microbiology Unit Children's cancer hospital Egypt 57357 Cairo Egypt. Department of clinical pathology Faculty of Medicine Cairo University Cairo Egypt. Genomics Program Children's cancer hospital Egypt 57357 Cairo Egypt. Bioinformatics Group Center of Informatics Sciences (CIS) Nile University Giza Egypt. Microbiology Unit Children's cancer hospital Egypt 57357 Cairo Egypt. Infectious disease unit Children's cancer hospital Egypt 57357 Cairo Egypt. Department of pediatric oncology National cancer Institute Cairo University Cairo Egypt. Genomics Program Children's cancer hospital Egypt 57357 Cairo Egypt. ahmad.sayed@***. Department of Biochemistry Faculty of Science Ain Shams University Cairo Egypt. ahmad.sayed@***.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Author Correction: SARS-CoV-2 infection engenders heterogeneous ribonucleoprotein interactions to impede translation elongation in the lungs

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EXPERIMENTAL AND MOLECULAR MEDICINE 2023年第12期55卷 2609-2609页

作者： Kim, Junsoo Youn, Daehwa Choi, Seunghoon Lee, Youn Woo Sumberzul, Dulguun Yoon, Jeongeun Lee, Hanju Bae, Jong Woo Noh, Hyuna On, Dain Hong, Seung-Min An, Se-Hee Jang, Hui Jeong Kim, Seo Yeon Kim, Young Been Hwang, Ji-Yeon Lee, Hyo-Jung Kim, Hong Bin Park, Jun Won Yun, Jun-Won Shin, Jeon-Soo Seo, Jun-Young Nam, Ki Taek Choi, Kang-Seuk Lee, Ho-Young Chang, Hyeshik Seong, Je Kyung Cho, Jun Center for RNA Research Institute for Basic Science (IBS) Seoul National University Seoul Republic of Korea Interdisciplinary Program in Bioinformatics Seoul National University Seoul Republic of Korea Department of Biomedical Science and Engineering Gwangju Institute of Science and Technology (GIST) Gwangju Republic of Korea Korea Mouse Phenotyping Center (KMPC) Seoul National University Seoul Republic of Korea Laboratory of Developmental Biology and Genomics Research Institute for Veterinary Science and BK 21 PLUS Program for Creative Veterinary Science Research College of Veterinary Medicine Seoul National University Seoul Republic of Korea Department of Nuclear Medicine Seoul National University Bundang Hospital Seongnam Republic of Korea School of Biological Sciences Seoul National University Seoul Republic of Korea Laboratory of Avian Diseases Research Institute for Veterinary Science and BK 21 PLUS Program for Creative Veterinary Science Research College of Veterinary Medicine Seoul National University Seoul Republic of Korea Preclinical Research Center Seoul National University Bundang Hospital Seongnam Republic of Korea Department of Periodontology Section of Dentistry Seoul National University Bundang Hospital Seongnam Republic of Korea Department of Internal Medicine Seoul National University Bundang Hospital Seoul National University College of Medicine Seongnam Republic of Korea Division of Biomedical Convergence College of Biomedical Science Kangwon National University ChunCheon Republic of Korea Laboratory of Veterinary Toxicology College of Veterinary Medicine Seoul National University Seoul Republic of Korea Severance Biomedical Science Institute Graduate School of Medical Science Brain Korea 21 Project Yonsei University College of Medicine Seoul Republic of Korea Department of Nuclear Medicine Seoul National University College of Medicine Seoul Republic of Korea Interdisciplinary Program and BIO MAX Institute Seoul National University

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Genome structures resolve the early diversification of teleost fishes

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Science (New York, N.Y.) 2023年第6632期379卷 572-575页

作者： Elise Parey Alexandra Louis Jerome Montfort Olivier Bouchez Céline Roques Carole Iampietro Jerome Lluch Adrien Castinel Cécile Donnadieu Thomas Desvignes Christabel Floi Bucao Elodie Jouanno Ming Wen Sahar Mejri Ron Dirks Hans Jansen Christiaan Henkel Wei-Jen Chen Margot Zahm Cédric Cabau Christophe Klopp Andrew W Thompson Marc Robinson-Rechavi Ingo Braasch Guillaume Lecointre Julien Bobe John H Postlethwait Camille Berthelot Hugues Roest Crollius Yann Guiguen Institut de Biologie de l'ENS (IBENS) Département de Biologie École Normale Supérieure CNRS INSERM Université PSL Paris France. INRAE LPGP Rennes France. GeT-PlaGe INRAE Genotoul Castanet-Tolosan France. Institute of Neuroscience University of Oregon Eugene OR USA. Department of Ecology and Evolution University of Lausanne Lausanne Switzerland. SIB Swiss Institute of Bioinformatics Lausanne Switzerland. State Key Laboratory of Developmental Biology of Freshwater Fish College of Life Science Hunan Normal University Changsha China. Florida Atlantic University Harbor Branch Oceanographic Institute Fort Pierce FL USA. Future Genomics Technologies Leiden Netherlands. Institute of Biology University of Leiden Leiden Netherlands. Faculty of Veterinary Medicine Norwegian University of Life Sciences Ås Norway. Institute of Oceanography National Taiwan University Taipei 10617 Taiwan. Sigenae GenPhySE INRAE ENVT Université de Toulouse Castanet Tolosan France. Sigenae Genotoul Bioinfo MIAT UR875 INRAE Castanet Tolosan France. Department of Integrative Biology Michigan State University East Lansing MI USA. Ecology Evolution and Behavior Program Michigan State University East Lansing MI USA. Department of Biological Sciences Western Michigan University Kalamazoo MI USA Institut Systématique Evolution Biodiversité (ISYEB) Muséum national d'Histoire naturelle CNRS SU EPHE UA Paris France. Institut Pasteur Université Paris Cité CNRS UMR 3525 INSERM UA12 Comparative Functional Genomics group F-75015 Paris France.

Accurate species phylogenies are a prerequisite for all evolutionary research. Teleosts are the largest and most diversified group of extant vertebrates, but relationships among their three oldest extant lineages remain unresolved. On the basis of seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the topology of the deepest branches of the teleost phylogeny using independent gene sequence and chromosomal rearrangement phylogenomic approaches. These analyses converged to a single scenario that unambiguously places the Elopomorpha and Osteoglossomorpha (arapaima, elephantnose fish) in a monophyletic sister group to all other teleosts, i.e., the Clupeocephala lineage (zebrafish, medaka). This finding resolves more than 50 years of controversy on the evolutionary relationships of these lineages and highlights the power of combining different levels of genome-wide information to solve complex phylogenies.

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