Author: "Shane A McCarthy" - Searchworks@Jio Institute Digital Library Search Results

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1. A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia illucens L.)

Author: Tomas N Generalovic, Shane A McCarthy, Ian A Warren, Jonathan M D Wood, James Torrance, Ying Sims, Michael Quail, Kerstin Howe, Miha Pipan, Richard Durbin, and Chris D Jiggins
Subjects: Genetics, QH426-470
Abstract: Abstract Hermetia illucens
Published: 2021
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2. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author: Ann M. Mc Cartney, Giulio Formenti, Alice Mouton, Diego De Panis, Luísa S. Marins, Henrique G. Leitão, Genevieve Diedericks, Joseph Kirangwa, Marco Morselli, Judit Salces-Ortiz, Nuria Escudero, Alessio Iannucci, Chiara Natali, Hannes Svardal, Rosa Fernández, Tim De Pooter, Geert Joris, Mojca Strazisar, Jonathan M. D. Wood, Katie E. Herron, Ole Seehausen, Phillip C. Watts, Felix Shaw, Robert P. Davey, Alice Minotto, José M. Fernández, Astrid Böhne, Carla Alegria, Tyler Alioto, Paulo C. Alves, Isabel R. Amorim, Jean-Marc Aury, Niclas Backstrom, Petr Baldrian, Laima Baltrunaite, Endre Barta, Bertrand BedHom, Caroline Belser, Johannes Bergsten, Laurie Bertrand, Helena Bilandija, Mahesh Binzer-Panchal, Iliana Bista, Mark Blaxter, Paulo A. V. Borges, Guilherme Borges Dias, Mirte Bosse, Tom Brown, Rémy Bruggmann, Elena Buena-Atienza, Josephine Burgin, Elena Buzan, Alessia Cariani, Nicolas Casadei, Matteo Chiara, Sergio Chozas, Fedor Čiampor, Angelica Crottini, Corinne Cruaud, Fernando Cruz, Love Dalen, Alessio De Biase, Javier del Campo, Teo Delic, Alice B. Dennis, Martijn F. L. Derks, Maria Angela Diroma, Mihajla Djan, Simone Duprat, Klara Eleftheriadi, Philine G. D. Feulner, Jean-François Flot, Giobbe Forni, Bruno Fosso, Pascal Fournier, Christine Fournier-Chambrillon, Toni Gabaldon, Shilpa Garg, Carmela Gissi, Luca Giupponi, Jessica Gomez-Garrido, Josefa González, Miguel L. Grilo, Björn Grüning, Thomas Guerin, Nadege Guiglielmoni, Marta Gut, Marcel P. Haesler, Christoph Hahn, Balint Halpern, Peter W. Harrison, Julia Heintz, Maris Hindrikson, Jacob Höglund, Kerstin Howe, Graham M. Hughes, Benjamin Istace, Mark J. Cock, Franc Janžekovič, Zophonias O. Jonsson, Sagane Joye-Dind, Janne J. Koskimäki, Boris Krystufek, Justyna Kubacka, Heiner Kuhl, Szilvia Kusza, Karine Labadie, Meri Lähteenaro, Henrik Lantz, Anton Lavrinienko, Lucas Leclère, Ricardo Jorge Lopes, Ole Madsen, Ghislaine Magdelenat, Giulia Magoga, Tereza Manousaki, Tapio Mappes, Joao Pedro Marques, Gemma I. Martinez Redondo, Florian Maumus, Shane A. McCarthy, Hendrik-Jan Megens, Jose Melo-Ferreira, Sofia L. Mendes, Matteo Montagna, Joao Moreno, Mai-Britt Mosbech, Mónica Moura, Zuzana Musilova, Eugene Myers, Will J. Nash, Alexander Nater, Pamela Nicholson, Manuel Niell, Reindert Nijland, Benjamin Noel, Karin Noren, Pedro H. Oliveira, Remi-Andre Olsen, Lino Ometto, Rebekah A. Oomen, Stephan Ossowski, Vaidas Palinauskas, Snaebjorn Palsson, Jerome P. Panibe, Joana Pauperio, Martina Pavlek, Emilie Payen, Julia Pawlowska, Jaume Pellicer, Graziano Pesole, Joao Pimenta, Martin Pippel, Anna Maria Pirttilä, Nikos Poulakakis, Jeena Rajan, Rúben M.C. Rego, Roberto Resendes, Philipp Resl, Ana Riesgo, Patrik Rodin-Morch, Andre E. R. Soares, Carlos Rodriguez Fernandes, Maria M. Romeiras, Guilherme Roxo, Lukas Rüber, Maria Jose Ruiz-Lopez, Urmas Saarma, Luis P. da Silva, Manuela Sim-Sim, Lucile Soler, Vitor C. Sousa, Carla Sousa Santos, Alberto Spada, Milomir Stefanovic, Viktor Steger, Josefin Stiller, Matthias Stöck, Torsten H. Struck, Hiranya Sudasinghe, Riikka Tapanainen, Christian Tellgren-Roth, Helena Trindade, Yevhen Tukalenko, Ilenia Urso, Benoit Vacherie, Steven M. Van Belleghem, Kees Van Oers, Carlos Vargas-Chavez, Nevena Velickovic, Noel Vella, Adriana Vella, Cristiano Vernesi, Sara Vicente, Sara Villa, Olga Vinnere Pettersson, Filip A. M. Volckaert, Judit Voros, Patrick Wincker, Sylke Winkler, Claudio Ciofi, Robert M. Waterhouse, and Camila J. Mazzoni
Subjects: General. Including nature conservation, geographical distribution, QH1-199.5
Abstract: Abstract A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.
Published: 2024
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3. A chromosomal reference genome sequence for the malaria mosquito, Anopheles marshallii, Theobald, 1903 [version 1; peer review: 2 approved]

Author: Ying Sims, Marcela Uliano-Silva, Diego Ayala, Jonathan M. D. Wood, Ksenia Krasheninnikova, Mara K. N. Lawniczak, Haynes Heaton, Martin G. Wagah, Alan Tracey, Harriet F Johnson, Sarah E. Pelan, Joanna C. Collins, Katharina von Wyschetzki, James W. Torrance, Alex Makunin, Damon-Lee B. Pointon, Daniel E. Neafsey, Shane A. McCarthy, Boris K. Makanga, Lemonde B. A. Bouafou, and Nil Rahola
Subjects: Anopheles marshallii, African malaria mosquito, genome sequence, chromosomal, eng, Medicine, Science
Abstract: We present a genome assembly from an individual female Anopheles marshallii (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae) from Lopé, Gabon. The genome sequence is 225.7 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.
Published: 2024
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4. Chromosomal reference genome sequences for the malaria mosquito, Anopheles coustani, Laveran, 1900 [version 1; peer review: 2 approved]

Author: Shane A. McCarthy, Damon-Lee B. Pointon, Jonathan M.D. Wood, Ying Sims, James W. Torrance, Mara K N Lawniczak, Marcela Uliano-Silva, Martin G. Wagah, Diego Ayala, Harriet F. Johnson, Ksenia Krasheninnikova, Haynes Heaton, Alan Tracey, Katharina von Wyschetzki, Alex Makunin, Daniel E. Neafsey, Boris K. Makanga, Lemonde B. A. Bouafou, Joanna C. Collins, Sarah E. Pelan, and Nil Rahola
Subjects: Anopheles coustani, African malaria mosquito, genome sequence, chromosomal, eng, Medicine, Science
Abstract: We present genome assembly from individual female An. coustani (African malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae) from Lopé, Gabon. The genome sequence is 270 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled for both species. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.
Published: 2024
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5. A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data.

