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Teng JLL, Tang Y, Wong SSY, Yeung ML, Cai JP, Chen C, Chan E, Fong JYH, Au-Yeung RKH, Xiong L, Lau TCK, Lau SKP, Woo PCY. Mycolyltransferase is important for biofilm formation and pathogenesis of Tsukamurella keratitis. Emerg Microbes Infect 2024; 13:2373317. [PMID: 38934251 DOI: 10.1080/22221751.2024.2373317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/22/2024] [Indexed: 06/28/2024]
Abstract
Tsukamurella, a group of multi-drug resistant, Gram-positive, aerobic, and partially acid-fast bacteria, are emerging causes of bacterial conjunctivitis and keratitis. However, the pathogenesis of Tsukamurella keratitis is largely unknown. To address this, we used New Zealand White rabbits to develop the first eye infection model and conducted in vitro tests to study the pathogenesis mechanisms of Tsukamurella. There is increasing evidence that biofilms play a significant role in ocular infections, leading us to hypothesize that biofilm formation is crucial for effective Tsukamurella infection. In order to look for potential candidate genes which are important in biofilm formation and Tsukamurella keratitis. We performed genome sequencing of two ocular isolates, T. pulmonis-PW1004 and T. tyrosinosolvens-PW899, to identify potential virulence factors. Through in vitro and in vivo studies, we characterized their biological roles in mediating Tsukamurella keratitis. Our findings confirmed that Tsukamurella is an ocular pathogen by fulfilling Koch's postulates, and using genome sequence data, we identified tmytC, encoding a mycolyltransferase, as a crucial gene in biofilm formation and causing Tsukamurella keratitis in the rabbit model. This is the first report demonstrating the novel role of mycolyltransferase in causing ocular infections. Overall, our findings contribute to a better understanding of Tsukamurella pathogenesis and provide a potential target for treatment. Specific inhibitors targeting TmytC could serve as an effective treatment option for Tsukamurella infections.
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Affiliation(s)
- Jade Lee-Lee Teng
- Faculty of Dentistry, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People's Republic of China
| | - Ying Tang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People's Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People's Republic of China
| | - Samson Sai-Yin Wong
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People's Republic of China
| | - Man Lung Yeung
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People's Republic of China
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People's Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People's Republic of China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, Hong Kong, People's Republic of China
| | - Jian-Pao Cai
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People's Republic of China
| | - Chen Chen
- Beijing Ditan Hospital, Capital Medical University, Beijing Key Laboratory of Emerging infectious Diseases, Beijing, People's Republic of China
| | - Elaine Chan
- Faculty of Dentistry, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People's Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People's Republic of China
| | - Jordan Yik-Hei Fong
- Faculty of Dentistry, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People's Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People's Republic of China
| | - Rex Kwok-Him Au-Yeung
- Department of Pathology, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People's Republic of China
| | - Lifeng Xiong
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People's Republic of China
| | - Terrence Chi-Kong Lau
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People's Republic of China
| | - Susanna Kar-Pui Lau
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People's Republic of China
| | - Patrick Chiu-Yat Woo
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People's Republic of China
- Doctoral Program in Translational Medicine and Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- The iEGG and Animal Biotechnology Research Center, National Chung Hsing University, Taichung, Taiwan
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2
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Do DT, Yang MR, Vo TNS, Le NQK, Wu YW. Unitig-centered pan-genome machine learning approach for predicting antibiotic resistance and discovering novel resistance genes in bacterial strains. Comput Struct Biotechnol J 2024; 23:1864-1876. [PMID: 38707536 PMCID: PMC11067008 DOI: 10.1016/j.csbj.2024.04.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 04/13/2024] [Accepted: 04/13/2024] [Indexed: 05/07/2024] Open
Abstract
In current genomic research, the widely used methods for predicting antimicrobial resistance (AMR) often rely on prior knowledge of known AMR genes or reference genomes. However, these methods have limitations, potentially resulting in imprecise predictions owing to incomplete coverage of AMR mechanisms and genetic variations. To overcome these limitations, we propose a pan-genome-based machine learning approach to advance our understanding of AMR gene repertoires and uncover possible feature sets for precise AMR classification. By building compacted de Brujin graphs (cDBGs) from thousands of genomes and collecting the presence/absence patterns of unique sequences (unitigs) for Pseudomonas aeruginosa, we determined that using machine learning models on unitig-centered pan-genomes showed significant promise for accurately predicting the antibiotic resistance or susceptibility of microbial strains. Applying a feature-selection-based machine learning algorithm led to satisfactory predictive performance for the training dataset (with an area under the receiver operating characteristic curve (AUC) of > 0.929) and an independent validation dataset (AUC, approximately 0.77). Furthermore, the selected unitigs revealed previously unidentified resistance genes, allowing for the expansion of the resistance gene repertoire to those that have not previously been described in the literature on antibiotic resistance. These results demonstrate that our proposed unitig-based pan-genome feature set was effective in constructing machine learning predictors that could accurately identify AMR pathogens. Gene sets extracted using this approach may offer valuable insights into expanding known AMR genes and forming new hypotheses to uncover the underlying mechanisms of bacterial AMR.
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Affiliation(s)
- Duyen Thi Do
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Ming-Ren Yang
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Department of Electrical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Tran Nam Son Vo
- Department of Business Administration, College of Management, Lunghwa University of Science and Technology, Taoyuan City, Taiwan
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei, Taiwan
- TMU Research Center for Digestive Medicine, Taipei Medical University, Taipei, Taiwan
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3
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Woo HJ, Kim J, Kim SM, Kim D, Moon JY, Park D, Lee JS. Context-dependent genomic locus effects on antibody production in recombinant Chinese hamster ovary cells generated through random integration. Comput Struct Biotechnol J 2024; 23:1654-1665. [PMID: 38680870 PMCID: PMC11046053 DOI: 10.1016/j.csbj.2024.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/30/2024] [Accepted: 04/07/2024] [Indexed: 05/01/2024] Open
Abstract
High-yield production of therapeutic protein using Chinese hamster ovary (CHO) cells requires stable cell line development (CLD). CLD typically uses random integration of transgenes; however, this results in clonal variation and subsequent laborious clone screening. Therefore, site-specific integration of a protein expression cassette into a desired chromosomal locus showing high transcriptional activity and stability, referred to as a hot spot, is emerging. Although positional effects are important for therapeutic protein expression, the sequence-specific mechanisms by which hotspots work are not well understood. In this study, we performed whole-genome sequencing (WGS) to locate randomly inserted vectors in the genome of recombinant CHO cells expressing high levels of monoclonal antibodies (mAbs) and experimentally validated these locations and vector compositions. The integration site was characterized by active histone marks and potential enhancer activities, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) mediated indel mutations in the region upstream of the integration site led to a significant reduction in specific antibody productivity by up to 30%. Notably, the integration site and its core region did not function equivalently outside the native genomic context, showing a minimal effect on the increase in exogenous protein expression in the host cell line. We also observed a superior production capacity of the mAb expressing cell line compared to that of the host cell line. Collectively, this study demonstrates that developing recombinant CHO cell lines to produce therapeutic proteins at high levels requires a balance of factors including transgene configuration, genomic locus landscape, and host cell properties.
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Affiliation(s)
- Hyun Jee Woo
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Jaehoon Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
- Molecular Science and Technology Research Center, Ajou University, Suwon 16499, Republic of Korea
| | - Seul Mi Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Dongwoo Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Jae Yun Moon
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Daechan Park
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
- Department of Biological Sciences, Ajou University, Suwon 16499, Republic of Korea
| | - Jae Seong Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 16499, Republic of Korea
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4
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Sorée M, Lozach S, Kéomurdjian N, Richard D, Hughes A, Delbarre-Ladrat C, Verrez-Bagnis V, Rincé A, Passerini D, Ritchie JM, Heath DH. Virulence phenotypes differ between toxigenic Vibrio parahaemolyticus isolated from western coasts of Europe. Microbiol Res 2024; 285:127744. [PMID: 38735242 DOI: 10.1016/j.micres.2024.127744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 04/19/2024] [Accepted: 04/30/2024] [Indexed: 05/14/2024]
Abstract
Vibrio parahaemolyticus is the leading bacterial cause of gastroenteritis associated with seafood consumption worldwide. Not all members of the species are thought to be pathogenic, thus identification of virulent organisms is essential to protect public health and the seafood industry. Correlations of human disease and known genetic markers (e.g. thermostable direct hemolysin (TDH), TDH-related hemolysin (TRH)) appear complex. Some isolates recovered from patients lack these factors, while their presence has become increasingly noted in isolates recovered from the environment. Here, we used whole-genome sequencing in combination with mammalian and insect models of infection to assess the pathogenic potential of V. parahaemolyticus isolated from European Atlantic shellfish production areas. We found environmental V. parahaemolyticus isolates harboured multiple virulence-associated genes, including TDH and/or TRH. However, carriage of these factors did not necessarily reflect virulence in the mammalian intestine, as an isolate containing TDH and the genes coding for a type 3 secretion system (T3SS) 2α virulence determinant, appeared avirulent. Moreover, environmental V. parahaemolyticus lacking TDH or TRH could be assigned to groups causing low and high levels of mortality in insect larvae, with experiments using defined bacterial mutants showing that a functional T3SS1 contributed to larval death. When taken together, our findings highlight the genetic diversity of V. parahaemolyticus isolates found in the environment, their potential to cause disease and the need for a more systematic evaluation of virulence in diverse V. parahaemolyticus to allow better genetic markers.
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Affiliation(s)
| | - Solen Lozach
- Ifremer, Univ Brest, CNRS, IRD, LEMAR, Plouzané F-29280, France
| | | | | | - Alexandra Hughes
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | | | | | - Alain Rincé
- Biotargen, Université de Caen Normandie, Saint-Contest F-14380, France
| | | | - Jennifer M Ritchie
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom.
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5
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Seng R, Chomkatekaew C, Tandhavanant S, Saiprom N, Phunpang R, Thaipadungpanit J, Batty EM, Day NPJ, Chantratita W, Eoin West T, Thomson NR, Parkhill J, Chewapreecha C, Chantratita N. Genetic diversity, determinants, and dissemination of Burkholderia pseudomallei lineages implicated in melioidosis in Northeast Thailand. Nat Commun 2024; 15:5699. [PMID: 38972886 DOI: 10.1038/s41467-024-50067-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 06/28/2024] [Indexed: 07/09/2024] Open
Abstract
Melioidosis is an often-fatal neglected tropical disease caused by an environmental bacterium Burkholderia pseudomallei. However, our understanding of the disease-causing bacterial lineages, their dissemination, and adaptive mechanisms remains limited. To address this, we conduct a comprehensive genomic analysis of 1,391 B. pseudomallei isolates collected from nine hospitals in northeast Thailand between 2015 and 2018, and contemporaneous isolates from neighbouring countries, representing the most densely sampled collection to date. Our study identifies three dominant lineages, each with unique gene sets potentially enhancing bacterial fitness in the environment. We find that recombination drives lineage-specific gene flow. Transcriptome analyses of representative clinical isolates from each dominant lineage reveal increased expression of lineage-specific genes under environmental conditions in two out of three lineages. This underscores the potential importance of environmental persistence for these dominant lineages. The study also highlights the influence of environmental factors such as terrain slope, altitude, and river direction on the geographical dispersal of B. pseudomallei. Collectively, our findings suggest that environmental persistence may play a role in facilitating the spread of B. pseudomallei, and as a prerequisite for exposure and infection, thereby providing useful insights for informing melioidosis prevention and control strategies.
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Affiliation(s)
- Rathanin Seng
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Chalita Chomkatekaew
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sarunporn Tandhavanant
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Natnaree Saiprom
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rungnapa Phunpang
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Janjira Thaipadungpanit
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Elizabeth M Batty
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas P J Day
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - T Eoin West
- Division of Pulmonary, Critical Care & Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Nicholas R Thomson
- Parasites and Microbes Wellcome Sanger Institute, Cambridge, UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Claire Chewapreecha
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
- Parasites and Microbes Wellcome Sanger Institute, Cambridge, UK.
- Previous Affiliations: Bioinformatics and Systems Biology Program, School of Bioresource and Technology, King Mongkut University of Technology Thonburi, Bangkok, Thailand.
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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6
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Weimann A, Dinan AM, Ruis C, Bernut A, Pont S, Brown K, Ryan J, Santos L, Ellison L, Ukor E, Pandurangan AP, Krokowski S, Blundell TL, Welch M, Blane B, Judge K, Bousfield R, Brown N, Bryant JM, Kukavica-Ibrulj I, Rampioni G, Leoni L, Harrison PT, Peacock SJ, Thomson NR, Gauthier J, Fothergill JL, Levesque RC, Parkhill J, Floto RA. Evolution and host-specific adaptation of Pseudomonas aeruginosa. Science 2024; 385:eadi0908. [PMID: 38963857 DOI: 10.1126/science.adi0908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/02/2024] [Indexed: 07/06/2024]
Abstract
The major human bacterial pathogen Pseudomonas aeruginosa causes multidrug-resistant infections in people with underlying immunodeficiencies or structural lung diseases such as cystic fibrosis (CF). We show that a few environmental isolates, driven by horizontal gene acquisition, have become dominant epidemic clones that have sequentially emerged and spread through global transmission networks over the past 200 years. These clones demonstrate varying intrinsic propensities for infecting CF or non-CF individuals (linked to specific transcriptional changes enabling survival within macrophages); have undergone multiple rounds of convergent, host-specific adaptation; and have eventually lost their ability to transmit between different patient groups. Our findings thus explain the pathogenic evolution of P. aeruginosa and highlight the importance of global surveillance and cross-infection prevention in averting the emergence of future epidemic clones.
