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      Ancient chicken remains reveal the origins of virulence in Marek’s disease virus

      1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 2 , 10 , 2 , 2 , 1 , 1 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 17 , 18 , 19 , 20 , 20 , 21 , 22 , 23 , 24 , 25 , 2 , 26 , 17 , 17 , 20 , 27 , 1 , 28 , 1 , 29 , 2 , 1 , 30 , 31
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      American Association for the Advancement of Science (AAAS)

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          Abstract

          The pronounced growth in livestock populations since the 1950s has altered the epidemiological and evolutionary trajectory of their associated pathogens. For example, Marek’s disease virus (MDV), which causes lymphoid tumors in chickens, has experienced a marked increase in virulence over the past century. Today, MDV infections kill >90% of unvaccinated birds, and controlling it costs more than US$1 billion annually. By sequencing MDV genomes derived from archeological chickens, we demonstrate that it has been circulating for at least 1000 years. We functionally tested the Meq oncogene, one of 49 viral genes positively selected in modern strains, demonstrating that ancient MDV was likely incapable of driving tumor formation. Our results demonstrate the power of ancient DNA approaches to trace the molecular basis of virulence in economically relevant pathogens.

          Editor’s summary

          Marek’s disease virus (MDV) causes tumors in chickens and has increased in virulence over the past century. Fiddaman et al . studied ancient DNA from chickens to reveal the evolutionary history of this once mild disease (see the Perspective by Duchene). They sequenced MDV DNA from 15 ancient chickens, finding that these strains were basal to modern ones and identifying multiple fixed genetic changes. Testing the ancient version of the gene Meq , a regulator of tumor formation, the authors found that virulence was greatly reduced compared with modern versions. These results shed light on the evolution of virulence in a major disease in modern agriculture. —Corinne Simonti

          Abstract

          Functional paleogenomics reveals the molecular basis for increased virulence in Marek’s disease virus.

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          Most cited references65

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            Fast gapped-read alignment with Bowtie 2.

            As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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              Is Open Access

              MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

              We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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                Author and article information

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                Journal
                Science
                Science
                American Association for the Advancement of Science (AAAS)
                0036-8075
                1095-9203
                December 15 2023
                December 15 2023
                : 382
                : 6676
                : 1276-1281
                Affiliations
                [1 ]Department of Biology, University of Oxford, Oxford, UK.
                [2 ]The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.
                [3 ]Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
                [4 ]Centre d’Anthropobiologie et de Génomique de Toulouse, CNRS/Université Toulouse III Paul Sabatier, Toulouse, France.
                [5 ]Instituto Nacional de Antropología y Pensamiento Latinoamericano, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina.
                [6 ]Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
                [7 ]Swiss Institute of Bioinformatics, Lausanne, Switzerland.
                [8 ]Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
                [9 ]Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium.
                [10 ]BioArCh, Department of Archaeology, University of York, York, UK.
                [11 ]Institute of Archaeology, Belgrade, Serbia.
                [12 ]Institute of Immunity and Transplantation, University College London, London, UK.
                [13 ]Silkie Club of Great Britain, Charing, UK.
                [14 ]Fishbourne Roman Palace, Fishbourne, UK.
                [15 ]Leibniz-Zentrum für Archäologie, Mainz, Germany.
                [16 ]Medieval Department, Budapest History Museum, Budapest, Hungary.
                [17 ]Laboratory of Biomonitoring, The Institute of Problems in Ecology and Mineral Wealth, Tatarstan Academy of Sciences, Kazan, Russia.
                [18 ]Archéologie Alsace–PAIR, Sélestat, Bas-Rhin, France.
                [19 ]Departament de Prehistòria, Universitat Autònoma de Barcelona, Barcelona, Spain.
                [20 ]Bioarchaeology Laboratory, Central Laboratory, University of Tehran, Tehran, Iran.
                [21 ]Department of Art and Architecture, Payame Noor University (PNU), Tehran, Iran.
                [22 ]Iranian Ministry of Cultural Heritage, Tourism, and Handicrafts, North Khorasan Office, Iran.
                [23 ]Department of Archaeology, School of History, Nanjing University, China.
                [24 ]Headland Archaeology, Edinburgh, UK.
                [25 ]Department of Archaeology, University of Exeter, Exeter, UK.
                [26 ]Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden.
                [27 ]CNRS, National Museum Natural History Paris, Paris, France.
                [28 ]Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK.
                [29 ]Viral Oncogenesis Group, Pirbright Institute, Woking, UK.
                [30 ]Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universitat, Munich, Germany.
                [31 ]School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
                Article
                10.1126/science.adg2238
                38096384
                cd5e85b5-28bc-4db3-b631-e97c4badecc6
                © 2023

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