Author: Petr Danecek, Shane A McCarthy, HipSci Consortium, and Richard Durbin
Subjects: Medicine, Science
Abstract: Genomic screening for chromosomal abnormalities is an important part of quality control when establishing and maintaining stem cell lines. We present a new method for sensitive detection of copy number alterations, aneuploidy, and contamination in cell lines using genome-wide SNP genotyping data. In contrast to other methods designed for identifying copy number variations in a single sample or in a sample composed of a mixture of normal and tumor cells, this new method is tailored for determining differences between cell lines and the starting material from which they were derived, which allows us to distinguish between normal and novel copy number variation. We implemented the method in the freely available BCFtools package and present results based on induced pluripotent stem cell lines obtained in the HipSci project.
Published: 2016
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6. Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author: Ann M. Mc Cartney, Giulio Formenti, Alice Mouton, Diego De Panis, Luísa S. Marins, Henrique G. Leitão, Genevieve Diedericks, Joseph Kirangwa, Marco Morselli, Judit Salces-Ortiz, Nuria Escudero, Alessio Iannucci, Chiara Natali, Hannes Svardal, Rosa Fernández, Tim De Pooter, Geert Joris, Mojca Strazisar, Jonathan M. D. Wood, Katie E. Herron, Ole Seehausen, Phillip C. Watts, Felix Shaw, Robert P. Davey, Alice Minotto, José M. Fernández, Astrid Böhne, Carla Alegria, Tyler Alioto, Paulo C. Alves, Isabel R. Amorim, Jean-Marc Aury, Niclas Backstrom, Petr Baldrian, Laima Baltrunaite, Endre Barta, Bertrand BedHom, Caroline Belser, Johannes Bergsten, Laurie Bertrand, Helena Bilandija, Mahesh Binzer-Panchal, Iliana Bista, Mark Blaxter, Paulo A. V. Borges, Guilherme Borges Dias, Mirte Bosse, Tom Brown, Rémy Bruggmann, Elena Buena-Atienza, Josephine Burgin, Elena Buzan, Alessia Cariani, Nicolas Casadei, Matteo Chiara, Sergio Chozas, Fedor Čiampor, Angelica Crottini, Corinne Cruaud, Fernando Cruz, Love Dalen, Alessio De Biase, Javier del Campo, Teo Delic, Alice B. Dennis, Martijn F. L. Derks, Maria Angela Diroma, Mihajla Djan, Simone Duprat, Klara Eleftheriadi, Philine G. D. Feulner, Jean-François Flot, Giobbe Forni, Bruno Fosso, Pascal Fournier, Christine Fournier-Chambrillon, Toni Gabaldon, Shilpa Garg, Carmela Gissi, Luca Giupponi, Jessica Gomez-Garrido, Josefa González, Miguel L. Grilo, Björn Grüning, Thomas Guerin, Nadege Guiglielmoni, Marta Gut, Marcel P. Haesler, Christoph Hahn, Balint Halpern, Peter W. Harrison, Julia Heintz, Maris Hindrikson, Jacob Höglund, Kerstin Howe, Graham M. Hughes, Benjamin Istace, Mark J. Cock, Franc Janžekovič, Zophonias O. Jonsson, Sagane Joye-Dind, Janne J. Koskimäki, Boris Krystufek, Justyna Kubacka, Heiner Kuhl, Szilvia Kusza, Karine Labadie, Meri Lähteenaro, Henrik Lantz, Anton Lavrinienko, Lucas Leclère, Ricardo Jorge Lopes, Ole Madsen, Ghislaine Magdelenat, Giulia Magoga, Tereza Manousaki, Tapio Mappes, Joao Pedro Marques, Gemma I. Martinez Redondo, Florian Maumus, Shane A. McCarthy, Hendrik-Jan Megens, Jose Melo-Ferreira, Sofia L. Mendes, Matteo Montagna, Joao Moreno, Mai-Britt Mosbech, Mónica Moura, Zuzana Musilova, Eugene Myers, Will J. Nash, Alexander Nater, Pamela Nicholson, Manuel Niell, Reindert Nijland, Benjamin Noel, Karin Noren, Pedro H. Oliveira, Remi-Andre Olsen, Lino Ometto, Rebekah A. Oomen, Stephan Ossowski, Vaidas Palinauskas, Snaebjorn Palsson, Jerome P. Panibe, Joana Pauperio, Martina Pavlek, Emilie Payen, Julia Pawlowska, Jaume Pellicer, Graziano Pesole, Joao Pimenta, Martin Pippel, Anna Maria Pirttilä, Nikos Poulakakis, Jeena Rajan, Rúben M.C. Rego, Roberto Resendes, Philipp Resl, Ana Riesgo, Patrik Rodin-Morch, Andre E. R. Soares, Carlos Rodriguez Fernandes, Maria M. Romeiras, Guilherme Roxo, Lukas Rüber, Maria Jose Ruiz-Lopez, Urmas Saarma, Luis P. da Silva, Manuela Sim-Sim, Lucile Soler, Vitor C. Sousa, Carla Sousa Santos, Alberto Spada, Milomir Stefanovic, Viktor Steger, Josefin Stiller, Matthias Stöck, Torsten H. Struck, Hiranya Sudasinghe, Riikka Tapanainen, Christian Tellgren-Roth, Helena Trindade, Yevhen Tukalenko, Ilenia Urso, Benoit Vacherie, Steven M. Van Belleghem, Kees Van Oers, Carlos Vargas-Chavez, Nevena Velickovic, Noel Vella, Adriana Vella, Cristiano Vernesi, Sara Vicente, Sara Villa, Olga Vinnere Pettersson, Filip A. M. Volckaert, Judit Voros, Patrick Wincker, Sylke Winkler, Claudio Ciofi, Robert M. Waterhouse, and Camila J. Mazzoni
Subjects: General. Including nature conservation, geographical distribution, QH1-199.5
Published: 2024
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7. A chromosomal reference genome sequence for the malaria mosquito, Anopheles gambiae, Giles, 1902, Ifakara strain [version 2; peer review: 2 approved]

Author: Ying Sims, Shane A. McCarthy, Damon-Lee B. Pointon, Jonathan MD Wood, James W. Torrance, Harriet Johnson, Ksenia Krasheninnikova, Haynes Heaton, Joanna Collins, Alan Tracey, Mara Lawniczak, Marcela Uliano Da Silva, Katharina von Wyschetzki, Alex Makunin, Daniel E. Neafsey, Mara K.N. Lawniczak, Tibebu Habtewold, Mgeni Mohamed Tambwe, Martin Wagah, Nikolai Windbichler, Sarah Moore, Sarah E. Pelan, and George Christophides
Subjects: Anopheles gambiae, African malaria mosquito, genome sequence, chromosomal, eng, Medicine, Science
Abstract: We present a genome assembly from an individual female Anopheles gambiae (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae), Ifakara strain. The genome sequence is 264 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.
Published: 2024
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8. MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

Author: Marcela Uliano-Silva, João Gabriel R. N. Ferreira, Ksenia Krasheninnikova, Darwin Tree of Life Consortium, Giulio Formenti, Linelle Abueg, James Torrance, Eugene W. Myers, Richard Durbin, Mark Blaxter, and Shane A. McCarthy
Subjects: MitoHiFi, Docker, Mitogenome, Heteroplasmy, Long reads, HiFi, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract: Abstract Background PacBio high fidelity (HiFi) sequencing reads are both long (15–20 kb) and highly accurate (> Q20). Because of these properties, they have revolutionised genome assembly leading to more accurate and contiguous genomes. In eukaryotes the mitochondrial genome is sequenced alongside the nuclear genome often at very high coverage. A dedicated tool for mitochondrial genome assembly using HiFi reads is still missing. Results MitoHiFi was developed within the Darwin Tree of Life Project to assemble mitochondrial genomes from the HiFi reads generated for target species. The input for MitoHiFi is either the raw reads or the assembled contigs, and the tool outputs a mitochondrial genome sequence fasta file along with annotation of protein and RNA genes. Variants arising from heteroplasmy are assembled independently, and nuclear insertions of mitochondrial sequences are identified and not used in organellar genome assembly. MitoHiFi has been used to assemble 374 mitochondrial genomes (368 Metazoa and 6 Fungi species) for the Darwin Tree of Life Project, the Vertebrate Genomes Project and the Aquatic Symbiosis Genome Project. Inspection of 60 mitochondrial genomes assembled with MitoHiFi for species that already have reference sequences in public databases showed the widespread presence of previously unreported repeats. Conclusions MitoHiFi is able to assemble mitochondrial genomes from a wide phylogenetic range of taxa from Pacbio HiFi data. MitoHiFi is written in python and is freely available on GitHub ( https://github.com/marcelauliano/MitoHiFi ). MitoHiFi is available with its dependencies as a Docker container on GitHub (ghcr.io/marcelauliano/mitohifi:master).
Published: 2023
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9. Genomics of cold adaptations in the Antarctic notothenioid fish radiation