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Affiliation(s)
- Aaron Weimann
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Adam M Dinan
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | - Christopher Ruis
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Audrey Bernut
- Laboratory of Pathogens and Host Immunity (LPHI), UMR5235, CNRS/Université de Montpellier, Montpellier, France
| | - Stéphane Pont
- Laboratory of Pathogens and Host Immunity (LPHI), UMR5235, CNRS/Université de Montpellier, Montpellier, France
| | - Karen Brown
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, UK
| | - Judy Ryan
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Lúcia Santos
- Department of Physiology, Bioscience Institute, University College Cork, Cork, Ireland
| | - Louise Ellison
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Emem Ukor
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, UK
| | - Arun P Pandurangan
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Sina Krokowski
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Tom L Blundell
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Beth Blane
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kim Judge
- Wellcome Sanger Institute, Hinxton, UK
| | - Rachel Bousfield
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals Trust, Cambridge, UK
| | | | | | - Irena Kukavica-Ibrulj
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Québec, Canada
| | - Giordano Rampioni
- Department of Science, University Roma Tre, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Livia Leoni
- Department of Science, University Roma Tre, Rome, Italy
| | - Patrick T Harrison
- Department of Physiology, Bioscience Institute, University College Cork, Cork, Ireland
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals Trust, Cambridge, UK
| | - Nicholas R Thomson
- Wellcome Sanger Institute, Hinxton, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Jeff Gauthier
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Québec, Canada
| | - Jo L Fothergill
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
| | - Roger C Levesque
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Québec, Canada
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - R Andres Floto
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals Trust, Cambridge, UK
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7
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Belman S, Lefrancq N, Nzenze S, Downs S, du Plessis M, Lo SW, McGee L, Madhi SA, von Gottberg A, Bentley SD, Salje H. Geographical migration and fitness dynamics of Streptococcus pneumoniae. Nature 2024:10.1038/s41586-024-07626-3. [PMID: 38961295 DOI: 10.1038/s41586-024-07626-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 05/30/2024] [Indexed: 07/05/2024]
Abstract
Streptococcus pneumoniae is a leading cause of pneumonia and meningitis worldwide. Many different serotypes co-circulate endemically in any one location1,2. The extent and mechanisms of spread and vaccine-driven changes in fitness and antimicrobial resistance remain largely unquantified. Here using geolocated genome sequences from South Africa (n = 6,910, collected from 2000 to 2014), we developed models to reconstruct spread, pairing detailed human mobility data and genomic data. Separately, we estimated the population-level changes in fitness of strains that are included (vaccine type (VT)) and not included (non-vaccine type (NVT)) in pneumococcal conjugate vaccines, first implemented in South Africa in 2009. Differences in strain fitness between those that are and are not resistant to penicillin were also evaluated. We found that pneumococci only become homogenously mixed across South Africa after 50 years of transmission, with the slow spread driven by the focal nature of human mobility. Furthermore, in the years following vaccine implementation, the relative fitness of NVT compared with VT strains increased (relative risk of 1.68; 95% confidence interval of 1.59-1.77), with an increasing proportion of these NVT strains becoming resistant to penicillin. Our findings point to highly entrenched, slow transmission and indicate that initial vaccine-linked decreases in antimicrobial resistance may be transient.
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Affiliation(s)
- Sophie Belman
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Global Health Resilience, Earth Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain.
| | - Noémie Lefrancq
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Susan Nzenze
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Sarah Downs
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
| | - Lesley McGee
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shabir A Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | | | - Henrik Salje
- Department of Genetics, University of Cambridge, Cambridge, UK
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8
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Thomas A, Battenfeld T, Kraiselburd I, Anastasiou O, Dittmer U, Dörr AK, Dörr A, Elsner C, Gosch J, Le-Trilling VTK, Magin S, Scholtysik R, Yilmaz P, Trilling M, Schöler L, Köster J, Meyer F. UnCoVar: a reproducible and scalable workflow for transparent and robust virus variant calling and lineage assignment using SARS-CoV-2 as an example. BMC Genomics 2024; 25:647. [PMID: 38943066 PMCID: PMC11214259 DOI: 10.1186/s12864-024-10539-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/18/2024] [Indexed: 07/01/2024] Open
Abstract
BACKGROUND At a global scale, the SARS-CoV-2 virus did not remain in its initial genotype for a long period of time, with the first global reports of variants of concern (VOCs) in late 2020. Subsequently, genome sequencing has become an indispensable tool for characterizing the ongoing pandemic, particularly for typing SARS-CoV-2 samples obtained from patients or environmental surveillance. For such SARS-CoV-2 typing, various in vitro and in silico workflows exist, yet to date, no systematic cross-platform validation has been reported. RESULTS In this work, we present the first comprehensive cross-platform evaluation and validation of in silico SARS-CoV-2 typing workflows. The evaluation relies on a dataset of 54 patient-derived samples sequenced with several different in vitro approaches on all relevant state-of-the-art sequencing platforms. Moreover, we present UnCoVar, a robust, production-grade reproducible SARS-CoV-2 typing workflow that outperforms all other tested approaches in terms of precision and recall. CONCLUSIONS In many ways, the SARS-CoV-2 pandemic has accelerated the development of techniques and analytical approaches. We believe that this can serve as a blueprint for dealing with future pandemics. Accordingly, UnCoVar is easily generalizable towards other viral pathogens and future pandemics. The fully automated workflow assembles virus genomes from patient samples, identifies existing lineages, and provides high-resolution insights into individual mutations. UnCoVar includes extensive quality control and automatically generates interactive visual reports. UnCoVar is implemented as a Snakemake workflow. The open-source code is available under a BSD 2-clause license at github.com/IKIM-Essen/uncovar.
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Affiliation(s)
- Alexander Thomas
- Data Science Research Group, Institute for Artificial Intelligence in Medicine (IKIM), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Thomas Battenfeld
- Data Science Research Group, Institute for Artificial Intelligence in Medicine (IKIM), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Ivana Kraiselburd
- Data Science Research Group, Institute for Artificial Intelligence in Medicine (IKIM), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Olympia Anastasiou
- Institute for Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Ann-Kathrin Dörr
- Data Science Research Group, Institute for Artificial Intelligence in Medicine (IKIM), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Adrian Dörr
- Data Science Research Group, Institute for Artificial Intelligence in Medicine (IKIM), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Carina Elsner
- Institute for Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Jule Gosch
- Data Science Research Group, Institute for Artificial Intelligence in Medicine (IKIM), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Vu Thuy Khanh Le-Trilling
- Institute for Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
- Institute for the Research on HIV & AIDS-associated Diseases, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Simon Magin
- Data Science Research Group, Institute for Artificial Intelligence in Medicine (IKIM), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - René Scholtysik
- Institute for the Research on HIV & AIDS-associated Diseases, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Pelin Yilmaz
- Data Science Research Group, Institute for Artificial Intelligence in Medicine (IKIM), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Mirko Trilling
- Institute for Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
- Institute for the Research on HIV & AIDS-associated Diseases, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Lara Schöler
- Institute for Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
- Institute for the Research on HIV & AIDS-associated Diseases, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
- Institute of Cell Biology (Cancer Research), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Johannes Köster
- Bioinformatics and Computational Oncology, Institute for Artificial Intelligence in Medicine (IKIM), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Harvard Medical School, Boston, MA, USA
| | - Folker Meyer
- Data Science Research Group, Institute for Artificial Intelligence in Medicine (IKIM), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany.
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9
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Fernandez MC, Sweeney YC, Suchland RJ, Carrell SJ, Soge OO, Phan IQ, Rockey DD, Patton DL, Hybiske K. CT135 mediates the resistance of Chlamydia trachomatis to primate interferon gamma stimulated immune defenses. iScience 2024; 27:110143. [PMID: 38947519 PMCID: PMC11214326 DOI: 10.1016/j.isci.2024.110143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/19/2024] [Accepted: 05/27/2024] [Indexed: 07/02/2024] Open
Abstract
Evading host innate immune defenses is a critical feature of Chlamydia trachomatis infections, and the mechanisms used by C. trachomatis to subvert these pathways are incompletely understood. We screened a library of chimeric C. trachomatis mutants for genetic factors important for interference with cell-autonomous immune defenses. Mutant strains with predicted truncations of the inclusion membrane protein CT135 were susceptible to interferon gamma-activated immunity in human cells. CT135 functions to prevent host-driven recruitment of ubiquitin and p62/SQSTM to the inclusion membrane. In a nonhuman primate model of C. trachomatis infection, a CT135-deficient strain was rapidly cleared, highlighting the importance of this virulence factor for C. trachomatis pathogenesis. Analysis of CT135 phenotypes in primary macaque cells revealed that cell-autonomous immune defenses against C. trachomatis are conserved between humans and nonhuman primates and connects mechanistic findings with in vivo infection outcomes.
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Affiliation(s)
- Mark C. Fernandez
- Department of Global Health, University of Washington, Seattle, WA 98109, USA
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, WA 98109, USA
| | | | - Robert J. Suchland
- Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Steven J. Carrell
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Olusegun O. Soge
- Department of Global Health, University of Washington, Seattle, WA 98109, USA
- Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Isabelle Q. Phan
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA 98109, USA
- Center for Global Infectious Disease Research, Seattle Children’s Hospital, Seattle, WA 98109, USA
| | - Daniel D. Rockey
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Dorothy L. Patton
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98109, USA
| | - Kevin Hybiske
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, WA 98109, USA
- Department of Medicine, University of Washington, Seattle, WA 98109, USA
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10
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Galià-Camps C, Araujo AK, Carmona L, Martín-Hervás MDR, Pola M, Palero F, Cervera JL. New mitogenomes of Runcinidae and Facelinidae: two understudied heterobranch families (Mollusca: Gastropoda). Mitochondrial DNA B Resour 2024; 9:771-776. [PMID: 38919811 PMCID: PMC11198154 DOI: 10.1080/23802359.2024.2363365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 05/29/2024] [Indexed: 06/27/2024] Open
Abstract
Here, we present the mitochondrial sequences of two sea slugs (Heterobranchia): Runcina aurata and Facelina auriculata, the latter being the type species of the family. The mitochondrial genomes are 14,282 and 14,171bp in length, respectively, with a complete set of 13 PCGs, 2 rRNAs, and 22 tRNAs. None of the mitogenomes show gene reorganization, keeping the standard mitogenomic structure of Heterobranchia. Nucleotide composition differs significantly between them, with R. aurata showing the most AT-rich mitogenome (25.7% GC content) reported to date in Heterobranchia, and F. auriculata showing a rich GC content (35%) compared with other heterobranch mitochondrial genomes.
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Affiliation(s)
- Carles Galià-Camps
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Ana Karla Araujo
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Campus de Excelencia Internacional del Mar (CEIMAR), Universidad de Cádiz, Puerto Real, Spain
- Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Puerto Real, Spain
| | - Leila Carmona
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Campus de Excelencia Internacional del Mar (CEIMAR), Universidad de Cádiz, Puerto Real, Spain
- Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Puerto Real, Spain
| | - María del Rosario Martín-Hervás
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Campus de Excelencia Internacional del Mar (CEIMAR), Universidad de Cádiz, Puerto Real, Spain
- Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Puerto Real, Spain
| | - Marta Pola
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, CSIC, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), CSIC, Madrid, Spain
| | - Ferran Palero
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Spain
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Juan Lucas Cervera
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Campus de Excelencia Internacional del Mar (CEIMAR), Universidad de Cádiz, Puerto Real, Spain
- Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Puerto Real, Spain
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11
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Jackson DJ, Cerveau N, Posnien N. De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms - a brief guide. Front Zool 2024; 21:17. [PMID: 38902827 PMCID: PMC11188175 DOI: 10.1186/s12983-024-00538-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
Many questions in biology benefit greatly from the use of a variety of model systems. High-throughput sequencing methods have been a triumph in the democratization of diverse model systems. They allow for the economical sequencing of an entire genome or transcriptome of interest, and with technical variations can even provide insight into genome organization and the expression and regulation of genes. The analysis and biological interpretation of such large datasets can present significant challenges that depend on the 'scientific status' of the model system. While high-quality genome and transcriptome references are readily available for well-established model systems, the establishment of such references for an emerging model system often requires extensive resources such as finances, expertise and computation capabilities. The de novo assembly of a transcriptome represents an excellent entry point for genetic and molecular studies in emerging model systems as it can efficiently assess gene content while also serving as a reference for differential gene expression studies. However, the process of de novo transcriptome assembly is non-trivial, and as a rule must be empirically optimized for every dataset. For the researcher working with an emerging model system, and with little to no experience with assembling and quantifying short-read data from the Illumina platform, these processes can be daunting. In this guide we outline the major challenges faced when establishing a reference transcriptome de novo and we provide advice on how to approach such an endeavor. We describe the major experimental and bioinformatic steps, provide some broad recommendations and cautions for the newcomer to de novo transcriptome assembly and differential gene expression analyses. Moreover, we provide an initial selection of tools that can assist in the journey from raw short-read data to assembled transcriptome and lists of differentially expressed genes.
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Affiliation(s)
- Daniel J Jackson
- University of Göttingen, Department of Geobiology, Goldschmidtstr.3, Göttingen, 37077, Germany.
| | - Nicolas Cerveau
- University of Göttingen, Department of Geobiology, Goldschmidtstr.3, Göttingen, 37077, Germany
| | - Nico Posnien
- University of Göttingen, Department of Developmental Biology, GZMB, Justus-Von-Liebig-Weg 11, Göttingen, 37077, Germany.
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12
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Wang T, Zhang L, Zhang Y, Tong P, Ma W, Wang Y, Liu Y, Su Z. Isolation and identification of specific Enterococcus faecalis phage C-3 and G21-7 against Avian pathogenic Escherichia coli and its application to one-day-old geese. Front Microbiol 2024; 15:1385860. [PMID: 38962142 PMCID: PMC11221357 DOI: 10.3389/fmicb.2024.1385860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 05/24/2024] [Indexed: 07/05/2024] Open
Abstract
Colibacillosis caused by Avian pathogenic Escherichia coli (APEC), including peritonitis, respiratory tract inflammation and ovaritis, is recognized as one of the most common and economically destructive bacterial diseases in poultry worldwide. In this study, the characteristics and inhibitory potential of phages were investigated by double-layer plate method, transmission electron microscopy, whole genome sequencing, bioinformatics analysis and animal experiments. The results showed that phages C-3 and G21-7 isolated from sewage around goose farms infected multiple O serogroups (O1, O2, O18, O78, O157, O26, O145, O178, O103 and O104) Escherichia coli (E.coli) with a multiplicity of infection (MOI) of 10 and 1, respectively. According to the one-step growth curve, the incubation time of both bacteriophage C-3 and G21-7 was 10 min. Sensitivity tests confirmed that C-3 and G21-6 are stable at 4 to 50 °C and pH in the range of 4 to 11. Based on morphological and phylogenetic analysis, phages C-3 and G21-7 belong to Enterococcus faecalis (E. faecalis) phage species of the genus Saphexavirus of Herelleviridae family. According to genomic analysis, phage C-3 and G21-7 were 58,097 bp and 57,339 bp in size, respectively, with G+C content of 39.91% and 39.99%, encoding proteins of 97 CDS (105 to 3,993 bp) and 96 CDS (105 to 3,993 bp), and both contained 2 tRNAs. Both phages contained two tail proteins and holin-endolysin system coding genes, and neither carried resistance genes nor virulence factors. Phage mixture has a good safety profile and has shown good survival probability and feed efficiency in both treatment and prophylaxis experiments with one-day-old goslings. These results suggest that phage C-3 and G21-7 can be used as potential antimicrobials for the prevention and treatment of APEC.