Author: Iliana Bista, Jonathan M. D. Wood, Thomas Desvignes, Shane A. McCarthy, Michael Matschiner, Zemin Ning, Alan Tracey, James Torrance, Ying Sims, William Chow, Michelle Smith, Karen Oliver, Leanne Haggerty, Walter Salzburger, John H. Postlethwait, Kerstin Howe, Melody S. Clark, H. William Detrich, C.-H. Christina Cheng, Eric A. Miska, and Richard Durbin
Subjects: Science
Abstract: Abstract Numerous novel adaptations characterise the radiation of notothenioids, the dominant fish group in the freezing seas of the Southern Ocean. To improve understanding of the evolution of this iconic fish group, here we generate and analyse new genome assemblies for 24 species covering all major subgroups of the radiation, including five long-read assemblies. We present a new estimate for the onset of the radiation at 10.7 million years ago, based on a time-calibrated phylogeny derived from genome-wide sequence data. We identify a two-fold variation in genome size, driven by expansion of multiple transposable element families, and use the long-read data to reconstruct two evolutionarily important, highly repetitive gene family loci. First, we present the most complete reconstruction to date of the antifreeze glycoprotein gene family, whose emergence enabled survival in sub-zero temperatures, showing the expansion of the antifreeze gene locus from the ancestral to the derived state. Second, we trace the loss of haemoglobin genes in icefishes, the only vertebrates lacking functional haemoglobins, through complete reconstruction of the two haemoglobin gene clusters across notothenioid families. Both the haemoglobin and antifreeze genomic loci are characterised by multiple transposon expansions that may have driven the evolutionary history of these genes.
Published: 2023
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10. A chromosomal reference genome sequence for the malaria mosquito, Anopheles moucheti, Evans, 1925 [version 1; peer review: 2 approved]

Author: Shane A. McCarthy, Damon-Lee B. Pointon, Ying Sims, James W. Torrance, Jean-Pierre Agbor, Sandrine N. Nsango, Martin G. Wagah, Diego Ayala, Harriet F. Johnson, Jonathan M. D. Wood, Joanna C. Collins, Ksenia Krasheninnikova, Haynes Heaton, Alan Tracey, Marcela Uliano Da Silva, Katharina von Wyschetzki, Alex Makunin, Daniel E. Neafsey, Mara Lawniczak, and Sarah E. Pelan
Subjects: Anopheles moucheti, African malaria mosquito, genome sequence, chromosomal, eng, Medicine, Science
Abstract: We present a genome assembly from an individual male Anopheles moucheti (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae), from a wild population in Cameroon. The genome sequence is 271 megabases in span. The majority of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.5 kilobases in length.
Published: 2023
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11. A chromosomal reference genome sequence for the malaria mosquito, Anopheles gambiae, Giles, 1902, Ifakara strain [version 1; peer review: 2 approved]

Author: Ying Sims, Shane A. McCarthy, Damon-Lee B. Pointon, Jonathan MD Wood, James W. Torrance, Harriet Johnson, Ksenia Krasheninnikova, Haynes Heaton, Joanna Collins, Alan Tracey, Marcela Uliano Da Silva, Katharina von Wyschetzki, Alex Makunin, Daniel E. Neafsey, Mara Lawniczak, Tibebu Habtewold, Mgeni Mohamed Tambwe, Martin Wagah, Nikolai Windbichler, Sarah Moore, Sarah E. Pelan, and George Christophides
Subjects: Anopheles gambiae, African malaria mosquito, genome sequence, chromosomal, eng, Medicine, Science
Abstract: We present a genome assembly from an individual female Anopheles gambiae (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae), Ifakara strain. The genome sequence is 264 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.
Published: 2023
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12. The genome sequence of the European turtle dove, Streptopelia turtur Linnaeus 1758 [version 1; peer review: 2 approved]

Author: Jenny C. Dunn, Michael A. Quail, James Torrance, Ying Sims, Marcela Uliano-Silva, Richard Challis, Antony J. Morris, Keith C. Hamer, Sarah Pelan, William Chow, Philip V. Grice, Mark Blaxter, Daniel Mead, Craig Corton, Michelle Smith, Jason Skelton, Karen Oliver, Emma Betteridge, Shane A. McCarthy, Jonathan Threlfall, Jale Dolucan, and Kerstin Howe
Subjects: Streptopelia turtur, European turtle dove, genome sequence, chromosomal, eng, Medicine, Science
Abstract: We present a genome assembly from an individual female Streptopelia turtur (the European turtle dove; Chordata; Aves; Columbidae). The genome sequence is 1.18 gigabases in span. The majority of the assembly is scaffolded into 35 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled.
Published: 2021
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13. Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians

Author: Vladimir Ovchinnikov, Marcela Uliano-Silva, Mark Wilkinson, Jonathan Wood, Michelle Smith, Karen Oliver, Ying Sims, James Torrance, Alexander Suh, Shane A McCarthy, Richard Durbin, Mary J O’Connell, Uliano-Silva, Marcela [0000-0001-6723-4715], McCarthy, Shane A [0000-0002-2715-4187], Durbin, Richard [0000-0002-9130-1006], O'Connell, Mary J [0000-0002-1877-1001], and Apollo - University of Cambridge Repository
Subjects: Genome, Acclimatization, Biochemistry and Molecular Biology, limblessness, Snakes, amphibia, Amphibians, Evolution, Molecular, Mice, Genetics, Gymnophiona, Animals, Hedgehog Proteins, vertebrate comparative genomics, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Biokemi och molekylärbiologi
Abstract: We present genome sequences for the caeciliansGeotrypetes seraphini(3.8Gb) andMicrocaecilia unicolor(4.7Gb), representatives of a limbless, mostly soil-dwelling amphibian clade with reduced eyes, and unique putatively chemosensory tentacles. More than 69% of both genomes are composed of repeats, with retrotransposons the most abundant. We identify 1,150 orthogroups which are unique to caecilians and enriched for functions in olfaction and detection of chemical signals. There are 379 orthogroups with signatures of positive selection on caecilian lineages with roles in organ development and morphogenesis, sensory perception and immunity amongst others. We discover that caecilian genomes are missing the ZRS enhancer of Sonic Hedgehog which is also mutated in snakes.In vivodeletions have shown ZRS is required for limb development in mice, thus revealing a shared molecular target implicated in the independent evolution of limblessness in snakes and caecilians.
Published: 2023

14. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Author: S. Cotton, M.P. McHugh, R. Dewar, J.G. Haas, K. Templeton, Samuel C. Robson, Thomas R. Connor, Nicholas J. Loman, Tanya Golubchik, Rocio T. Martinez Nunez, David Bonsall, Andrew Rambaut, Luke B. Snell, Rich Livett, Catherine Ludden, Sally Corden, Eleni Nastouli, Gaia Nebbia, Ian Johnston, Jacqui A. Prieto, Kordo Saeed, David K. Jackson, Catherine Houlihan, Dan Frampton, William L. Hamilton, Adam A. Witney, Giselda Bucca, Cassie F. Pope, Catherine Moore, Emma C. Thomson, Teresa Cutino-Moguel, Ewan M. Harrison, Colin P. Smith, Fiona Rogan, Shaun M. Beckwith, Abigail Murray, Dawn Singleton, Kirstine Eastick, Liz A. Sheridan, Paul Randell, Leigh M. Jackson, Cristina V. Ariani, Sónia Gonçalves, Derek J. Fairley, Matthew W. Loose, Joanne Watkins, Samuel Moses, Sam Nicholls, Matthew Bull, Roberto Amato, Darren L. Smith, David M. Aanensen, Jeffrey C. Barrett, Beatrix Kele, Dinesh Aggarwal, James G. Shepherd, Martin D. Curran, Surendra Parmar, Matthew D. Parker, Catryn Williams, Sharon Glaysher, Anthony P. Underwood, Matthew Bashton, Nicole Pacchiarini, Katie F. Loveson, Matthew Byott, Alessandro M. Carabelli, Kate E. Templeton, Sharon J. Peacock, Thushan I. de Silva, Dennis Wang, Cordelia F. Langford, John Sillitoe, Rory N. Gunson, Simon Cottrell, Justin O’Grady, Dominic Kwiatkowski, Patrick J. Lillie, Nicholas Cortes, Nathan Moore, Claire Thomas, Phillipa J. Burns, Tabitha W. Mahungu, Steven Liggett, Angela H. Beckett, Matthew TG. Holden, Lisa J. Levett, Husam Osman, Mohammed O. Hassan-Ibrahim, David A. Simpson, Meera Chand, Ravi K. Gupta, Alistair C. Darby, Steve Paterson, Oliver G. Pybus, Erik M. Volz, Daniela de Angelis, David L. Robertson, Andrew J. Page, Inigo Martincorena, Louise Aigrain, Andrew R. Bassett, Nick Wong, Yusri Taha, Michelle J. Erkiert, Michael H. Spencer Chapman, Rebecca Dewar, Martin P. McHugh, Siddharth Mookerjee, Stephen Aplin, Matthew Harvey, Thea Sass, Helen Umpleby, Helen Wheeler, James P. McKenna, Ben Warne, Joshua F. Taylor, Yasmin Chaudhry, Rhys Izuagbe, Aminu S. Jahun, Gregory R. Young, Claire McMurray, Clare M. McCann, Andrew Nelson, Scott Elliott, Hannah Lowe, Anna Price, Matthew R. Crown, Sara Rey, Sunando Roy, Ben Temperton, Sharif Shaaban, Andrew R. Hesketh, Kenneth G. Laing, Irene M. Monahan, Judith Heaney, Emanuela Pelosi, Siona Silviera, Eleri Wilson-Davies, Helen Fryer, Helen Adams, Louis du Plessis, Rob Johnson, William T. Harvey, Joseph Hughes, Richard J. Orton, Lewis G. Spurgin, Yann Bourgeois, Chris Ruis, Áine O'Toole, Marina Gourtovaia, Theo Sanderson, Christophe Fraser, Jonathan Edgeworth, Judith Breuer, Stephen L. Michell, John A. Todd, Michaela John, David Buck, Kavitha Gajee, Gemma L. Kay, David Heyburn, Themoula Charalampous, Adela Alcolea-Medina, Katie Kitchman, Alan McNal, David T. Pritch, Samir Dervisevic, Peter Muir, Esther Robinson, Barry B. Vipond, Newara A. Ramadan, Christopher Jeanes, Danni Weldon, Jana Catalan, Neil Jones, Ana da Silva Filipe, Chris Williams, Marc Fuchs, Julia Miskelly, Aaron R. Jeffries, Karen Oliver, Naomi R. Park, Amy Ash, Cherian Koshy, Magdalena Barrow, Sarah L. Buchan, Anna Mantzouratou, Gemma Clark, Christopher W. Holmes, Sharon Campbell, Thomas Davis, Ngee Keong Tan, Julianne R. Brown, Kathryn A. Harris, Stephen P. Kidd, Paul R. Grant, Li Xu-McCrae, Alison Cox, Pinglawathee Madona, Marcus Pond, Paul A. Randell, Karen T. Withell, Cheryl Williams, Clive Graham, Rebecca Denton-Smith, Emma Swindells, Robyn Turnbull, Tim J. Sloan, Andrew Bosworth, Stephanie Hutchings, Hannah M. Pymont, Anna Casey, Liz Ratcliffe, Christopher R. Jones, Bridget A. Knight, Tanzina Haque, Jennifer Hart, Dianne Irish-Tavares, Eric Witele, Craig Mower, Louisa K. Watson DipHE, Jennifer Collins, Gary Eltringham, Dorian Crudgington, Ben Macklin, Miren Iturriza-Gomara, Anita O. Lucaci, Patrick C. McClure, Matthew Carlile, Nadine Holmes, Christopher Moore, Nathaniel Storey, Stefan Rooke, Gonzalo Yebra, Noel Craine, Malorie Perry, Nabil-Fareed Alikhan, Stephen Bridgett, Kate F. Cook, Christopher Fearn, Salman Goudarzi, Ronan A. Lyons, Thomas Williams, Sam T. Haldenby, Jillian Durham, Steven Leonard, Robert M. Davies, Rahul Batra, Beth Blane, Moira J. Spyer, Perminder Smith, Mehmet Yavus, Rachel J. Williams, Adhyana IK. Mahanama, Buddhini Samaraweera, Sophia T. Girgis, Samantha E. Hansford, Angie Green, Charlotte Beaver, Katherine L. Bellis, Matthew J. Dorman, Sally Kay, Liam Prestwood, Shavanthi Rajatileka, Joshua Quick, Radoslaw Poplawski, Nicola Reynolds, Andrew Mack, Arthur Morriss, Thomas Whalley, Bindi Patel, Iliana Georgana, Myra Hosmillo, Malte L. Pinckert, Joanne Stockton, John H. Henderson, Amy Hollis, William Stanley, Wen C. Yew, Richard Myers, Alicia Thornton, Alexander Adams, Tara Annett, Hibo Asad, Alec Birchley, Jason Coombes, Johnathan M. Evans, Laia Fina, Bree Gatica-Wilcox, Lauren Gilbert, Lee Graham, Jessica Hey, Ember Hilvers, Sophie Jones, Hannah Jones, Sara Kumziene-Summerhayes, Caoimhe McKerr, Jessica Powell, Georgia Pugh, Sarah Taylor, Alexander J. Trotter, Charlotte A. Williams, Leanne M. Kermack, Benjamin H. Foulkes, Marta Gallis, Hailey R. Hornsby, Stavroula F. Louka, Manoj Pohare, Paige Wolverson, Peijun Zhang, George MacIntyre-Cockett, Amy Trebes, Robin J. Moll, Lynne Ferguson, Emily J. Goldstein, Alasdair Maclean, Rachael Tomb, Igor Starinskij, Laura Thomson, Joel Southgate, Moritz UG. Kraemer, Jayna Raghwani, Alex E. Zarebski, Olivia Boyd, Lily Geidelberg, Chris J. Illingworth, Chris Jackson, David Pascall, Sreenu Vattipally, Timothy M. Freeman, Sharon N. Hsu, Benjamin B. Lindsey, Keith James, Kevin Lewis, Gerry Tonkin-Hill, Jaime M. Tovar-Corona, MacGregor Cox, Khalil Abudahab, Mirko Menegazzo, Ben EW. Taylor, Corin A. Yeats, Afrida Mukaddas, Derek W. Wright, Leonardo de Oliveira Martins, Rachel Colquhoun, Verity Hill, Ben Jackson, J.T. McCrone, Nathan Medd, Emily Scher, Jon-Paul Keatley, Tanya Curran, Sian Morgan, Patrick Maxwell, Ken Smith, Sahar Eldirdiri, Anita Kenyon, Alison H. Holmes, James R. Price, Tim Wyatt, Alison E. Mather, Timofey Skvortsov, John A. Hartley, Martyn Guest, Christine Kitchen, Ian Merrick, Robert Munn, Beatrice Bertolusso, Jessica Lynch, Gabrielle Vernet, Stuart Kirk, Elizabeth Wastnedge, Rachael Stanley, Giles Idle, Declan T. Bradley, Nicholas F. Killough, Jennifer Poyner, Matilde Mori, Owen