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Affiliation(s)
- Tianli Wang
- College of Veterinary Medicine, Xinjiang Agricultural University, Xinjiang, China
- Xinjiang Key Laboratory of Herbivore Drug Research and Creation, College of Veterinary Medicine, Xinjiang Agricultural University, Xinjiang, China
| | - Ling Zhang
- College of Veterinary Medicine, Xinjiang Agricultural University, Xinjiang, China
- Xinjiang Key Laboratory of Herbivore Drug Research and Creation, College of Veterinary Medicine, Xinjiang Agricultural University, Xinjiang, China
| | - Yi Zhang
- College of Veterinary Medicine, Xinjiang Agricultural University, Xinjiang, China
- Xinjiang Key Laboratory of Herbivore Drug Research and Creation, College of Veterinary Medicine, Xinjiang Agricultural University, Xinjiang, China
| | - Panpan Tong
- College of Veterinary Medicine, Xinjiang Agricultural University, Xinjiang, China
- Xinjiang Key Laboratory of Herbivore Drug Research and Creation, College of Veterinary Medicine, Xinjiang Agricultural University, Xinjiang, China
| | - Wanpeng Ma
- College of Veterinary Medicine, Xinjiang Agricultural University, Xinjiang, China
- Xinjiang Key Laboratory of Herbivore Drug Research and Creation, College of Veterinary Medicine, Xinjiang Agricultural University, Xinjiang, China
| | - Yan Wang
- College of Veterinary Medicine, Xinjiang Agricultural University, Xinjiang, China
- Xinjiang Key Laboratory of Herbivore Drug Research and Creation, College of Veterinary Medicine, Xinjiang Agricultural University, Xinjiang, China
| | - Yifan Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Xinjiang, China
- Xinjiang Key Laboratory of Herbivore Drug Research and Creation, College of Veterinary Medicine, Xinjiang Agricultural University, Xinjiang, China
| | - Zhanqiang Su
- College of Veterinary Medicine, Xinjiang Agricultural University, Xinjiang, China
- Xinjiang Key Laboratory of Herbivore Drug Research and Creation, College of Veterinary Medicine, Xinjiang Agricultural University, Xinjiang, China
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13
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Yamashita T, Rhoads DD, Pummill J. A robust genome assembly with transcriptomic data from the striped bark scorpion, Centruroides vittatus. G3 (BETHESDA, MD.) 2024:jkae120. [PMID: 38885085 DOI: 10.1093/g3journal/jkae120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024]
Abstract
Scorpions, a seemingly primitive, stinging arthropod taxa, are known to exhibit marked diversity in their venom components. These venoms are known for their human pathology, but they are also important as models for therapeutic and drug development applications. In this study, we report a high-quality genome assembly and annotation of the striped bark scorpion, Centruroides vittatus, created with several shotgun libraries. The final assembly is 760 Mb in size, with a BUSCO score of 97.8%, a 30.85% GC, and an N50 of 2.35 Mb. We estimated 36,189 proteins with 37.32% assigned to Gene Ontology (GO) terms in our GO annotation analysis. We mapped venom toxin genes to 18 contigs and 2 scaffolds. We were also able to identify expression differences between venom gland (telson) and body tissue (carapace) with 19 sodium toxin and 14 potassium toxin genes to 18 contigs and 2 scaffolds. This assembly, along with our transcriptomic data, provides further data to investigate scorpion venom genomics.
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Affiliation(s)
- Tsunemi Yamashita
- Department of Biological Sciences, Arkansas Tech University, Russellville, AR 72801, USA
| | - Douglas D Rhoads
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR 72701, USA
| | - Jeff Pummill
- High Performance Computing Center, University of Arkansas-Fayetteville, Fayetteville, AR 72701, USA
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14
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Tran TA, Sridhar S, Reece ST, Lunguya O, Jacobs J, Van Puyvelde S, Marks F, Dougan G, Thomson NR, Nguyen BT, Bao PT, Baker S. Combining machine learning with high-content imaging to infer ciprofloxacin susceptibility in isolates of Salmonella Typhimurium. Nat Commun 2024; 15:5074. [PMID: 38871710 PMCID: PMC11176356 DOI: 10.1038/s41467-024-49433-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 06/05/2024] [Indexed: 06/15/2024] Open
Abstract
Antimicrobial resistance (AMR) is a growing public health crisis that requires innovative solutions. Current susceptibility testing approaches limit our ability to rapidly distinguish between antimicrobial-susceptible and -resistant organisms. Salmonella Typhimurium (S. Typhimurium) is an enteric pathogen responsible for severe gastrointestinal illness and invasive disease. Despite widespread resistance, ciprofloxacin remains a common treatment for Salmonella infections, particularly in lower-resource settings, where the drug is given empirically. Here, we exploit high-content imaging to generate deep phenotyping of S. Typhimurium isolates longitudinally exposed to increasing concentrations of ciprofloxacin. We apply machine learning algorithms to the imaging data and demonstrate that individual isolates display distinct growth and morphological characteristics that cluster by time point and susceptibility to ciprofloxacin, which occur independently of ciprofloxacin exposure. Using a further set of S. Typhimurium clinical isolates, we find that machine learning classifiers can accurately predict ciprofloxacin susceptibility without exposure to it or any prior knowledge of resistance phenotype. These results demonstrate the principle of using high-content imaging with machine learning algorithms to predict drug susceptibility of clinical bacterial isolates. This technique may be an important tool in understanding the morphological impact of antimicrobials on the bacterial cell to identify drugs with new modes of action.
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Affiliation(s)
- Tuan-Anh Tran
- The Department of Medicine, University of Cambridge, Cambridge, UK
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sushmita Sridhar
- The Department of Medicine, University of Cambridge, Cambridge, UK
- The Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Stephen T Reece
- The Department of Medicine, University of Cambridge, Cambridge, UK
- Sanofi, Kymab, Babraham Research Campus, Cambridge, UK
| | - Octavie Lunguya
- Department of Microbiology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Jan Jacobs
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sandra Van Puyvelde
- The Department of Medicine, University of Cambridge, Cambridge, UK
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Florian Marks
- The Department of Medicine, University of Cambridge, Cambridge, UK
- International Vaccine Institute, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
- Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany
- Madagascar Institute for Vaccine Research, University of Antananarivo, Antananarivo, Madagascar
| | - Gordon Dougan
- The Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nicholas R Thomson
- The Wellcome Sanger Institute, Hinxton, Cambridge, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Binh T Nguyen
- Faculty of Mathematics and Computer Science, University of Science, Vietnam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Pham The Bao
- Information Science Faculty, Saigon University, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- The Department of Medicine, University of Cambridge, Cambridge, UK.
- IAVI, Chelsea and Westminster Hospital, London, UK.
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15
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Ze M, Ma F, Zhang J, Duan J, Feng D, Shen Y, Chen G, Hu X, Dong M, Qi T, Zou L. Beneficial effects of Bacillus mojavensis strain MTC-8 on plant growth, immunity and disease resistance against Magnaporthe oryzae. Front Microbiol 2024; 15:1422476. [PMID: 38933037 PMCID: PMC11199545 DOI: 10.3389/fmicb.2024.1422476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Rice blast, a prevalent and highly destructive rice disease that significantly impacts rice yield, is caused by the rice blast fungus. In the present study, a strain named MTC-8, identified as Bacillus mojavensis, was demonstrated has strong antagonistic activity against the rice blast fungus, Rhizoctonia solani, Ustilaginoidea virens, and Bipolaria maydis. The potential biocontrol agents were identified using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) analysis and chromatography. Further investigations elucidated the inhibitory mechanism of the isolated compound and demonstrated its ability to suppress spore germination, alter hyphal morphology, disrupt cell membrane integrity, and induce defense-related gene expression in rice. MTC-8 promoted plant growth and may lead to the development of a biocontrol agent that meets agricultural standards. Overall, the Bacillus mojavensis MTC-8 strain exerted beneficial effects on plant growth, immunity and disease resistance against rice blast fungus. In this study, we isolated and purified a bioactive substance from fermentation broth, and the results provide a foundation for the development and application of biopesticides. Elucidation of the inhibitory mechanism against rice blast fungus provides theoretical support for the identification of molecular targets. The successful development of a biocontrol agent lays the groundwork for its practical application in agriculture.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Tuo Qi
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Teachers' College, Mianyang, China
| | - Lijuan Zou
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Teachers' College, Mianyang, China
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16
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Ghasemian E, Holland MJ. Genomic profiling and characterization of ocular Chlamydia trachomatis reference strain B/HAR36. Microbiol Resour Announc 2024; 13:e0002924. [PMID: 38700340 DOI: 10.1128/mra.00029-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/13/2024] [Indexed: 05/05/2024] Open
Abstract
The human pathogen Chlamydia trachomatis has multiple serovariants that have distinct organotropisms. We recently revised genomic sequence data linked to ocular reference strain, B/HAR36. Now linked to its correct genomic data in the European Nucleotide Archive, we describe its genomic features.
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Affiliation(s)
- Ehsan Ghasemian
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Martin J Holland
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
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17
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Dickey AM, Schmidt JW, Bono JL, Guragain M. The GEA pipeline for characterizing Escherichia coli and Salmonella genomes. Sci Rep 2024; 14:13257. [PMID: 38858528 PMCID: PMC11164923 DOI: 10.1038/s41598-024-63832-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024] Open
Abstract
Salmonella enterica and Escherichia coli are major food-borne human pathogens, and their genomes are routinely sequenced for clinical surveillance. Computational pipelines designed for analyzing pathogen genomes should both utilize the most current information from annotation databases and increase the coverage of these databases over time. We report the development of the GEA pipeline to analyze large batches of E. coli and S. enterica genomes. The GEA pipeline takes as input paired Illumina raw reads files which are then assembled followed by annotation. Alternatively, assemblies can be provided as input and directly annotated. The pipeline provides predictive genome annotations for E. coli and S. enterica with a focus on the Center for Genomic Epidemiology tools. Annotation results are provided as a tab delimited text file. The GEA pipeline is designed for large-scale E. coli and S. enterica genome assembly and characterization using the Center for Genomic Epidemiology command-line tools and high-performance computing. Large scale annotation is demonstrated by an analysis of more than 14,000 Salmonella genome assemblies. Testing the GEA pipeline on E. coli raw reads demonstrates reproducibility across multiple compute environments and computational usage is optimized on high performance computers.
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Affiliation(s)
- Aaron M Dickey
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, 844 Rd 313, PO Box 165, Clay Center, NE, 68933, USA.
| | - John W Schmidt
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, 844 Rd 313, PO Box 165, Clay Center, NE, 68933, USA
| | - James L Bono
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, 844 Rd 313, PO Box 165, Clay Center, NE, 68933, USA
| | - Manita Guragain
- US Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA.
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18
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Chen S, Wang H, Zhang D, Chen R, Luo J. Readon: a novel algorithm to identify read-through transcripts with long-read sequencing data. Bioinformatics 2024; 40:btae336. [PMID: 38808568 PMCID: PMC11162696 DOI: 10.1093/bioinformatics/btae336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/30/2024] [Accepted: 05/26/2024] [Indexed: 05/30/2024] Open
Abstract
MOTIVATION There are many clustered transcriptionally active regions in the human genome, in which the transcription complex cannot immediately terminate transcription at the upstream gene termination site, but instead continues to transcribe intergenic regions and downstream genes, resulting in read-through transcripts. Several studies have demonstrated the regulatory roles of read-through transcripts in tumorigenesis and development. However, limited by the read length of next-generation sequencing, discovery of read-through transcripts has been slow. For long but also erroneous third-generation sequencing data, this study developed a novel minimizer sketch algorithm to accurately and quickly identify read-through transcripts. RESULTS Readon initially splits the reference sequence into distinct active regions. It employs a sliding window approach within each region, calculates minimizers, and constructs the specialized structured arrays for query indexing. Following initial alignment anchor screening of candidate read-through transcripts, further confirmation steps are executed. Comparative assessments against existing software reveal Readon's superior performance on both simulated and validated real data. Additionally, two downstream tools are provided: one for predicting whether a read-through transcript is likely to undergo nonsense-mediated decay or encodes a protein, and another for visualizing splicing patterns. AVAILABILITY AND IMPLEMENTATION Readon is freely available on GitHub (https://github.com/Bulabula45/Readon).
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Affiliation(s)
- Siang Chen
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Wang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongdong Zhang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Runsheng Chen
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianjun Luo
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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19
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Shrestha H, McCulloch K, Chisholm RH, Armoo SK, Veriegh F, Sirwani N, Crawford KE, Osei-Atweneboana MY, Grant WN, Hedtke SM. Synthesizing environmental, epidemiological and vector and parasite genetic data to assist decision making for disease elimination. Mol Ecol 2024; 33:e17357. [PMID: 38683054 DOI: 10.1111/mec.17357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/27/2024] [Accepted: 04/05/2024] [Indexed: 05/01/2024]
Abstract
We present a framework for identifying when conditions are favourable for transmission of vector-borne diseases between communities by incorporating predicted disease prevalence mapping with landscape analysis of sociological, environmental and host/parasite genetic data. We explored the relationship between environmental features and gene flow of a filarial parasite of humans, Onchocerca volvulus, and its vector, blackflies in the genus Simulium. We generated a baseline microfilarial prevalence map from point estimates from 47 locations in the ecological transition separating the savannah and forest in Ghana, where transmission of O. volvulus persists despite onchocerciasis control efforts. We generated movement suitability maps based on environmental correlates with mitochondrial population structure of 164 parasites from 15 communities and 93 vectors from only four sampling sites, and compared these to the baseline prevalence map. Parasite genetic distance between sampling locations was significantly associated with elevation (r = .793, p = .005) and soil moisture (r = .507, p = .002), while vector genetic distance was associated with soil moisture (r = .788, p = .0417) and precipitation (r = .835, p = .0417). The correlation between baseline prevalence and parasite resistance surface maps was stronger than that between prevalence and vector resistance surface maps. The centre of the study area had high prevalence and suitability for parasite and vector gene flow, potentially contributing to persistent transmission and suggesting the importance of re-evaluating transmission zone boundaries. With suitably dense sampling, this framework can help delineate transmission zones for onchocerciasis and would be translatable to other vector-borne diseases.