Jones, Victoria Wright, Ellena Brooks, Carol M. Churcher, Laia Delgado Callico, Mireille Fragakis, Katerina Galai, Andrew Jermy, Sarah Judges, Anna Markov, Georgina M. McManus, Kim S. Smith, Peter MD. Thomas-McEwen, Elaine Westwick, Stephen W. Attwood, Frances Bolt, Alisha Davies, Elen De Lacy, Fatima Downing, Sue Edwards, Lizzie Meadows, Sarah Jeremiah, Nikki Smith, Luke Foulser, Amita Patel, Louise Berry, Tim Boswell, Vicki M. Fleming, Hannah C. Howson-Wells, Amelia Joseph, Manjinder Khakh, Michelle M. Lister, Paul W. Bird, Karlie Fallon, Thomas Helmer, Claire L. McMurray, Mina Odedra, Jessica Shaw, Julian W. Tang, Nicholas J. Willford, Victoria Blakey, Veena Raviprakash, Nicola Sheriff, Lesley-Anne Williams, Theresa Feltwell, Luke Bedford, James S. Cargill, Warwick Hughes, Jonathan Moore, Susanne Stonehouse, Laura Atkinson, Jack CD. Lee, Divya Shah, Natasha Ohemeng-Kumi, John Ramble, Jasveen Sehmi, Rebecca Williams, Wendy Chatterton, Monika Pusok, William Everson, Anibolina Castigador, Emily Macnaughton, Kate El Bouzidi, Temi Lampejo, Malur Sudhanva, Cassie Breen, Graciela Sluga, Shazaad SY. Ahmad, Ryan P. George, Nicholas W. Machin, Debbie Binns, Victoria James, Rachel Blacow, Lindsay Coupland, Louise Smith, Edward Barton, Debra Padgett, Garren Scott, Aidan Cross, Mariyam Mirfenderesky, Jane Greenaway, Kevin Cole, Phillip Clarke, Nichola Duckworth, Sarah Walsh, Kelly Bicknell, Robert Impey, Sarah Wyllie, Richard Hopes, Chloe Bishop, Vicki Chalker, Ian Harrison, Laura Gifford, Zoltan Molnar, Cressida Auckland, Cariad Evans, Kate Johnson, David G. Partridge, Mohammad Raza, Paul Baker, Stephen Bonner, Sarah Essex, Leanne J. Murray, Andrew I. Lawton, Shirelle Burton-Fanning, Brendan AI. Payne, Sheila Waugh, Andrea N. Gomes, Maimuna Kimuli, Darren R. Murray, Paula Ashfield, Donald Dobie, Fiona Ashford, Angus Best, Liam Crawford, Nicola Cumley, Megan Mayhew, Oliver Megram, Jeremy Mirza, Emma Moles-Garcia, Benita Percival, Megan Driscoll, Leah Ensell, Helen L. Lowe, Laurentiu Maftei, Matteo Mondani, Nicola J. Chaloner, Benjamin J. Cogger, Lisa J. Easton, Hannah Huckson, Jonathan Lewis, Sarah Lowdon, Cassandra S. Malone, Florence Munemo, Manasa Mutingwende, Roberto Nicodemi, Olga Podplomyk FD, Thomas Somassa, Andrew Beggs, Alex Richter, Claire Cormie, Joana Dias, Sally Forrest, Ellen E. Higginson, Mailis Maes, Jamie Young, Rose K. Davidson, Kathryn A. Jackson, Alexander J. Keeley, Jonathan Ball, Timothy Byaruhanga, Joseph G. Chappell, Jayasree Dey, Jack D. Hill, Emily J. Park, Arezou Fanaie, Rachel A. Hilson, Geraldine Yaze, Stephanie Lo, Safiah Afifi, Robert Beer, Joshua Maksimovic, Kathryn McCluggage, Karla Spellman, Catherine Bresner, William Fuller, Angela Marchbank, Trudy Workma, Ekaterina Shelest, Johnny Debebe, Fei Sang, Sarah Francois, Bernardo Gutierrez, Tetyana I. Vasylyeva, Flavia Flaviani, Manon Ragonnet-Cronin, Katherine L. Smollett, Alice Broos, Daniel Mair, Jenna Nichols, Kyriaki Nomikou, Lily Tong, Ioulia Tsatsani, Sarah O'Brien, Steven Rushton, Roy Sanderson, Jon Perkins, Seb Cotton, Abbie Gallagher, Elias Allara, Clare Pearson, David Bibby, Gavin Dabrer, Nicholas Ellaby, Eileen Gallagher, Jonathan Hubb, Angie Lackenby, David Lee, Nikos Manesis, Tamyo Mbisa, Steven Platt, Katherine A. Twohig, Mari Morgan, Alp Aydin, David J. Baker, Ebenezer Foster-Nyarko, Sophie J. Prosolek, Steven Rudder, Chris Baxter, Sílvia F. Carvalho, Deborah Lavin, Arun Mariappan, Clara Radulescu, Aditi Singh, Miao Tang, Helen Morcrette, Nadua Bayzid, Marius Cotic, Carlos E. Balcazar, Michael D. Gallagher, Daniel Maloney, Thomas D. Stanton, Kathleen A. Williamson, Robin Manley, Michelle L. Michelsen, Christine M. Sambles, David J. Studholme, Joanna Warwick-Dugdale, Richard Eccles, Matthew Gemmell, Richard Gregory, Margaret Hughes, Charlotte Nelson, Lucille Rainbow, Edith E. Vamos, Hermione J. Webster, Mark Whitehead, Claudia Wierzbicki, Adrienn Angyal, Luke R. Green, Max Whiteley, Emma Betteridge, Iraad F. Bronner, Ben W. Farr, Scott Goodwin, Stefanie V. Lensing, Shane A. McCarthy, Michael A. Quail, Diana Rajan, Nicholas M. Redshaw, Carol Scott, Lesley Shirley, Scott AJ. Thurston, Will Rowe, Amy Gaskin, Thanh Le-Viet, James Bonfield, Jennifier Liddle, Andrew Whitwham, University of St Andrews. School of Medicine, University of St Andrews. Infection and Global Health Division, and Apollo - University of Cambridge Repository
Subjects: Microbiology (medical), MCC, Introduction, SARS-CoV-2, NDAS, COVID-19, Care homes, General Medicine, NIS, Patient Discharge, Hospitals, Hospitalization, Infectious Diseases, SDG 3 - Good Health and Well-being, RA0421, RA0421 Public health. Hygiene. Preventive Medicine, Humans, Hospital discharge
Abstract: COG-UK is supported by funding from the MRC part of UK Research & Innovation, the National Institute of Health Research (Grant code MC_PC_19027), and Genome Research Limited, operating as the Welcome Sanger Institute. Background The first epidemic wave of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over one-third of care homes reported an outbreak, while there was limited testing of hospital patients discharged to care homes. Aim To investigate patients discharged from hospitals as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave. Methods A clinical review was performed for all patients discharges from hospitals to care homes from 1st March 2020 to 31st May 2020. Episodes were ruled out based on coronavirus disease 2019 (COVID-19) test history, clinical assessment at discharge, whole-genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis using Cluster Investigation and Virus Epidemiological Tool software. Patient timelines were obtained using electronic hospital records. Findings In total, 787 patients discharged from hospitals to care homes were identified. Of these, 776 (99%) were ruled out for subsequent introduction of SARS-CoV-2 into care homes. However, for 10 episodes, the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data were available. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission, leading to 10 positive cases in their care home. Conclusion The majority of patients discharged from hospitals were ruled out for introduction of SARS-CoV-2 into care homes, highlighting the importance of screening all new admissions when faced with a novel emerging virus and no available vaccine. Publisher PDF
Published: 2023