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Affiliation(s)
- Himal Shrestha
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
| | - Karen McCulloch
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
| | - Rebecca H Chisholm
- Department of Mathematical and Physical Sciences, La Trobe University, Bundoora, Victoria, Australia
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Samuel K Armoo
- Biomedical and Public Health Research Unit, CSIR-Water Research Institute, Accra, Ghana
| | - Francis Veriegh
- Biomedical and Public Health Research Unit, CSIR-Water Research Institute, Accra, Ghana
| | - Neha Sirwani
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
| | - Katie E Crawford
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
| | | | - Warwick N Grant
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
| | - Shannon M Hedtke
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
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20
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Ferreira CP, Moreira RS, Bastolla CLV, Saldaña-Serrano M, Lima D, Gomes CHAM, Bainy ACD, Lüchmann KH. Transcriptomic investigation and biomarker discovery for zinc response in oysters Crassostrea gasar. Mar Genomics 2024; 75:101109. [PMID: 38603950 DOI: 10.1016/j.margen.2024.101109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 03/03/2024] [Accepted: 03/24/2024] [Indexed: 04/13/2024]
Abstract
In an era of unprecedented industrial and agricultural growth, metal contamination in marine environments is a pressing concern. Sentinel organisms such as the mangrove oyster Crassostrea gasar provide valuable insights into these environments' health. However, a comprehensive understanding of the molecular mechanisms underlying their response to metal exposure remains elusive. To address this gap, we reanalyzed the 454-sequencing data of C. gasar, utilizing an array of bioinformatics workflow of CDTA (Combined De Novo Transcriptome Assembly) to generate a more representative assembly. In parallel, C. gasar individuals were exposed to two concentrations of zinc (850 and 4500 μg L-1 Zn) for 48 h to understand their molecular responses. We utilized Trinotate workflow for the 11,684-CDTA unigenes annotation, with most transcripts aligning with the genus Crassostrea. Our analysis indicated that 67.3% of transcript sequences showed homology with Pfam, while 51.4% and 54.5%, respectively had GO and KO terms annotated. We identified potential metal pollution biomarkers, focusing on metal-related genes, such as those related to the GSH biosynthesis (CHAC1 and GCLC-like), to zinc transporters (ZNT2-like), and metallothionein (MT-like). The evolutionary conservation of these genes within the Crassostrea genus was assessed through phylogenetic analysis. Further, these genes were evaluated by qPCR in the laboratory exposed oysters. All target genes exhibited significant upregulation upon exposure to Zn at both 850 and 4500 μg L-1, except for GCLC-like, which showed upregulation only at the higher concentration of 4500 μg L-1. This result suggests distinct activation thresholds and complex interactions among these genes in response to varying Zn concentrations. Our study provides insights into the molecular responses of C. gasar to Zn, adding valuable tools for monitoring metal pollution in marine ecosystems using the mangrove oyster as a sentinel organism.
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Affiliation(s)
- Clarissa P Ferreira
- Multicentric PostGraduate Program in Biochemistry and Molecular Biology - PMBqBM, Santa Catarina State University, Lages 88520-000, Brazil
| | - Renato S Moreira
- Federal Institute of Santa Catarina, Gaspar 89111-009, Brazil; Bioinformatic Laboratory, Federal University of Santa Catarina, Florianópolis 88040-970, Brazil
| | - Camila L V Bastolla
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry - LABCAI, Federal University of Santa Catarina, Florianópolis 88034-257, Brazil
| | - Miguel Saldaña-Serrano
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry - LABCAI, Federal University of Santa Catarina, Florianópolis 88034-257, Brazil
| | - Daína Lima
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry - LABCAI, Federal University of Santa Catarina, Florianópolis 88034-257, Brazil
| | - Carlos H A M Gomes
- Laboratory of Marine Mollusks (LMM), Department of Aquaculture, Center of Agricultural Science, Federal University of Santa Catarina, UFSC, Florianópolis, Santa Catarina, Brazil
| | - Afonso C D Bainy
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry - LABCAI, Federal University of Santa Catarina, Florianópolis 88034-257, Brazil
| | - Karim H Lüchmann
- Department of Scientific and Technological Education, Santa Catarina State University, Florianópolis 88035-001, Brazil.
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21
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Chen Y, Guo S, Jiang L, Yan F, Hao K, Wang Z, An M, Xia Z, Li F, Zhou X, Wu Y. Molecular characterization and pathogenicity of a novel monopartite geminivirus infecting tobacco in China. Virology 2024; 594:110061. [PMID: 38518441 DOI: 10.1016/j.virol.2024.110061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 03/24/2024]
Abstract
The occurrence of geminiviruses causes significant economic losses in many economically important crops. In this study, a novel geminivirus isolated from tobacco in Sichuan province of China, named tomato leaf curl Chuxiong virus (TLCCxV), was characterized by small RNA-based deep sequencing. The full-length of TLCCxV genome was determined to be 2744 nucleotides (nt) encoding six open reading frames. Phylogenetic and genome-wide pairwise identity analysis revealed that TLCCxV shared less than 91% identities with reported geminiviruses. A TLCCxV infectious clone was constructed and successfully infected Nicotiana benthamiana, N. tabacum, N. glutinosa, Solanum lycopersicum and Petunia hybrida plants. Furthermore, expression of the V2, C1 and C4 proteins through a potato virus X vector caused severe chlorosis or necrosis symptom in N. benthamiana. Taken together, we identified a new geminivirus in tobacco plants, and found that V2, C1 and C4 contribute to symptom development.
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Affiliation(s)
- Yuan Chen
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China
| | - Shiping Guo
- Sichuan Tobacco Company, Chengdu, Sichuan, 610000, China
| | - Lianqiang Jiang
- Liangshan Branch of Sichuan Tobacco Company, Xichang, Sichuan, 615000, China
| | - Fangfang Yan
- Panzhihua Branch of Sichuan Tobacco Company, Panzhihua, Sichuan, 617000, China
| | - Kaiqiang Hao
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China
| | - Zhiping Wang
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China
| | - Mengnan An
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China
| | - Zihao Xia
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xueping Zhou
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China; State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Yuanhua Wu
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China.
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Casimiro-Ramos A, Bautista-Crescencio C, Vidal-Montiel A, González GM, Hernández-García JA, Hernández-Rodríguez C, Villa-Tanaca L. Comparative Genomics of the First Resistant Candida auris Strain Isolated in Mexico: Phylogenomic and Pan-Genomic Analysis and Mutations Associated with Antifungal Resistance. J Fungi (Basel) 2024; 10:392. [PMID: 38921378 PMCID: PMC11204476 DOI: 10.3390/jof10060392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/19/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024] Open
Abstract
Candida auris is an emerging multidrug-resistant and opportunistic pathogenic yeast. Whole-genome sequencing analysis has defined five major clades, each from a distinct geographic region. The current study aimed to examine the genome of the C. auris 20-1498 strain, which is the first isolate of this fungus identified in Mexico. Based on whole-genome sequencing, the draft genome was found to contain 70 contigs. It had a total genome size of 12.86 Mbp, an N50 value of 1.6 Mbp, and an average guanine-cytosine (GC) content of 45.5%. Genome annotation revealed a total of 5432 genes encoding 5515 proteins. According to the genomic analysis, the C. auris 20-1498 strain belongs to clade IV (containing strains endemic to South America). Of the two genes (ERG11 and FKS1) associated with drug resistance in C. auris, a mutation was detected in K143R, a gene located in a mutation hotspot of ERG11 (lanosterol 14-α-demethylase), an antifungal drug target. The focus on whole-genome sequencing and the identification of mutations linked to the drug resistance of fungi could lead to the discovery of new therapeutic targets and new antifungal compounds.
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Affiliation(s)
- Arturo Casimiro-Ramos
- Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala, Casco de Santo Tomás, Ciudad de México 11340, Mexico; (A.C.-R.); (C.B.-C.); (A.V.-M.); (J.A.H.-G.); (C.H.-R.)
| | - Celia Bautista-Crescencio
- Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala, Casco de Santo Tomás, Ciudad de México 11340, Mexico; (A.C.-R.); (C.B.-C.); (A.V.-M.); (J.A.H.-G.); (C.H.-R.)
| | - Alvaro Vidal-Montiel
- Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala, Casco de Santo Tomás, Ciudad de México 11340, Mexico; (A.C.-R.); (C.B.-C.); (A.V.-M.); (J.A.H.-G.); (C.H.-R.)
| | - Gloria M. González
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Hospital Universitario “Dr. José Eleuterio Gonzalez”, Av. Madero y Calle Dr. Eduardo Aguirre Pequeño s/n, Colonia Mitras Centro, Monterrey 64460, Nuevo Leon, Mexico;
| | - Juan Alfredo Hernández-García
- Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala, Casco de Santo Tomás, Ciudad de México 11340, Mexico; (A.C.-R.); (C.B.-C.); (A.V.-M.); (J.A.H.-G.); (C.H.-R.)
| | - César Hernández-Rodríguez
- Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala, Casco de Santo Tomás, Ciudad de México 11340, Mexico; (A.C.-R.); (C.B.-C.); (A.V.-M.); (J.A.H.-G.); (C.H.-R.)
| | - Lourdes Villa-Tanaca
- Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala, Casco de Santo Tomás, Ciudad de México 11340, Mexico; (A.C.-R.); (C.B.-C.); (A.V.-M.); (J.A.H.-G.); (C.H.-R.)
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23
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Li H, Marin M, Farhat MR. Exploring gene content with pangene graphs. ARXIV 2024:arXiv:2402.16185v3. [PMID: 38463499 PMCID: PMC10925376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Motivation The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is applicable to collections of large eukaryotic genomes such as the human pangenome. Results We developed pangene, a computational tool to identify gene orientation, gene order and gene copy-number changes in a collection of genomes. Pangene aligns a set of input protein sequences to the genomes, resolves redundancies between protein sequences and constructs a gene graph with each genome represented as a walk in the graph. It additionally finds subgraphs, which we call bibubbles, that capture gene content changes. Applied to the human pangenome, pangene identifies known gene-level variations and reveals complex haplotypes that are not well studied before. Pangene also works with high-quality bacterial pangenome and reports similar numbers of core and accessory genes in comparison to existing tools. Availability and implementation Source code at https://github.com/lh3/pangene; pre-built pangene graphs can be downloaded from https://zenodo.org/records/8118576 and visualized at https://pangene.bioinweb.org.
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Affiliation(s)
- Heng Li
- Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02215, USA
- Harvard Medical School, 10 Shattuck St, Boston, MA 02215, USA
- Broad Insitute of Harvard and MIT, 415 Main St, Cambridge, MA 02142, USA
| | | | - Maha Reda Farhat
- Harvard Medical School, 10 Shattuck St, Boston, MA 02215, USA
- Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, USA
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24
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Carpio LE, Olivares M, Benítez-Paez A, Serrano-Candelas E, Barigye SJ, Sanz Y, Gozalbes R. Comparative Binding Study of Gliptins to Bacterial DPP4-like Enzymes for the Treatment of Type 2 Diabetes Mellitus (T2DM). Int J Mol Sci 2024; 25:5744. [PMID: 38891933 PMCID: PMC11171585 DOI: 10.3390/ijms25115744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
The role of the gut microbiota and its interplay with host metabolic health, particularly in the context of type 2 diabetes mellitus (T2DM) management, is garnering increasing attention. Dipeptidyl peptidase 4 (DPP4) inhibitors, commonly known as gliptins, constitute a class of drugs extensively used in T2DM treatment. However, their potential interactions with gut microbiota remain poorly understood. In this study, we employed computational methodologies to investigate the binding affinities of various gliptins to DPP4-like homologs produced by intestinal bacteria. The 3D structures of DPP4 homologs from gut microbiota species, including Segatella copri, Phocaeicola vulgatus, Bacteroides uniformis, Parabacteroides merdae, and Alistipes sp., were predicted using computational modeling techniques. Subsequently, molecular dynamics simulations were conducted for 200 ns to ensure the stability of the predicted structures. Stable structures were then utilized to predict the binding interactions with known gliptins through molecular docking algorithms. Our results revealed binding similarities of gliptins toward bacterial DPP4 homologs compared to human DPP4. Specifically, certain gliptins exhibited similar binding scores to bacterial DPP4 homologs as they did with human DPP4, suggesting a potential interaction of these drugs with gut microbiota. These findings could help in understanding the interplay between gliptins and gut microbiota DPP4 homologs, considering the intricate relationship between the host metabolism and microbial communities in the gut.
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Affiliation(s)
- Laureano E. Carpio
- ProtoQSAR SL, CEEI (Centro Europeo de Empresas Innovadoras), Parque Tecnológico de Valencia, 46980 Valencia, Spain; (L.E.C.); (E.S.-C.)
- MolDrug AI Systems SL, 46018 Valencia, Spain
| | - Marta Olivares
- Microbial Ecology, Nutrition and Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), 46980 Valencia, Spain; (M.O.); (A.B.-P.); (Y.S.)
| | - Alfonso Benítez-Paez
- Microbial Ecology, Nutrition and Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), 46980 Valencia, Spain; (M.O.); (A.B.-P.); (Y.S.)
| | - Eva Serrano-Candelas
- ProtoQSAR SL, CEEI (Centro Europeo de Empresas Innovadoras), Parque Tecnológico de Valencia, 46980 Valencia, Spain; (L.E.C.); (E.S.-C.)
| | | | - Yolanda Sanz
- Microbial Ecology, Nutrition and Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), 46980 Valencia, Spain; (M.O.); (A.B.-P.); (Y.S.)
| | - Rafael Gozalbes
- ProtoQSAR SL, CEEI (Centro Europeo de Empresas Innovadoras), Parque Tecnológico de Valencia, 46980 Valencia, Spain; (L.E.C.); (E.S.-C.)
- MolDrug AI Systems SL, 46018 Valencia, Spain
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25
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Masuda Y, Mise K, Xu Z, Zhang Z, Shiratori Y, Senoo K, Itoh H. Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome. MICROBIOME 2024; 12:95. [PMID: 38790049 PMCID: PMC11127431 DOI: 10.1186/s40168-024-01812-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 04/09/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N2-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome. RESULTS After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments). CONCLUSION Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.
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Affiliation(s)
- Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Kazumori Mise
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.
| | - Zhenxing Xu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Zhengcheng Zhang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yutaka Shiratori
- Niigata Agricultural Research Institute, 857 Nagakura-machi, Nagaoka, Niigata, 940-0826, Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hideomi Itoh
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.
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26
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Wang JH, Huang PT, Huang YT, Mao YC, Lai CH, Yeh TK, Tseng CH, Kao CC. Characterization of CRISPR-Cas Systems in Shewanella algae and Shewanella haliotis: Insights into the Adaptation and Survival of Marine Pathogens. Pathogens 2024; 13:439. [PMID: 38921737 PMCID: PMC11207072 DOI: 10.3390/pathogens13060439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/25/2024] [Accepted: 05/15/2024] [Indexed: 06/27/2024] Open
Abstract
CRISPR-Cas systems are adaptive immune mechanisms present in most prokaryotes that play an important role in the adaptation of bacteria and archaea to new environments. Shewanella algae is a marine zoonotic pathogen with worldwide distribution, which accounts for the majority of clinical cases of Shewanella infections. However, the characterization of Shewanella algae CRISPR-Cas systems has not been well investigated yet. Through whole genome sequence analysis, we characterized the CRISPR-Cas systems in S. algae. Our results indicate that CRISPR-Cas systems are prevalent in S. algae, with the majority of strains containing the Type I-F system. This study provides new insights into the diversity and function of CRISPR-Cas systems in S. algae and highlights their potential role in the adaptation and survival of these marine pathogens.
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Affiliation(s)
- Jui-Hsing Wang
- Division of Infectious Disease, Department of Internal Medicine, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung 427213, Taiwan;
- Department of Internal Medicine, School of Medicine, Tzu Chi University, Hualien 970374, Taiwan
| | - Po-Tsang Huang
- Division of Pharmacy, Kaohsiung Armed Forces General Hospital, Kaohsiung 802301, Taiwan;
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi 621301, Taiwan;
| | - Yan-Chiao Mao
- Division of Clinical Toxicology, Department of Emergency Medicine, Taichung Veterans General Hospital, Taichung 407219, Taiwan;
| | - Chung-Hsu Lai
- Division of Infectious Diseases, Department of Internal Medicine, E-Da Hospital, Kaohsiung 824005, Taiwan;
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 840301, Taiwan
| | - Ting-Kuang Yeh
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 407219, Taiwan;
- Genomic Center for Infectious Diseases, Taichung Veterans General Hospital, Taichung 407219, Taiwan
| | - Chien-Hao Tseng
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 407219, Taiwan;
- Genomic Center for Infectious Diseases, Taichung Veterans General Hospital, Taichung 407219, Taiwan
| | - Chih-Chuan Kao
- Division of Infectious Disease, Department of Internal Medicine, Tungs’ Taichung Metroharbor Hospital, Taichung 435403, Taiwan
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27
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Chen JR, Aguirre-Carvajal K, Xue DY, Chang HC, Arone-Maxwell L, Lin YP, Armijos-Jaramillo V, Oliva R. Exploring the genetic makeup of Xanthomonas species causing bacterial spot in Taiwan: evidence of population shift and local adaptation. Front Microbiol 2024; 15:1408885. [PMID: 38846563 PMCID: PMC11153759 DOI: 10.3389/fmicb.2024.1408885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/13/2024] [Indexed: 06/09/2024] Open
Abstract
The introduction of plant pathogens can quickly reshape disease dynamics in island agro-ecologies, representing a continuous challenge for local crop management strategies. Xanthomonas pathogens causing tomato bacterial spot were probably introduced in Taiwan several decades ago, creating a unique opportunity to study the genetic makeup and adaptive response of this alien population. We examined the phenotypic and genotypic identity of 669 pathogen entries collected across different regions of Taiwan in the last three decades. The analysis detected a major population shift, where X. euvesicatoria and X. vesicatoria races T1 and T2 were replaced by new races of X. perforans. After its introduction, race T4 quickly became dominant in all tomato-growing areas of the island. The genomic analysis of 317 global genomes indicates that the Xanthomonas population in Taiwan has a narrow genetic background, most likely resulting from a small number of colonization events. However, despite the apparent genetic uniformity, X. perforans race T4 shows multiple phenotypic responses in tomato lines. Additionally, an in-depth analysis of effector composition suggests diversification in response to local adaptation. These include unique mutations on avrXv3 which might allow the pathogen to overcome Xv3/Rx4 resistance gene. The findings underscore the dynamic evolution of a pathogen when introduced in a semi-isolated environment and provide insights into the potential management strategies for this important disease of tomato.
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Affiliation(s)
- Jaw-Rong Chen
- Safe and Sustainable Value Chain, World Vegetable Center, Shanhua, Taiwan
| | - Kevin Aguirre-Carvajal
- Research Center of Information and Communication Technologies, University of A Coruña, A Coruña, Spain
- Bio-Cheminformatics Research Group, Universidad de Las Américas, Quito, Ecuador
| | - Dao-Yuan Xue
- Seed and Seedling Management Section, Taiwan Seed Improvement and Propagation Station, Ministry of Agriculture, Taichung, Taiwan
| | - Hung-Chia Chang
- Safe and Sustainable Value Chain, World Vegetable Center, Shanhua, Taiwan
| | | | - Ya-Ping Lin
- Safe and Sustainable Value Chain, World Vegetable Center, Shanhua, Taiwan
| | - Vinicio Armijos-Jaramillo
- Bio-Cheminformatics Research Group, Universidad de Las Américas, Quito, Ecuador
- Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
| | - Ricardo Oliva
- Safe and Sustainable Value Chain, World Vegetable Center, Shanhua, Taiwan
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28
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Wade KJ, Suseno R, Kizer K, Williams J, Boquett J, Caillier S, Pollock NR, Renschen A, Santaniello A, Oksenberg JR, Norman PJ, Augusto DG, Hollenbach JA. MHConstructor: A high-throughput, haplotype-informed solution to the MHC assembly challenge. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.20.595060. [PMID: 38826378 PMCID: PMC11142050 DOI: 10.1101/2024.05.20.595060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The extremely high levels of genetic polymorphism within the human major histocompatibility complex (MHC) limit the usefulness of reference-based alignment methods for sequence assembly. We incorporate a short read de novo assembly algorithm into a workflow for novel application to the MHC. MHConstructor is a containerized pipeline designed for high-throughput, haplotype-informed, reproducible assembly of both whole genome sequencing and target-capture short read data in large, population cohorts. To-date, no other self-contained tool exists for the generation of de novo MHC assemblies from short read data. MHConstructor facilitates wide-spread access to high quality, alignment-free MHC sequence analysis.
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Affiliation(s)
- Kristen J. Wade
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Rayo Suseno
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Kerry Kizer
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Jacqueline Williams
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Juliano Boquett
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Stacy Caillier
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Nicholas R. Pollock
- Department of Biomedical Informatics, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
- Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
| | - Adam Renschen
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Adam Santaniello
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Jorge R. Oksenberg
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Paul J. Norman
- Department of Biomedical Informatics, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
- Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
| | - Danillo G. Augusto
- Department of Biological Sciences, University of North Carolina Charlotte, Charlotte, NC, United States
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Jill A. Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, United States
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29
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Graham AS, Patel F, Little F, van der Kouwe A, Kaba M, Holmes MJ. Using short-read 16S rRNA sequencing of multiple variable regions to generate high-quality results to a species level. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.591068. [PMID: 38798511 PMCID: PMC11118338 DOI: 10.1101/2024.05.13.591068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Introduction Short-read amplicon sequencing studies have typically focused on 1-2 variable regions of the 16S rRNA gene. Species-level resolution is limited in these studies, as each variable region enables the characterisation of a different subsection of the microbiome. Although long-read sequencing techniques take advantage of all 9 variable regions by sequencing the entire 16S rRNA gene, they are substantially more expensive. This work assessed the feasibility of accurate species-level resolution and reproducibility using a relatively new sequencing kit and bioinformatics pipeline developed for short-read sequencing of multiple variable regions of the 16S rRNA gene. In addition, we evaluated the potential impact of different sample collection methods on our outcomes. Methods Using xGen™ 16S Amplicon Panel v2 kits, sequencing of all 9 variable regions of the 16S rRNA gene was carried out on an Illumina MiSeq platform. Mock cells and mock DNA for 8 bacterial species were included as extraction and sequencing controls respectively. Within-run and between-run replicate samples, and pairs of stool and rectal swabs collected at 0-5 weeks from the same participants, were incorporated. Observed relative abundances of each species were compared to theoretical abundances provided by ZymoBIOMICS. Paired Wilcoxon rank sum tests and distance-based intraclass correlation coefficients were used to statistically compare alpha and beta diversity measures, respectively, for pairs of replicates and stool/rectal swab sample pairs. Results Using multiple variable regions of the 16S ribosomal Ribonucleic Acid (rRNA) gene, we found that we could accurately identify taxa to a species level and obtain highly reproducible results at a species level. Yet, the microbial profiles of stool and rectal swab sample pairs differed substantially despite being collected concurrently from the same infants. Conclusion This protocol provides an effective means for studying infant gut microbial samples at a species level. However, sample collection approaches need to be accounted for in any downstream analysis.
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Affiliation(s)
- Amy S Graham
- Imaging Sciences, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Human Biology, Division of Biomedical Engineering, University of Cape Town, Cape Town, South Africa
| | - Fadheela Patel
- Department of Pathology, Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa
| | - Francesca Little
- Department of Statistical Sciences, University of Cape Town, Cape Town, South Africa
| | - Andre van der Kouwe
- Athinoula A. Martinos Centre for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Mamadou Kaba
- Department of Pathology, Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa
| | - Martha J Holmes
- Imaging Sciences, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Human Biology, Division of Biomedical Engineering, University of Cape Town, Cape Town, South Africa
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
- ImageTech, Simon Fraser University, Surrey, BC, Canada
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30
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Břinda K, Lima L, Pignotti S, Quinones-Olvera N, Salikhov K, Chikhi R, Kucherov G, Iqbal Z, Baym M. Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.15.536996. [PMID: 37131636 PMCID: PMC10153118 DOI: 10.1101/2023.04.15.536996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Comprehensive collections approaching millions of sequenced genomes have become central information sources in the life sciences. However, the rapid growth of these collections has made it effectively impossible to search these data using tools such as BLAST and its successors. Here, we present a technique called phylogenetic compression, which uses evolutionary history to guide compression and efficiently search large collections of microbial genomes using existing algorithms and data structures. We show that, when applied to modern diverse collections approaching millions of genomes, lossless phylogenetic compression improves the compression ratios of assemblies, de Bruijn graphs, and k -mer indexes by one to two orders of magnitude. Additionally, we develop a pipeline for a BLAST-like search over these phylogeny-compressed reference data, and demonstrate it can align genes, plasmids, or entire sequencing experiments against all sequenced bacteria until 2019 on ordinary desktop computers within a few hours. Phylogenetic compression has broad applications in computational biology and may provide a fundamental design principle for future genomics infrastructure.
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31
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Tsai HK, Sabbagh MF, Montesion M, Williams EA, Arbini A, Boué DR, Harris EM, Wachter F, Grimmett L, Place AE, Lucas F, Nardi V, Kim AS, Brugnara C, Degar B, Pollard J, Harris MH, Bledsoe JR. Acute Promyelocytic Leukemia With Torque Teno Mini Virus::RARA Fusion: An Approach to Screening and Diagnosis. Mod Pathol 2024; 37:100509. [PMID: 38704030 DOI: 10.1016/j.modpat.2024.100509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 04/20/2024] [Indexed: 05/06/2024]
Abstract
Acute promyelocytic leukemia (APL) with variant RARA translocation is linked to over 15 partner genes. Recent publications encompassing 6 cases have expanded the spectrum of RARA partners to torque teno mini virus (TTMV). This entity is likely underrecognized due to the lack of clinician and pathologist familiarity, inability to detect the fusion using routine testing modalities, and informatic challenges in its recognition within next-generation sequencing (NGS) data. We describe a clinicopathologic approach and provide the necessary tools to screen and diagnose APL with TTMV::RARA using existing clinical DNA- or RNA-based NGS assays, which led to the identification of 4 cases, all without other known cytogenetic/molecular drivers. One was identified prospectively and 3 retrospectively, including 2 from custom automated screening of multiple data sets (50,257 cases of hematopoietic malignancy, including 4809 acute myeloid leukemia/myeloid sarcoma/APL cases). Two cases presented as myeloid sarcoma, including 1 with multiple relapses after acute myeloid leukemia-type chemotherapy and hematopoietic stem cell transplant. Two cases presented as leukemia, had a poor response to induction chemotherapy, but achieved remission upon reinduction (including all-trans retinoic acid in 1 case) and subsequent hematopoietic stem cell transplant. Neoplastic cells demonstrated features of APL including frequent azurophilic granules and dim/absent CD34 and HLA-DR expression. RARA rearrangement was not detected by karyotype or fluorescent in situ hybridization. Custom analysis of NGS fusion panel data identified TTMV::RARA rearrangements and, in the prospectively identified case, facilitated monitoring in sequential bone marrow samples. APL with TTMV::RARA is a rare leukemia with a high rate of treatment failure in described cases. The diagnosis should be considered in leukemias with features of APL that lack detectable RARA fusions and other drivers, and may be confirmed by appropriate NGS tests with custom informatics. Incorporation of all-trans retinoic acid may have a role in treatment but requires accurate recognition of the fusion for appropriate classification as APL.
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Affiliation(s)
- Harrison K Tsai
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts; Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mark F Sabbagh
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Erik A Williams
- Department of Pathology and Laboratory Medicine, University of Miami, Sylvester Comprehensive Cancer Center, and Jackson Memorial Hospitals, Miami, Florida; Foundation Medicine Inc, Boston, Massachusetts
| | - Arnaldo Arbini
- Department of Pathology, NYU Grossman School of Medicine, New York City, New York
| | - Daniel R Boué
- Department of Pathology & Laboratory Medicine, Nationwide Children's Hospital and The Ohio State University, Columbus, Ohio
| | - Emily M Harris
- Dana Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Franziska Wachter
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Leslie Grimmett
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Andrew E Place
- Dana Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Fabienne Lucas
- Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Annette S Kim
- Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Carlo Brugnara
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Barbara Degar
- Dana Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Jessica Pollard
- Dana Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jacob R Bledsoe
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts; Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts.
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32
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Ariffin N, Newman DW, Nelson MG, O’cualain R, Hubbard SJ. Proteogenomic Gene Structure Validation in the Pineapple Genome. J Proteome Res 2024; 23:1583-1592. [PMID: 38651221 PMCID: PMC11077482 DOI: 10.1021/acs.jproteome.3c00675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 03/15/2024] [Accepted: 04/12/2024] [Indexed: 04/25/2024]
Abstract
MD2 pineapple (Ananas comosus) is the second most important tropical crop that preserves crassulacean acid metabolism (CAM), which has high water-use efficiency and is fast becoming the most consumed fresh fruit worldwide. Despite the significance of environmental efficiency and popularity, until very recently, its genome sequence has not been determined and a high-quality annotated proteome has not been available. Here, we have undertaken a pilot proteogenomic study, analyzing the proteome of MD2 pineapple leaves using liquid chromatography-mass spectrometry (LC-MS/MS), which validates 1781 predicted proteins in the annotated F153 (V3) genome. In addition, a further 603 peptide identifications are found that map exclusively to an independent MD2 transcriptome-derived database but are not found in the standard F153 (V3) annotated proteome. Peptide identifications derived from these MD2 transcripts are also cross-referenced to a more recent and complete MD2 genome annotation, resulting in 402 nonoverlapping peptides, which in turn support 30 high-quality gene candidates novel to both pineapple genomes. Many of the validated F153 (V3) genes are also supported by an independent proteomics data set collected for an ornamental pineapple variety. The contigs and peptides have been mapped to the current F153 genome build and are available as bed files to display a custom gene track on the Ensembl Plants region viewer. These analyses add to the knowledge of experimentally validated pineapple genes and demonstrate the utility of transcript-derived proteomics to discover both novel genes and genetic structure in a plant genome, adding value to its annotation.