15. TheHypolimnas misippusgenome supports a common origin of the W chromosome in Lepidoptera

Author: Anna Orteu, Shane A. McCarthy, Emily A. Hornett, Mathew Gemmel, Louise A. Reynolds, Ian A. Warren, Ian J. Gordon, Gregory D. D. Hurst, Richard Durbin, Simon H. Martin, and Chris D. Jiggins
Abstract: Moths and butterflies (Lepidoptera) have a heterogametic sex chromosome system with females carrying ZW chromosomes and males ZZ. The lack of W chromosomes in early diverging lepidopteran lineages has led to the suggestion of an ancestral Z0 system in this clade and a B chromosome origin of the W. This contrasts with the canonical model of W chromosome evolution in which the W would have originated from the same homologous autosomal pair as the Z chromosome. Despite the distinct models proposed, the rapid evolution of the W chromosome has hindered the elucidation of its origin. Here, we present high-quality, chromosome-level genome assemblies of twoHypolimnasspecies (Hypolimnas bolinaandHypolimnas misippus)and use theH. misippusassembly to explore the evolution of W chromosomes in butterflies and moths. We show that inH. misippusthe W chromosome has higher similarity to the Z chromosome than any other chromosome, which could suggest a possible origin from the same homologous autosome pair as the Z chromosome. However, using genome assemblies of closely related species (ditrysian lineages) containing assembled W chromosomes, we present contrasting evidence suggesting that the W chromosome might have evolved from a B chromosome instead. Crucially, by using a synteny analysis to infer homology, we show that W chromosomes are likely to share a common evolutionary origin in Lepidoptera. This study highlights the difficulty of studying the evolution of W chromosomes and contributes to better understanding its evolutionary origins.SignificanceButterflies and moths have a sex determination system in which females carry two different sex chromosomes, Z and W, while males carry two copies of the Z. The evolutionary origin of the W chromosome has been elusive, with many possible scenarios being suggested, such as the independent evolution of W chromosomes in many butterfly and moth species. Here, we present genome assemblies of twoHypolimnasbutterfly species and use one of them to shed light on the evolution of the W chromosome. We show that W chromosomes across butterflies and moths are very similar which suggests a shared common origin.
Published: 2023

16. Casirivimab and Imdevimab Treatment Reduces Viral Load and Improves Clinical Outcomes in Seropositive Hospitalized COVID-19 Patients with Nonneutralizing or Borderline Neutralizing Antibodies

Author: Andrea T. Hooper, Selin Somersan-Karakaya, Shane E. McCarthy, Eleftherios Mylonakis, Shazia Ali, Jingning Mei, Rafia Bhore, Adnan Mahmood, Gregory P. Geba, Paula Dakin, David M. Weinreich, George D. Yancopoulos, Gary A. Herman, and Jennifer D. Hamilton
Subjects: Virology, Microbiology
Abstract: The clinical benefit of CAS+IMD in hospitalized seronegative patients with COVID-19 has previously been demonstrated, although these studies observed no clinical benefit in seropositive patients. As the prevalence of SARS-CoV-2-seropositive individuals rises due to both vaccination and previous infection, it is important to understand whether there is a subset of hospitalized patients with COVID-19 with antibodies against SARS-CoV-2 who could benefit from anti-SARS-CoV-2 monoclonal antibody treatment.
Published: 2022