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Affiliation(s)
- Norazrin Ariffin
- School
of Biological Sciences, Faculty of Biology Medicine and Health, MAHSC, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
- Department
of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor Darul Ehsan, Malaysia
| | - David Wells Newman
- School
of Biological Sciences, Faculty of Biology Medicine and Health, MAHSC, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
| | - Michael G. Nelson
- School
of Biological Sciences, Faculty of Biology Medicine and Health, MAHSC, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
| | - Ronan O’cualain
- School
of Biological Sciences, Faculty of Biology Medicine and Health, MAHSC, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
| | - Simon J. Hubbard
- School
of Biological Sciences, Faculty of Biology Medicine and Health, MAHSC, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
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33
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Opulente DA, LaBella AL, Harrison MC, Wolters JF, Liu C, Li Y, Kominek J, Steenwyk JL, Stoneman HR, VanDenAvond J, Miller CR, Langdon QK, Silva M, Gonçalves C, Ubbelohde EJ, Li Y, Buh KV, Jarzyna M, Haase MAB, Rosa CA, ČCadež N, Libkind D, DeVirgilio JH, Hulfachor AB, Kurtzman CP, Sampaio JP, Gonçalves P, Zhou X, Shen XX, Groenewald M, Rokas A, Hittinger CT. Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts. Science 2024; 384:eadj4503. [PMID: 38662846 DOI: 10.1126/science.adj4503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 03/22/2024] [Indexed: 05/03/2024]
Abstract
Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Two general paradigms have been proposed to explain this variation: (i) trade-offs between performance efficiency and breadth and (ii) the joint influence of extrinsic (environmental) and intrinsic (genomic) factors. We assembled genomic, metabolic, and ecological data from nearly all known species of the ancient fungal subphylum Saccharomycotina (1154 yeast strains from 1051 species), grown in 24 different environmental conditions, to examine niche breadth evolution. We found that large differences in the breadth of carbon utilization traits between yeasts stem from intrinsic differences in genes encoding specific metabolic pathways, but we found limited evidence for trade-offs. These comprehensive data argue that intrinsic factors shape niche breadth variation in microbes.
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Affiliation(s)
- Dana A Opulente
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Biology Department, Villanova University, Villanova, PA 19085, USA
| | - Abigail Leavitt LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- North Carolina Research Center (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Kannapolis, NC 28081, USA
| | - Marie-Claire Harrison
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - John F Wolters
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Chao Liu
- College of Agriculture and Biotechnology and Centre for Evolutionary and Organismal Biology, Zhejiang University, Hangzhou 310058, China
| | - Yonglin Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Jacek Kominek
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- LifeMine Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hayley R Stoneman
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jenna VanDenAvond
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Caroline R Miller
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Quinn K Langdon
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Margarida Silva
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Carla Gonçalves
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Emily J Ubbelohde
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Yuanning Li
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Kelly V Buh
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Martin Jarzyna
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Graduate Program in Neuroscience and Department of Biology, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Max A B Haase
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Vilcek Institute of Graduate Biomedical Sciences and Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Carlos A Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Neža ČCadež
- Food Science and Technology Department, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Universidad Nacional del Comahue, CONICET, CRUB, Quintral 1250, San Carlos de Bariloche, 8400, Río Negro, Argentina
| | - Jeremy H DeVirgilio
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, IL 61604, USA
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Cletus P Kurtzman
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, IL 61604, USA
| | - José Paulo Sampaio
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Paula Gonçalves
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- College of Agriculture and Biotechnology and Centre for Evolutionary and Organismal Biology, Zhejiang University, Hangzhou 310058, China
| | | | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
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Park S, An B, Park S. Dynamic changes in the plastid and mitochondrial genomes of the angiosperm Corydalis pauciovulata (Papaveraceae). BMC PLANT BIOLOGY 2024; 24:303. [PMID: 38644497 PMCID: PMC11034061 DOI: 10.1186/s12870-024-05025-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 04/15/2024] [Indexed: 04/23/2024]
Abstract
BACKGROUND Corydalis DC., the largest genus in the family Papaveraceae, comprises > 465 species. Complete plastid genomes (plastomes) of Corydalis show evolutionary changes, including syntenic arrangements, gene losses and duplications, and IR boundary shifts. However, little is known about the evolution of the mitochondrial genome (mitogenome) in Corydalis. Both the organelle genomes and transcriptomes are needed to better understand the relationships between the patterns of evolution in mitochondrial and plastid genomes. RESULTS We obtained complete plastid and mitochondrial genomes from Corydalis pauciovulata using a hybrid assembly of Illumina and Oxford Nanopore Technologies reads to assess the evolutionary parallels between the organelle genomes. The mitogenome and plastome of C. pauciovulata had sizes of 675,483 bp and 185,814 bp, respectively. Three ancestral gene clusters were missing from the mitogenome, and expanded IR (46,060 bp) and miniaturized SSC (202 bp) regions were identified in the plastome. The mitogenome and plastome of C. pauciovulata contained 41 and 67 protein-coding genes, respectively; the loss of genes was a plastid-specific event. We also generated a draft genome and transcriptome for C. pauciovulata. A combination of genomic and transcriptomic data supported the functional replacement of acetyl-CoA carboxylase subunit β (accD) by intracellular transfer to the nucleus in C. pauciovulata. In contrast, our analyses suggested a concurrent loss of the NADH-plastoquinone oxidoreductase (ndh) complex in both the nuclear and plastid genomes. Finally, we performed genomic and transcriptomic analyses to characterize DNA replication, recombination, and repair (DNA-RRR) genes in C. pauciovulata as well as the transcriptomes of Liriodendron tulipifera and Nelumbo nuicifera. We obtained 25 DNA-RRR genes and identified their structure in C. pauciovulata. Pairwise comparisons of nonsynonymous (dN) and synonymous (dS) substitution rates revealed that several DNA-RRR genes in C. pauciovulata have higher dN and dS values than those in N. nuicifera. CONCLUSIONS The C. pauciovulata genomic data generated here provide a valuable resource for understanding the evolution of Corydalis organelle genomes. The first mitogenome of Papaveraceae provides an example that can be explored by other researchers sequencing the mitogenomes of related plants. Our results also provide fundamental information about DNA-RRR genes in Corydalis and their related rate variation, which elucidates the relationships between DNA-RRR genes and organelle genome stability.
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Affiliation(s)
- Seongjun Park
- Institute of Natural Science, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea.
| | - Boram An
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea.
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35
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Sakamoto T, Ikematsu S, Nakayama H, Mandáková T, Gohari G, Sakamoto T, Li G, Hou H, Matsunaga S, Lysak MA, Kimura S. A chromosome-level genome assembly for the amphibious plant Rorippa aquatica reveals its allotetraploid origin and mechanisms of heterophylly upon submergence. Commun Biol 2024; 7:431. [PMID: 38637665 PMCID: PMC11026429 DOI: 10.1038/s42003-024-06088-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 03/21/2024] [Indexed: 04/20/2024] Open
Abstract
The ability to respond to varying environments is crucial for sessile organisms such as plants. The amphibious plant Rorippa aquatica exhibits a striking type of phenotypic plasticity known as heterophylly, a phenomenon in which leaf form is altered in response to environmental factors. However, the underlying molecular mechanisms of heterophylly are yet to be fully understood. To uncover the genetic basis and analyze the evolutionary processes driving heterophylly in R. aquatica, we assembled the chromosome-level genome of the species. Comparative chromosome painting and chromosomal genomics revealed that allopolyploidization and subsequent post-polyploid descending dysploidy occurred during the speciation of R. aquatica. Based on the obtained genomic data, the transcriptome analyses revealed that ethylene signaling plays a central role in regulating heterophylly under submerged conditions, with blue light signaling acting as an attenuator of ethylene signal. The assembled R. aquatica reference genome provides insights into the molecular mechanisms and evolution of heterophylly.
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Affiliation(s)
- Tomoaki Sakamoto
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan
| | - Shuka Ikematsu
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan
| | - Hokuto Nakayama
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan
- Graduate School of Science, Department of Biological Sciences, The University of Tokyo, Science Build. #2, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
- Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, CA, USA
| | - Terezie Mandáková
- CEITEC - Central European Institute of Technology, Masaryk University, CZ-625 00, Brno, Czech Republic
| | - Gholamreza Gohari
- Department of Horticulture, Faculty of Agriculture, University of Maragheh, Maragheh, Iran
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, Japan
- Faculty of Science, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa, Japan
| | - Gaojie Li
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Hongwei Hou
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Sachihiro Matsunaga
- Department of Integrated Biosciences, Graduate School of Frontier Science, The University of Tokyo, Chiba, Japan
| | - Martin A Lysak
- CEITEC - Central European Institute of Technology, Masaryk University, CZ-625 00, Brno, Czech Republic
| | - Seisuke Kimura
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan.
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan.
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36
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Blackburn MB, Tannières M, Sparks ME, Gundersen-Rindal DE, Bon MC. Serratia montpellierensis sp. nov., Isolated from Laboratory-Reared Parasitic Wasps Psyttalia lounsburyii Silvestri and Psyttalia ponerophaga Silvestri (Hymenoptera: Braconidae). Curr Microbiol 2024; 81:146. [PMID: 38634927 DOI: 10.1007/s00284-024-03666-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 03/09/2024] [Indexed: 04/19/2024]
Abstract
Two strains of bacteria, PsyLou2AT and PsyPon4B, were isolated from adult braconid wasps Psyttalia lounsburyii and Psyttalia ponerophaga, respectively. These laboratory-reared wasps were investigated as agents for biological control of the olive fruit fly, Bactrocera oleae. Analysis of 16S rRNA genes of the two isolates demonstrated that they were highly related and belonged to the genus Serratia. Genomic sequencing of these isolates revealed genomes of 5,152,551 bp and 5,154,385 bp for PsyLou2AT and PsyPon4B, respectively, and both genomes had a mol% G+C content of 59.6%. Phylogenetic analyses using BLAST-based average nucleotide identity (ANIb), and digital DNA-DNA hybridization methods indicated that PsyLou2AT was most closely related to Serratia nevei S15T, producing ANIb and dDDH values of 96.11% and 70.2%, respectively. Since these values were literally on the species cutoff threshold, additional S. nevei genome assemblies were analyzed using ANIb and dDDH calculations. This revealed that among assemblies that were clearly identifiable as S. nevei, S. nevei S15T was the most closely related to PsyLou2AT, and that a majority of assemblies produced dDDH values of 68.3-68.7% relative to PsyLou2AT. Additionally, PsyLou2AT differed biochemically from S. nevei S15T in that it produced positive Voges Proskauer tests, produced protease, lacked arginine dihydrolase, and did not utilize D-lactose. Hence, PsyLou2AT represents a novel taxon within the Serratia, for which we propose the name Serratia montpellierensis sp. nov. The type strain is PsyLou2AT (=LMG 32817T =NRRL B-65689T).
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Affiliation(s)
- Michael B Blackburn
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, MD, 20705, USA.
| | - Mélanie Tannières
- USDA-ARS European Biological Control Laboratory, Montferrier sur Lez, France
| | - Michael E Sparks
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, MD, 20705, USA
| | | | - Marie-Claude Bon
- USDA-ARS European Biological Control Laboratory, Montferrier sur Lez, France
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37
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Bouzalas I, Apostolidi ED, Scalas D, Davidopoulou E, Chassalevris T, Rosati S, Colitti B. A Combined Approach for the Characterization of Small Ruminant Lentivirus Strains Circulating in the Islands and Mainland of Greece. Animals (Basel) 2024; 14:1119. [PMID: 38612358 PMCID: PMC11010947 DOI: 10.3390/ani14071119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
Small ruminant lentiviruses are a group of viruses infecting goat and sheep worldwide. These viruses exhibit an extraordinary degree of genetic and antigenic variability that severely influence in vivo and in vitro features, as well as diagnostic test results. Small ruminant farming is the most important animal farming business in Greece, with a high impact on the Greek primary economy. Although SRLV infection and its impact on animal production are well established in the country, little is known about the circulating SRLV strains and their prevalence. The aim of this study was to characterize SRLVs circulating in Greece with a combined serological and molecular approach, using the bulk milk matrix collected from 60 farms in different municipalities. This study allowed us to estimate a seroprevalence of around 52% at the herd level. The B1, B2 and A3 subtypes and a novel A viral cluster were identified. Moreover, the amplicon sequencing method allowed us to identify more than one viral subtype in a sample. These results again confirm the high variability of these viruses and highlight the importance of the constant monitoring of viral evolution, in particular in antigens of diagnostic interest.
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Affiliation(s)
- Ilias Bouzalas
- Hellenic Agricultural Organization—DEMETER, Veterinary Research Institute, Campus of Thermi, 57001 Thessaloniki, Greece; (I.B.); (E.D.A.); (T.C.)
| | - Evangelia D. Apostolidi
- Hellenic Agricultural Organization—DEMETER, Veterinary Research Institute, Campus of Thermi, 57001 Thessaloniki, Greece; (I.B.); (E.D.A.); (T.C.)
| | - Daniela Scalas
- Department of Veterinary Sciences, University of Turin, L. Braccini 2, 10095 Torino, Italy; (D.S.); (S.R.)
| | | | - Taxiarchis Chassalevris
- Hellenic Agricultural Organization—DEMETER, Veterinary Research Institute, Campus of Thermi, 57001 Thessaloniki, Greece; (I.B.); (E.D.A.); (T.C.)
| | - Sergio Rosati
- Department of Veterinary Sciences, University of Turin, L. Braccini 2, 10095 Torino, Italy; (D.S.); (S.R.)
| | - Barbara Colitti
- Department of Veterinary Sciences, University of Turin, L. Braccini 2, 10095 Torino, Italy; (D.S.); (S.R.)
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38
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Yang J, Park CG, Cho MS, Kim SC. Wasabi Gone Wild? Origin and Characterization of the Complete Plastomes of Ulleung Island Wasabi ( Eutrema japonicum; Brassicaceae) and Other Cultivars in Korea. Genes (Basel) 2024; 15:457. [PMID: 38674391 PMCID: PMC11049635 DOI: 10.3390/genes15040457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
Korean wasabi occurs naturally on the young oceanic, volcanic Ulleung Island off the east coast of the Korean Peninsula. Although the Ulleung Island wasabi is reported as Eutrema japonicum and has been suggested to be morphologically identical to cultivars in Korea, very little is known about its taxonomic identity and relationship with other cultivars. In this study, we sequenced the complete chloroplast DNA sequences of three naturally occurring Ulleung Island wasabi plants and six cultivars ('Daewang', 'Daruma', 'Micado', 'Orochi', 'Green Thumb', and 'Shogun') from continental Korea and determined the taxonomic identity of Korean wasabi on Ulleung Island. The size and organization of the complete chloroplast genomes of the nine accessions were nearly identical to those of previously reported wasabi cultivars. In addition, phylogenetic analysis based on the complete plastomes suggested that Ulleung Island wasabi most likely comprises various wasabi cultivars with three chlorotypes ('Shogun', 'Green Thumb', and a unique Chusan type). Based on the complete plastomes, we identified eight chlorotypes for the major wasabi cultivars and the Ulleung Island wasabi. Two major groups (1-'Mazuma' and 'Daruma', and 2-'Fujidaruma'/'Shimane No. 3'/Ulleung Island wasabi/five cultivars in Korea) were also identified based on mother line genealogical history. Furthermore, different types of variations (mutations, insertions/deletions (indels), mononucleotide repeats, and inversions) in plastomes were identified to distinguish different cultivar lines and five highly divergent hotspots. The nine newly obtained complete plastomes are valuable organelle genomic resources for species identification and infraspecific phylogeographic studies on wild and cultivated wasabi.
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Affiliation(s)
- JiYoung Yang
- Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea;
| | - Cheon Gyoo Park
- Gangwondo Agricultural Research and Extension Services, Wild Vegetable Reseaerch Institute, Alpine Agricultural Experiment Station, Taebaek-si 26046, Republic of Korea;
| | - Myong-Suk Cho
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon 16419, Republic of Korea;
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon 16419, Republic of Korea;
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39
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Xie P, Guo Y, Teng Y, Zhou W, Yu Y. GeneMiner: A tool for extracting phylogenetic markers from next-generation sequencing data. Mol Ecol Resour 2024; 24:e13924. [PMID: 38197287 DOI: 10.1111/1755-0998.13924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/11/2024]
Abstract
The advancement of next-generation sequencing (NGS) technologies has been revolutionary for the field of evolutionary biology. This technology has led to an abundance of available genomes and transcriptomes for researchers to mine. Specifically, researchers can mine for various types of molecular markers that are vital for phylogenetic, evolutionary and ecological studies. Numerous tools have been developed to extract these molecular markers from NGS data. However, due to an insufficient number of well-annotated reference genomes for non-model organisms, it remains challenging to obtain these markers accurately and efficiently. Here, we present GeneMiner, an improved and expanded version of our previous tool, Easy353. GeneMiner combines the reference-guided de Bruijn graph assembly with seed self-discovery and greedy extension. Additionally, it includes a verification step using a parameter-bootstrap method to reduce the pitfalls associated with using a relatively distant reference. Our results, using both experimental and simulation data, showed GeneMiner can accurately acquire phylogenetic molecular markers for plants using transcriptomic, genomic and other NGS data. GeneMiner is designed to be user-friendly, fast and memory-efficient. Further, it is compatible with Linux, Windows and macOS. All source codes are publicly available on GitHub (https://github.com/sculab/GeneMiner) and Gitee (https://gitee.com/sculab/GeneMiner) for easy accessibility and transparency.
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Affiliation(s)
- Pulin Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yongling Guo
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yue Teng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wenbin Zhou
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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40
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Bossert S, Pauly A, Danforth BN, Orr MC, Murray EA. Lessons from assembling UCEs: A comparison of common methods and the case of Clavinomia (Halictidae). Mol Ecol Resour 2024; 24:e13925. [PMID: 38183389 DOI: 10.1111/1755-0998.13925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 01/08/2024]
Abstract
Sequence data assembly is a foundational step in high-throughput sequencing, with untold consequences for downstream analyses. Despite this, few studies have interrogated the many methods for assembling phylogenomic UCE data for their comparative efficacy, or for how outputs may be impacted. We study this by comparing the most commonly used assembly methods for UCEs in the under-studied bee lineage Nomiinae and a representative sampling of relatives. Data for 63 UCE-only and 75 mixed taxa were assembled with five methods, including ABySS, HybPiper, SPAdes, Trinity and Velvet, and then benchmarked for their relative performance in terms of locus capture parameters and phylogenetic reconstruction. Unexpectedly, Trinity and Velvet trailed the other methods in terms of locus capture and DNA matrix density, whereas SPAdes performed favourably in most assessed metrics. In comparison with SPAdes, the guided-assembly approach HybPiper generally recovered the highest quality loci but in lower numbers. Based on our results, we formally move Clavinomia to Dieunomiini and render Epinomia once more a subgenus of Dieunomia. We strongly advise that future studies more closely examine the influence of assembly approach on their results, or, minimally, use better-performing assembly methods such as SPAdes or HybPiper. In this way, we can move forward with phylogenomic studies in a more standardized, comparable manner.
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Affiliation(s)
- Silas Bossert
- Department of Entomology, Washington State University, Pullman, Washington, USA
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Alain Pauly
- Royal Belgian Institute of Natural Sciences, O.D. Taxonomy and Phylogeny, Brussels, Belgium
| | - Bryan N Danforth
- Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Michael C Orr
- Entomologie, Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
| | - Elizabeth A Murray
- Department of Entomology, Washington State University, Pullman, Washington, USA
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41
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Park S, Kwak M, Park S. Complete organelle genomes of Korean fir, Abies koreana and phylogenomics of the gymnosperm genus Abies using nuclear and cytoplasmic DNA sequence data. Sci Rep 2024; 14:7636. [PMID: 38561351 PMCID: PMC10985005 DOI: 10.1038/s41598-024-58253-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 03/27/2024] [Indexed: 04/04/2024] Open
Abstract
Abies koreana E.H.Wilson is an endangered evergreen coniferous tree that is native to high altitudes in South Korea and susceptible to the effects of climate change. Hybridization and reticulate evolution have been reported in the genus; therefore, multigene datasets from nuclear and cytoplasmic genomes are needed to better understand its evolutionary history. Using the Illumina NovaSeq 6000 and Oxford Nanopore Technologies (ONT) PromethION platforms, we generated complete mitochondrial (1,174,803 bp) and plastid (121,341 bp) genomes from A. koreana. The mitochondrial genome is highly dynamic, transitioning from cis- to trans-splicing and breaking conserved gene clusters. In the plastome, the ONT reads revealed two structural conformations of A. koreana. The short inverted repeats (1186 bp) of the A. koreana plastome are associated with different structural types. Transcriptomic sequencing revealed 1356 sites of C-to-U RNA editing in the 41 mitochondrial genes. Using A. koreana as a reference, we additionally produced nuclear and organelle genomic sequences from eight Abies species and generated multiple datasets for maximum likelihood and network analyses. Three sections (Balsamea, Momi, and Pseudopicea) were well grouped in the nuclear phylogeny, but the phylogenomic relationships showed conflicting signals in the mitochondrial and plastid genomes, indicating a complicated evolutionary history that may have included introgressive hybridization. The obtained data illustrate that phylogenomic analyses based on sequences from differently inherited organelle genomes have resulted in conflicting trees. Organelle capture, organelle genome recombination, and incomplete lineage sorting in an ancestral heteroplasmic individual can contribute to phylogenomic discordance. We provide strong support for the relationships within Abies and new insights into the phylogenomic complexity of this genus.
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Affiliation(s)
- Seongjun Park
- Institute of Natural Science, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea
| | - Myounghai Kwak
- National Institute of Biological Resources, Incheon, 22689, South Korea.
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea.
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42
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Liu X, Liu Y, Liu J, Zhang H, Shan C, Guo Y, Gong X, Cui M, Li X, Tang M. Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence. Neural Regen Res 2024; 19:833-845. [PMID: 37843219 PMCID: PMC10664138 DOI: 10.4103/1673-5374.382223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/19/2023] [Accepted: 06/17/2023] [Indexed: 10/17/2023] Open
Abstract
A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis. As a contributing factor, microbiota dysbiosis always occurs in pathological changes of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. High-throughput sequencing technology has helped to reveal that the bidirectional communication between the central nervous system and the enteric nervous system is facilitated by the microbiota's diverse microorganisms, and for both neuroimmune and neuroendocrine systems. Here, we summarize the bioinformatics analysis and wet-biology validation for the gut metagenomics in neurodegenerative diseases, with an emphasis on multi-omics studies and the gut virome. The pathogen-associated signaling biomarkers for identifying brain disorders and potential therapeutic targets are also elucidated. Finally, we discuss the role of diet, prebiotics, probiotics, postbiotics and exercise interventions in remodeling the microbiome and reducing the symptoms of neurodegenerative diseases.
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Affiliation(s)
- Xiaoyan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
- Institute of Animal Husbandry, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China
| | - Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Chaofan Shan
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Yinglu Guo
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Xun Gong
- Department of Rheumatology & Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Mengmeng Cui
- Department of Neurology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province, China
| | - Xiubin Li
- Department of Neurology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province, China
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
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Li W, Lim CH, Zhao Z, Wang Y, Conway PL, Loo SCJ. In Vitro Profiling of Potential Fish Probiotics, Enterococcus hirae Strains, Isolated from Jade Perch, and Safety Properties Assessed Using Whole Genome Sequencing. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10244-0. [PMID: 38498111 DOI: 10.1007/s12602-024-10244-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2024] [Indexed: 03/20/2024]
Abstract
The demands of intensified aquaculture production and escalating disease prevalence underscore the need for efficacious probiotic strategies to enhance fish health. This study focused on isolating and characterising potential probiotics from the gut microbiota of the emerging aquaculture species jade perch (Scortum barcoo). Eighty-seven lactic acid bacteria and 149 other bacteria were isolated from the digestive tract of five adult jade perch. The screening revealed that 24 Enterococcus hirae isolates inhibited the freshwater pathogens Aeromonas sobria and Streptococcus iniae. Co-incubating E. hirae with the host gut suspensions demonstrated a two- to five-fold increase in the size of growth inhibition zones compared to the results when using gut suspensions from tilapia (a non-host), indicating host-specificity. Genome analysis of the lead isolate, E. hirae R44, predicted the presence of antimicrobial compounds like enterolysin A, class II lanthipeptide, and terpenes, which underlay its antibacterial attributes. Isolate R44 exhibited desirable probiotic characteristics, including survival at pH values within the range of 3 to 12, bile tolerance, antioxidant activity, ampicillin sensitivity, and absence of transferable antimicrobial resistance genes and virulence factors commonly associated with hospital Enterococcus strains (IS16, hylEfm, and esp). This study offers a foundation for sourcing host-adapted probiotics from underexplored aquaculture species. Characterisation of novel probiotics like E. hirae R44 can expedite the development of disease mitigation strategies to support aquaculture intensification.
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Affiliation(s)
- Wenrui Li
- NTU Institute for Health Technologies, Interdisciplinary Graduate Programme, Nanyang Technological University, 61 Nanyang Drive, Singapore, 637335, Singapore
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Chiun Hao Lim
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Zhongtian Zhao
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Yulan Wang
- Singapore Phenome Centre, Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Patricia Lynne Conway
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- Centre for Marine Science Innovation, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Say Chye Joachim Loo
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore.
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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Minařík M, Modrell MS, Gillis JA, Campbell AS, Fuller I, Lyne R, Micklem G, Gela D, Pšenička M, Baker CVH. Identification of multiple transcription factor genes potentially involved in the development of electrosensory versus mechanosensory lateral line organs. Front Cell Dev Biol 2024; 12:1327924. [PMID: 38562141 PMCID: PMC10982350 DOI: 10.3389/fcell.2024.1327924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/19/2024] [Indexed: 04/04/2024] Open
Abstract
In electroreceptive jawed vertebrates, embryonic lateral line placodes give rise to electrosensory ampullary organs as well as mechanosensory neuromasts. Previous reports of shared gene expression suggest that conserved mechanisms underlie electroreceptor and mechanosensory hair cell development and that electroreceptors evolved as a transcriptionally related "sister cell type" to hair cells. We previously identified only one transcription factor gene, Neurod4, as ampullary organ-restricted in the developing lateral line system of a chondrostean ray-finned fish, the Mississippi paddlefish (Polyodon spathula). The other 16 transcription factor genes we previously validated in paddlefish were expressed in both ampullary organs and neuromasts. Here, we used our published lateral line organ-enriched gene-set (arising from differential bulk RNA-seq in late-larval paddlefish), together with a candidate gene approach, to identify 25 transcription factor genes expressed in the developing lateral line system of a more experimentally tractable chondrostean, the sterlet (Acipenser ruthenus, a small sturgeon), and/or that of paddlefish. Thirteen are expressed in both ampullary organs and neuromasts, consistent with conservation of molecular mechanisms. Seven are electrosensory-restricted on the head (Irx5, Irx3, Insm1, Sp5, Satb2, Mafa and Rorc), and five are the first-reported mechanosensory-restricted transcription factor genes (Foxg1, Sox8, Isl1, Hmx2 and Rorb). However, as previously reported, Sox8 is expressed in ampullary organs as well as neuromasts in a catshark (Scyliorhinus canicula), suggesting the existence of lineage-specific differences between cartilaginous and ray-finned fishes. Overall, our results support the hypothesis that ampullary organs and neuromasts develop via largely conserved transcriptional mechanisms, and identify multiple transcription factors potentially involved in the formation of electrosensory versus mechanosensory lateral line organs.
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Affiliation(s)
- Martin Minařík
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Melinda S. Modrell
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - J. Andrew Gillis
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Alexander S. Campbell
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Isobel Fuller
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Rachel Lyne
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Gos Micklem
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - David Gela
- Faculty of Fisheries and Protection of Waters, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Martin Pšenička
- Faculty of Fisheries and Protection of Waters, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Clare V. H. Baker
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
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He X, Kusuya Y, Hagiwara D, Toyotome T, Arai T, Bian C, Nagayama M, Shibata S, Watanabe A, Takahashi H. Genomic diversity of the pathogenic fungus Aspergillus fumigatus in Japan reveals the complex genomic basis of azole resistance. Commun Biol 2024; 7:274. [PMID: 38486002 PMCID: PMC10940670 DOI: 10.1038/s42003-024-05902-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 02/08/2024] [Indexed: 03/18/2024] Open
Abstract
Aspergillus fumigatus is a pathogenic fungus with a global distribution. The emergence of azole-resistant A. fumigatus (ARAf) other than the TR-mutants is a problem in Japan. Additionally, the genetic diversity of A. fumigatus strains in Japan remains relatively unknown. Here we show the diversity in the A. fumigatus strains isolated in Japan as well as the complexity in the global distribution of the pathogenic strains. First, we analyzed the genome sequences of 171 strains from Japan as well as the antifungal susceptibility of these strains. Next, we conducted a population analysis of 876 strains by combining the available genomic data for strains isolated worldwide, which were grouped in six clusters. Finally, a genome-wide association study identified the genomic loci associated with ARAf strains, but not the TR-mutants. These results highlight the complexity of the genomic mechanism underlying the emergence of ARAf strains other than the TR-mutants.