17. Towards complete and error-free genome assemblies of all vertebrate species

Author: Richard Hall, Tandy Warnow, Tanya M. Lama, Oliver A. Ryder, David Haussler, Matthew T. Biegler, Klaus-Peter Koepfli, Ivo Gut, Paul Flicek, Mark Chaisson, James Torrance, Guojie Zhang, Andrew J. Crawford, Federica Di Palma, Michael Hiller, Jennifer A. Marshall Graves, Sadye Paez, Sarah E. London, Mark Wilkinson, Kateryna D. Makova, Byung June Ko, Jimin George, Farooq O. Al-Ajli, Emma C. Teeling, George F. Turner, Robert H. S. Kraus, Sonja C. Vernes, Zev N. Kronenberg, Michelle Smith, Jonas Korlach, Daryl Eason, Jonathan Wood, Simona Secomandi, Claudio V. Mello, Arkarachai Fungtammasan, Arang Rhie, Tomas Marques-Bonet, Benedict Paten, Ekaterina Osipova, Richard Durbin, M. Thomas P. Gilbert, Beth Shapiro, Ivan Sović, Bruce C. Robertson, Richard E. Green, Eugene W. Myers, Leanne Haggerty, Sergey Koren, Martin Pippel, Bettina Haase, Patrick Masterson, Jay Ghurye, Maria Simbirsky, Samantha R. Friedrich, Chul Hee Lee, Luis R Nassar, Lindsey J. Cantin, Kerstin Howe, Erich D. Jarvis, Marlys L. Houck, Jason T. Howard, Jacquelyn Mountcastle, Mark Mooney, Paolo Franchini, Giulio Formenti, Siddarth Selvaraj, Robel E. Dagnew, Brett T. Hannigan, Brian P. Walenz, Alan Tracey, Heebal Kim, Constantina Theofanopoulou, Nicholas H. Putnam, Karen Clark, Iliana Bista, H. William Detrich, Dengfeng Guan, David Iorns, Andrew Digby, Trevor Pesout, Zemin Ning, Gregory Gedman, Woori Kwak, Maximilian Wagner, Joanna Collins, Harris A. Lewin, Hannes Svardal, Milan Malinsky, Byrappa Venkatesh, Françoise Thibaud-Nissen, Joana Damas, Andreas F. Kautt, Olivier Fedrigo, Christopher Dunn, William Chow, Warren E. Johnson, Yang Zhou, Adam M. Phillippy, Taylor Edwards, Paul Medvedev, Peter V. Lovell, Joyce V. Lee, Sylke Winkler, Stephen J. O'Brien, Wesley C. Warren, Alex Hastie, Marcela Uliano-Silva, Kevin L. Howe, Sarah B. Kingan, Fergal J. Martin, Christopher N. Balakrishnan, David F. Clayton, Ying Sims, Robert W. Murphy, Axel Meyer, Dave W Burt, Shane A. McCarthy, Sarah Pelan, Erik Garrison, Mark Diekhans, Frank Grützner, Gavin J. P. Naylor, Robert S. Harris, Hiram Clawson, Jinna Hoffman, Ann C Misuraca, J. H. Kim, University of St Andrews. School of Biology, University of St Andrews. St Andrews Bioinformatics Unit, Rhie, Arang [0000-0002-9809-8127], Fedrigo, Olivier [0000-0002-6450-7551], Formenti, Giulio [0000-0002-7554-5991], Koren, Sergey [0000-0002-1472-8962], Uliano-Silva, Marcela [0000-0001-6723-4715], Thibaud-Nissen, Francoise [0000-0003-4957-7807], Mountcastle, Jacquelyn [0000-0003-1078-4905], Winkler, Sylke [0000-0002-0915-3316], Vernes, Sonja C. [0000-0003-0305-4584], Grutzner, Frank [0000-0002-3088-7314], Balakrishnan, Christopher N. [0000-0002-0788-0659], Burt, Dave [0000-0002-9991-1028], George, Julia M. [0000-0001-6194-6914], Digby, Andrew [0000-0002-1870-8811], Robertson, Bruce [0000-0002-5348-2731], Edwards, Taylor [0000-0002-7235-6175], Meyer, Axel [0000-0002-0888-8193], Kautt, Andreas F. [0000-0001-7792-0735], Franchini, Paolo [0000-0002-8184-1463], Detrich, H. William, III [0000-0002-0783-4505], Pippel, Martin [0000-0002-8134-5929], Malinsky, Milan [0000-0002-1462-6317], Kingan, Sarah B. [0000-0002-4900-0189], Hall, Richard [0000-0001-6490-8227], Dunn, Christopher [0000-0002-0601-3254], Lee, Joyce [0000-0002-3492-1102], Putnam, Nicholas H. [0000-0002-1315-782X], Gut, Ivo [0000-0001-7219-632X], Tracey, Alan [0000-0002-4805-9058], Guan, Dengfeng [0000-0002-6376-3940], London, Sarah E. [0000-0002-7839-2644], Clayton, David F. [0000-0002-6395-3488], Mello, Claudio V. [0000-0002-9826-8421], Friedrich, Samantha R. [0000-0003-0570-6080], Osipova, Ekaterina [0000-0002-6769-7223], Al-Ajli, Farooq O. [0000-0002-4692-7106], Secomandi, Simona [0000-0001-8597-6034], Kim, Heebal [0000-0003-3064-1303], Theofanopoulou, Constantina [0000-0003-2014-7563], Zhou, Yang [0000-0003-1247-5049], Martin, Fergal [0000-0002-1672-050X], Flicek, Paul [0000-0002-3897-7955], Walenz, Brian P. [0000-0001-8431-1428], Diekhans, Mark [0000-0002-0430-0989], Paten, Benedict [0000-0001-8863-3539], Crawford, Andrew J. [0000-0003-3153-6898], Gilbert, M. Thomas P. [0000-0002-5805-7195], Zhang, Guojie [0000-0001-6860-1521], Venkatesh, Byrappa [0000-0003-3620-0277], Shapiro, Beth [0000-0002-2733-7776], Johnson, Warren E. [0000-0002-5954-186X], Marques-Bonet, Tomas [0000-0002-5597-3075], Teeling, Emma C. [0000-0002-3309-1346], Ryder, Oliver A. [0000-0003-2427-763X], Haussler, David [0000-0003-1533-4575], Korlach, Jonas [0000-0003-3047-4250], Lewin, Harris A. [0000-0002-1043-7287], Howe, Kerstin [0000-0003-2237-513X], Myers, Eugene W. [0000-0002-6580-7839], Durbin, Richard [0000-0002-9130-1006], Phillippy, Adam M. [0000-0003-2983-8934], Jarvis, Erich D. [0000-0001-8931-5049], Apollo - University of Cambridge Repository, National Institutes of Health (US), National Human Genome Research Institute (US), Ministry of Health and Welfare (South Korea), Wellcome Trust, European Molecular Biology Laboratory, Howard Hughes Medical Institute, Rockefeller University, Robert and Rosabel Osborne Endowment, European Commission, National Library of Medicine (US), Korea Institute of Marine Science & Technology, Ministry of Oceans and Fisheries (South Korea), Alfred P. Sloan Foundation, Max Planck Society, Maine Department of Inland Fisheries & Wildlife, National Science Foundation (US), University of Queensland, Science Exchange, Northeastern University (US), Federal Ministry of Education and Research (Germany), EMBO, National Key Research and Development Program (China), Qatar Society of Al-Gannas (Algannas), Katara Cultural Village, Government of Qatar, Monash University Malaysia, Hessen State Ministry of Higher Education, Research and the Arts, Ministry of Science, Research and Art Baden-Württemberg, Agency for Science, Technology and Research A*STAR (Singapore), European Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Fundación 'la Caixa', Generalitat de Catalunya, Irish Research Council, Danish National Research Foundation, Australian Research Council, Vernes, Sonja C [0000-0003-0305-4584], Balakrishnan, Christopher N [0000-0002-0788-0659], George, Julia M [0000-0001-6194-6914], Kautt, Andreas F [0000-0001-7792-0735], Detrich, H William [0000-0002-0783-4505], Kingan, Sarah B [0000-0002-4900-0189], Putnam, Nicholas H [0000-0002-1315-782X], London, Sarah E [0000-0002-7839-2644], Clayton, David F [0000-0002-6395-3488], Mello, Claudio V [0000-0002-9826-8421], Friedrich, Samantha R [0000-0003-0570-6080], Al-Ajli, Farooq O [0000-0002-4692-7106], Walenz, Brian P [0000-0001-8431-1428], Crawford, Andrew J [0000-0003-3153-6898], Gilbert, M Thomas P [0000-0002-5805-7195], Johnson, Warren E [0000-0002-5954-186X], Teeling, Emma C [0000-0002-3309-1346], Ryder, Oliver A [0000-0003-2427-763X], Lewin, Harris A [0000-0002-1043-7287], Myers, Eugene W [0000-0002-6580-7839], Phillippy, Adam M [0000-0003-2983-8934], and Jarvis, Erich D [0000-0001-8931-5049]
Subjects: QH301 Biology, Genome, 0302 clinical medicine, Genome Size, Vertebrats, Uncategorized, 64, 0303 health sciences, Sex Chromosomes, Multidisciplinary, High-Throughput Nucleotide Sequencing, Genomics, Mitochondrial, Vertebrates, Identification (biology), Engineering sciences. Technology, Sequence Analysis, Neuroinformatics, 45/23, QH426 Genetics, Biology, Article, Evolutionary genetics, 38, Birds, QH301, 03 medical and health sciences, Molecular evolution, ddc:570, Genome assembly algorithms, Animals, 631/181/735, 14. Life underwater, Genomes, QH426, Gene, Gene Library, Genome, Mitochondrial, Haplotypes, Molecular Sequence Annotation, Sequence Alignment, Sequence Analysis, DNA, 030304 developmental biology, 45/91, 631/61/212/2302, 45, Human evolutionary genetics, Haplotype, DAS, DNA, Research data, 706/648/697, 631/181/2474, Evolutionary biology, Genètica, 030217 neurology & neurosurgery, Reference genome
Abstract: High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1,2,3,4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences., We thank them for their permission to publish. A.R., S.K., B.P.W. and A.M.P. were supported by the Intramural Research Program of the NHGRI, NIH (1ZIAHG200398). A.R. was also supported by the Korea Health Technology R&D Project through KHIDI, funded by the Ministry of Health & Welfare, Republic of Korea (HI17C2098). S.A.M., I.B. and R.D. were supported by Wellcome Trust grant WT207492; W.C., M. Smith, Z.N., Y.S., J.C., S. Pelan, J.T., A.T., J.W. and Kerstin Howe by WT206194; L.H., F.M., Kevin Howe and P. Flicek by WT108749/Z/15/Z, WT218328/B/19/Z and the European Molecular Biology Laboratory. O.F. and E.D.J. were supported by Howard Hughes Medical Institute and Rockefeller University start-up funds for this project. J.D. and H.A.L. were supported by the Robert and Rosabel Osborne Endowment. M.U.-S. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement (750747). F.T.-N., J. Hoffman, P. Masterson and K.C. were supported by the Intramural Research Program of the NLM, NIH. C.L., B.J.K., J. Kim and H.K. were supported by the Marine Biotechnology Program of KIMST, funded by the Ministry of Ocean and Fisheries, Republic of Korea (20180430). M.C. was supported by Sloan Research Fellowship (FG-2020-12932). S.C.V. was funded by a Max Planck Research Group award from the Max Planck Society, and a Human Frontiers Science Program (HFSP) Research grant (RGP0058/2016). T.M.L., W.E.J. and the Canada lynx genome were funded by the Maine Department of Inland Fisheries & Wildlife (F11AF01099), including when W.E.J. held a National Research Council Research Associateship Award at the Walter Reed Army Institute of Research (WRAIR). C.B. was supported by the NSF (1457541 and 1456612). D.B. was funded by The University of Queensland (HFSP - RGP0030/2015). D.I. was supported by Science Exchange Inc. (Palo Alto, CA). H.W.D. was supported by NSF grants (OPP-0132032 ICEFISH 2004 Cruise, PLR-1444167 and OPP-1955368) and the Marine Science Center at Northeastern University (416). G.J.P.N. and the thorny skate genome were funded by Lenfest Ocean Program (30884). M.P. was funded by the German Federal Ministry of Education and Research (01IS18026C). M. Malinsky was supported by an EMBO fellowship (ALTF 456-2016). The following authors’ contributions were supported by the NIH: S. Selvaraj (R44HG008118); C.V.M., S.R.F., P.V.L. (R21 DC014432/DC/NIDCD); K.D.M. (R01GM130691); H.C. (5U41HG002371-19); M.D. (U41HG007234); and B.P. (R01HG010485). D.G. was supported by the National Key Research and Development Program of China (2017YFC1201201, 2018YFC0910504 and 2017YFC0907503). F.O.A. was supported by Al-Gannas Qatari Society and The Cultural Village Foundation-Katara, Doha, State of Qatar and Monash University Malaysia. C.T. was supported by The Rockefeller University. M. Hiller was supported by the LOEWE-Centre for Translational Biodiversity Genomics (TBG) funded by the Hessen State Ministry of Higher Education, Research and the Arts (HMWK). H.C. was supported by the NHGRI (5U41HG002371-19). R.H.S.K. was funded by the Max Planck Society with computational resources at the bwUniCluster and BinAC funded by the Ministry of Science, Research and the Arts Baden-Württemberg and the Universities of the State of Baden-Württemberg, Germany (bwHPC-C5). B.V. was supported by the Biomedical Research Council of A*STAR, Singapore. T.M.-B. was funded by the European Research Council under the European Union’s Horizon 2020 research and innovation programme (864203), MINECO/FEDER, UE (BFU2017-86471-P), Unidad de Excelencia María de Maeztu, AEI (CEX2018-000792-M), a Howard Hughes International Early Career award, Obra Social “La Caixa” and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880). E.C.T. was supported by the European Research Council (ERC-2012-StG311000) and an Irish Research Council Laureate Award. M.T.P.G. was supported by an ERC Consolidator Award 681396-Extinction Genomics, and a Danish National Research Foundation Center Grant (DNRF143). T.W. was supported by the NSF (1458652). J. M. Graves was supported by the Australian Research Council (CEO561477). E.W.M. was partially supported by the German Federal Ministry of Education and Research (01IS18026C). Complementary sequencing support for the Anna’s hummingbird and several genomes was provided by Pacific Biosciences, Bionano Genomics, Dovetail Genomics, Arima Genomics, Phase Genomics, 10X Genomics, NRGene, Oxford Nanopore Technologies, Illumina, and DNAnexus. All other sequencing and assembly were conducted at the Rockefeller University, Sanger Institute, and Max Planck Institute Dresden genome labs. Part of this work used the computational resources of the NIH HPC Biowulf cluster (https://hpc.nih.gov). We acknowledge funding from the Wellcome Trust (108749/Z/15/Z) and the European Molecular Biology Laboratory., With funding from the Spanish government through the "Severo Ochoa Centre of Excellence" accreditation (CEX2018-000792-M).
Published: 2021