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Affiliation(s)
- Xiaohui He
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan
| | - Yoko Kusuya
- Biological Resource Center, National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, 292-0818, Japan
| | - Daisuke Hagiwara
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Takahito Toyotome
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-11, Inadacho, Obihiro, 080-8555, Japan
| | - Teppei Arai
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan
| | - Cai Bian
- BGI-Shenzhen, Yantian District, Shenzhen, 518083, China
| | - Masaki Nagayama
- Graduate School of Medical and Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Saho Shibata
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan
| | - Akira Watanabe
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan
| | - Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan.
- Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan.
- Plant Molecular Science Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan.
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Carasso S, Zaatry R, Hajjo H, Kadosh-Kariti D, Ben-Assa N, Naddaf R, Mandelbaum N, Pressman S, Chowers Y, Gefen T, Jeffrey KL, Jofre J, Coyne MJ, Comstock LE, Sharon I, Geva-Zatorsky N. Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota. Cell Host Microbe 2024; 32:322-334.e9. [PMID: 38423015 PMCID: PMC10939037 DOI: 10.1016/j.chom.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 12/11/2023] [Accepted: 02/06/2024] [Indexed: 03/02/2024]
Abstract
Reversible genomic DNA inversions control the expression of numerous gut bacterial molecules, but how this impacts disease remains uncertain. By analyzing metagenomic samples from inflammatory bowel disease (IBD) cohorts, we identified multiple invertible regions where a particular orientation correlated with disease. These include the promoter of polysaccharide A (PSA) of Bacteroides fragilis, which induces regulatory T cells (Tregs) and ameliorates experimental colitis. The PSA promoter was mostly oriented "OFF" in IBD patients, which correlated with increased B. fragilis-associated bacteriophages. Similarly, in mice colonized with a healthy human microbiota and B. fragilis, induction of colitis caused a decline of PSA in the "ON" orientation that reversed as inflammation resolved. Monocolonization of mice with B. fragilis revealed that bacteriophage infection increased the frequency of PSA in the "OFF" orientation, causing reduced PSA expression and decreased Treg cells. Altogether, we reveal dynamic bacterial phase variations driven by bacteriophages and host inflammation, signifying bacterial functional plasticity during disease.
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Affiliation(s)
- Shaqed Carasso
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Rappaport Technion Integrated Cancer Center (RTICC), Haifa 32000, Israel
| | - Rawan Zaatry
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Rappaport Technion Integrated Cancer Center (RTICC), Haifa 32000, Israel
| | - Haitham Hajjo
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Rappaport Technion Integrated Cancer Center (RTICC), Haifa 32000, Israel
| | - Dana Kadosh-Kariti
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Rappaport Technion Integrated Cancer Center (RTICC), Haifa 32000, Israel
| | - Nadav Ben-Assa
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Rappaport Technion Integrated Cancer Center (RTICC), Haifa 32000, Israel
| | - Rawi Naddaf
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Rappaport Technion Integrated Cancer Center (RTICC), Haifa 32000, Israel
| | - Noa Mandelbaum
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Rappaport Technion Integrated Cancer Center (RTICC), Haifa 32000, Israel
| | - Sigal Pressman
- Department of Gastroenterology, Rambam Health Care Campus, Haifa 3109601, Israel; Clinical Research Institute, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Yehuda Chowers
- Department of Gastroenterology, Rambam Health Care Campus, Haifa 3109601, Israel; Clinical Research Institute, Rambam Health Care Campus, Haifa 3109601, Israel; Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Tal Gefen
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Rappaport Technion Integrated Cancer Center (RTICC), Haifa 32000, Israel
| | - Kate L Jeffrey
- Moderna, Inc., Cambridge, MA 02139, USA; Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, Avda. Diagonal 643 08028, Barcelona, Spain
| | - Michael J Coyne
- Duchossois Family Institute and Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Laurie E Comstock
- Duchossois Family Institute and Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Itai Sharon
- Migal-Galilee Research Institute, P.O. Box 831, Kiryat Shmona 11016, Israel; Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee 1220800, Israel
| | - Naama Geva-Zatorsky
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Rappaport Technion Integrated Cancer Center (RTICC), Haifa 32000, Israel; CIFAR, MaRS Centre, West Tower 661, Suite 505, Toronto, ON M5G 1M1, Canada.
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Rossini E, Bazzucchi M, Trocchi V, Merzoni F, Bertasio C, Knauf S, Lavazza A, Cavadini P. Identification and Characterisation of a Myxoma Virus Detected in the Italian Hare ( Lepus corsicanus). Viruses 2024; 16:437. [PMID: 38543802 PMCID: PMC10975712 DOI: 10.3390/v16030437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/08/2024] [Accepted: 03/09/2024] [Indexed: 05/23/2024] Open
Abstract
Myxoma virus (MYXV) is a Leporipoxvirus (genus) belonging to the family Poxviridae; it is characterised by a genome of approximately 161 kb dsDNA encoding for several proteins that play an essential role in both host spectrum determination and immunomodulation. The healthy reservoir of the virus is Sylvilagus spp. At the same time, in wild and domestic European rabbits (Oryctolagus cuniculus), MYXV is the etiologic agent of myxomatosis, a disease with an extremely high mortality rate. In 2014, an interspecies jump of MYXV was reported in Lepus europaeus in the UK. In 2018, myxomatosis induced by a new recombinant strain called MYXV-To was identified during a large outbreak in Iberian hares (Lepus granatensis) in Spain. Here, we describe the case of myxomatosis in another hare species: an adult male Italian hare (Lepus corsicanus) found dead in 2018 in Sicily with lesions suggestive of myxomatosis and treponema infection. Laboratory tests, e.g., end-point PCR and negative staining electron microscopy, confirmed the presence of both pathogens. MYXV was then isolated from tissue samples in permissive cells and sequenced using NGS technology. Main genomic differences concerning known MYXV strains are discussed.
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Affiliation(s)
- Elisa Rossini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini” (IZSLER), Via Antonio Bianchi, 7/9, 25124 Brescia, Italy; (E.R.); (F.M.); (C.B.); (A.L.); (P.C.)
- WOAH Reference Laboratories for Myxomatosis and for RHD, Via Antonio Bianchi, 7/9, 25124 Brescia, Italy
| | - Moira Bazzucchi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini” (IZSLER), Via Antonio Bianchi, 7/9, 25124 Brescia, Italy; (E.R.); (F.M.); (C.B.); (A.L.); (P.C.)
- WOAH Reference Laboratories for Myxomatosis and for RHD, Via Antonio Bianchi, 7/9, 25124 Brescia, Italy
| | - Valter Trocchi
- Federazione Italiana della Caccia (FIDC), Via Garigliano 57, 00198 Roma, Italy;
| | - Francesca Merzoni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini” (IZSLER), Via Antonio Bianchi, 7/9, 25124 Brescia, Italy; (E.R.); (F.M.); (C.B.); (A.L.); (P.C.)
- WOAH Reference Laboratories for Myxomatosis and for RHD, Via Antonio Bianchi, 7/9, 25124 Brescia, Italy
| | - Cristina Bertasio
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini” (IZSLER), Via Antonio Bianchi, 7/9, 25124 Brescia, Italy; (E.R.); (F.M.); (C.B.); (A.L.); (P.C.)
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich Loeffler Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany;
- Professorship for One Health/International Animal Health, Faculty of Veterinary Medicine, Justus Liebig University, 35392 Giessen, Germany
| | - Antonio Lavazza
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini” (IZSLER), Via Antonio Bianchi, 7/9, 25124 Brescia, Italy; (E.R.); (F.M.); (C.B.); (A.L.); (P.C.)
- WOAH Reference Laboratories for Myxomatosis and for RHD, Via Antonio Bianchi, 7/9, 25124 Brescia, Italy
| | - Patrizia Cavadini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini” (IZSLER), Via Antonio Bianchi, 7/9, 25124 Brescia, Italy; (E.R.); (F.M.); (C.B.); (A.L.); (P.C.)
- WOAH Reference Laboratories for Myxomatosis and for RHD, Via Antonio Bianchi, 7/9, 25124 Brescia, Italy
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48
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Luan T, Cepeda V, Liu B, Bowen Z, Ayyangar U, Almeida M, Hill CM, Koren S, Treangen TJ, Porter A, Pop M. MetaCompass: Reference-guided Assembly of Metagenomes. ARXIV 2024:arXiv:2403.01578v1. [PMID: 38903742 PMCID: PMC11188144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in a metagenomic context. Here we describe the first effective approach for reference-guided metagenomic assembly that can complement and improve upon de novo metagenomic assembly methods for certain organisms. Such approaches will be increasingly useful as more genomes are sequenced and made publicly available.
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Affiliation(s)
- Tu Luan
- Department of Computer Science, University of Maryland, College Park, Maryland, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Victoria Cepeda
- Department of Computer Science, University of Maryland, College Park, Maryland, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Bo Liu
- Department of Computer Science, University of Maryland, College Park, Maryland, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Zac Bowen
- Fraunhofer USA Center Mid-Atlantic, Riverdale, Maryland, USA
| | - Ujjwal Ayyangar
- Fraunhofer USA Center Mid-Atlantic, Riverdale, Maryland, USA
| | - Mathieu Almeida
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Christopher M. Hill
- Department of Computer Science, University of Maryland, College Park, Maryland, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Todd J. Treangen
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Adam Porter
- Department of Computer Science, University of Maryland, College Park, Maryland, USA
| | - Mihai Pop
- Department of Computer Science, University of Maryland, College Park, Maryland, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
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Tan M, Zhang Y, Bo H, Li X, Zou S, Yang L, Liu J, Chen Q, Xu X, Zhu W, Wang D. Rapid adaptive substitution of L226Q in HA protein increases the pathogenicity of H9N2 viruses in mice. INFECTIOUS MEDICINE 2024; 3:100090. [PMID: 38444745 PMCID: PMC10914417 DOI: 10.1016/j.imj.2024.100090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/04/2023] [Accepted: 12/10/2023] [Indexed: 03/07/2024]
Abstract
Background Since the first human infection with H9N2 virus was reported in 1998, the number of cases of H9N2 infection has exceeded one hundred by 2021. However, there is no systematic description of the biological characteristics of H9N2 viruses isolated from humans. Methods Therefore, this study analyzed the pathogenicity in mice of all available H9N2 viruses isolated from human cases in China from 2013 to 2021. Results Although most of the H9N2 viruses analyzed showed low or no pathogenicity in mice, the leucine to glutamine substitution at residue 226 (L226Q) in the hemagglutinin (HA) protein rapidly emerged during the adaptation of H9N2 viruses, and was responsible for severe infections and even fatalities. HA amino acid 226Q conferred a remarkable competitive advantage on H9N2 viruses in mice relative to viruses containing 226L, increasing their virulence, infectivity, and replication. Conclusion Thus, our study demonstrates that the adaptive substitution HA L226Q rapidly acquired by H9N2 viruses during the course of infection in mice contributed to their high pathogenicity.
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Affiliation(s)
- Min Tan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Beijing 102206, China
| | - Ye Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Beijing 102206, China
| | - Hong Bo
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Beijing 102206, China
| | - Xiyan Li
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Beijing 102206, China
| | - Shumei Zou
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Beijing 102206, China
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Beijing 102206, China
| | - Jia Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Beijing 102206, China
| | - Qi Chen
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Beijing 102206, China
- School of Public Health, Sun Yat-sen University, Guangdong 510275, China
| | - Xiaohao Xu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Beijing 102206, China
- School of Public Health, Sun Yat-sen University, Guangdong 510275, China
| | - Wenfei Zhu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Beijing 102206, China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Beijing 102206, China
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50
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Marlétaz F, Timoshevskaya N, Timoshevskiy VA, Parey E, Simakov O, Gavriouchkina D, Suzuki M, Kubokawa K, Brenner S, Smith JJ, Rokhsar DS. The hagfish genome and the evolution of vertebrates. Nature 2024; 627:811-820. [PMID: 38262590 PMCID: PMC10972751 DOI: 10.1038/s41586-024-07070-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
As the only surviving lineages of jawless fishes, hagfishes and lampreys provide a crucial window into early vertebrate evolution1-3. Here we investigate the complex history, timing and functional role of genome-wide duplications4-7 and programmed DNA elimination8,9 in vertebrates in the light of a chromosome-scale genome sequence for the brown hagfish Eptatretus atami. Combining evidence from syntenic and phylogenetic analyses, we establish a comprehensive picture of vertebrate genome evolution, including an auto-tetraploidization (1RV) that predates the early Cambrian cyclostome-gnathostome split, followed by a mid-late Cambrian allo-tetraploidization (2RJV) in gnathostomes and a prolonged Cambrian-Ordovician hexaploidization (2RCY) in cyclostomes. Subsequently, hagfishes underwent extensive genomic changes, with chromosomal fusions accompanied by the loss of genes that are essential for organ systems (for example, genes involved in the development of eyes and in the proliferation of osteoclasts); these changes account, in part, for the simplification of the hagfish body plan1,2. Finally, we characterize programmed DNA elimination in hagfish, identifying protein-coding genes and repetitive elements that are deleted from somatic cell lineages during early development. The elimination of these germline-specific genes provides a mechanism for resolving genetic conflict between soma and germline by repressing germline and pluripotency functions, paralleling findings in lampreys10,11. Reconstruction of the early genomic history of vertebrates provides a framework for further investigations of the evolution of cyclostomes and jawed vertebrates.
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Affiliation(s)
- Ferdinand Marlétaz
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
| | | | | | - Elise Parey
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Oleg Simakov
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Department for Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria
| | - Daria Gavriouchkina
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- UK Dementia Research Institute, University College London, London, UK
| | - Masakazu Suzuki
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Kaoru Kubokawa
- Ocean Research Institute, The University of Tokyo, Tokyo, Japan
| | - Sydney Brenner
- Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, KY, USA.
| | - Daniel S Rokhsar
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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