18. Genome sequence assembly evaluation using long-range sequencing data

Author: Dengfeng Guan, Shane A. McCarthy, Jonathan M. D. Wood, Ying Sims, William Chow, Zemin Ning, Kerstin Howe, Guohua Wang, Yadong Wang, and Richard Durbin
Abstract: Genome sequences are computationally assembled from millions of much shorter sequencing reads. Although this process can be impressively accurate with long reads, it is still subject to a variety of types of errors, including large structural misassembly errors in addition to localised base pair substitutions. Recent advances in long single molecule sequencing in combination with other long-range technologies such as synthetic long read clouds and Hi-C have dramatically increased the contiguity of assembly. This makes it all the more important to be able to validate the structural integrity of the chromosomal scale assemblies now being generated. Here we describe a novel assembly evaluation tool, Asset, which evaluates the consistency of a proposed genome assembly with multiple primary long-range data sets, identifying both supported regions and putative structural misassemblies. We present tests on three de novo assemblies from a human, a goat and a fish species, demonstrating that Asset can identify structural misassemblies accurately by combining regionally supported evidence from long read and other raw sequencing data. Not only can Asset be used to assess overall assembly confidence, and discover specific problematic regions for downstream genome curation, a process that leads to improvement in genome quality, but it can also provide feedback to automated assembly pipelines.
Published: 2022

19. Efficient iterative Hi-C scaffolder based on N-best neighbors

Author: Yadong Wang, Zemin Ning, Richard Durbin, Guohua Wang, Shane A. McCarthy, Dengfeng Guan, Apollo - University of Cambridge Repository, McCarthy, Shane [0000-0002-2715-4187], and Durbin, Richard [0000-0002-9130-1006]
Subjects: Scaffold, Chromosome number, Computer science, QH301-705.5, Computer applications to medicine. Medical informatics, R858-859.7, Machine learning, computer.software_genre, Scaffolding, Biochemistry, Chromosomes, Task (project management), 03 medical and health sciences, 0302 clinical medicine, Structural Biology, Scaffolder, Hi-C, Biology (General), Molecular Biology, 030304 developmental biology, Genome scaffolding, 0303 health sciences, Genome, business.industry, Applied Mathematics, High-Throughput Nucleotide Sequencing, Construct (python library), Genomics, Sequence Analysis, DNA, Computer Science Applications, A priori and a posteriori, Graph (abstract data type), Artificial intelligence, business, computer, 030217 neurology & neurosurgery, Software
Abstract: Background Efficient and effective genome scaffolding tools are still in high demand for generating reference-quality assemblies. While long read data itself is unlikely to create a chromosome-scale assembly for most eukaryotic species, the inexpensive Hi-C sequencing technology, capable of capturing the chromosomal profile of a genome, is now widely used to complete the task. However, the existing Hi-C based scaffolding tools either require a priori chromosome number as input, or lack the ability to build highly continuous scaffolds. Results We design and develop a novel Hi-C based scaffolding tool, pin_hic, which takes advantage of contact information from Hi-C reads to construct a scaffolding graph iteratively based on N-best neighbors of contigs. Subsequent to scaffolding, it identifies potential misjoins and breaks them to keep the scaffolding accuracy. Through our tests on three long read based de novo assemblies from three different species, we demonstrate that pin_hic is more efficient than current standard state-of-art tools, and it can generate much more continuous scaffolds, while achieving a higher or comparable accuracy. Conclusions Pin_hic is an efficient Hi-C based scaffolding tool, which can be useful for building chromosome-scale assemblies. As many sequencing projects have been launched in the recent years, we believe pin_hic has potential to be applied in these projects and makes a meaningful contribution.
Published: 2021

20. Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant

Author: Mohammad Raza, Alison E. Mather, Gilberto Betancor, Ian Merrick, Ben Taylor, Mathew A. Beale, Helen Ward, Samir Dervisevic, Michelle Cronin, Aaron R. Jeffries, Louise Smith, Steven Rudder, Mara K. N. Lawniczak, Sascha Ott, Ashok Dadrah, Luke Bedford, Gabrielle Vernet, Erik M. Volz, Rahul Batra, Johnny Debebe, Caoimhe McKerr, Samantha McGuigan, Oliver Megram, Katie Jones, Mailis Maes, Rebecca Dewar, Emma Swindells, Robert E. Johnson, Myra Hosmillo, Wen C Yew, Vineet Patel, Scott Aj Thurston, Matthew Bashton, Luke B Snell, Lynn Monaghan, David Buck, Gregory R Young, Garren Scott, Louis du Plessis, Sara Kumziene-Summerhayes, David M. Aanensen, Carl Jones, Nadine Holmes, Bernardo Gutierrez, Elizabeth Wastenge, Stavroula F Louka, Dennis Wang, Richard I. Gregory, M. Estée Török, Alistair C. Darby, Ulf Schaefer, Marc Niebel, David Robertson, E. Thomson, Carol Churcher, Patrick C McClure, Scott Elliott, Sarah Jeremiah, Katerina Galai, Matthew W. Loose, Megan Mayhew, Adhyana I K Mahanama, Angeliki Karamani, Naomi R Park, David J. Williams, Lance Turtle, Lucy R. Frost, Alicia Thornton, Jennifier Liddle, M Morgan, Tim Wyatt, Paul W Bird, Chloe Bishop, Esther Robinson, Alasdair MacLean, Inigo Martincorena, Bridget A. Knight, Emma Meader, Thomas R. Connor, Hermione J. Webster, Peter Muir, Sarah Walsh, Stephanie W. Lo, Andrew Bosworth, Hannah E Bridgewater, David Simpson, Radoslaw Poplawski, Angus I. Best, David Baker, Laura Letchford, Cassie Breen, Yann Bourgeois, Matthew Gemmell, Nikki Smith, Alison Holmes, Iliana Georgana, Christophe Fraser, Natasha Jesudason, Johnathan M Evans, Rachael Stanley, Lesley-Anne Williams, Jessica Lynch, Hannah Lowe, Eleri Wilson-Davies, Paul A. Baker, Alex Makunin, James Bonfield, Helen Adams, Christopher Fearn, Peter J. Diggle, Harry D Wilson, Carmen F. Manso, Nichola Duckworth, D Haw, Anna L. Casey, Audrey Farbos, Sam Haldenby, Vicki Chalker, Roberto Amato, Elen De Lacy, Ben Farr, Eric Witele, Buddhini Samaraweera, G MacIntyre-Cockett, Husam Osman, Jane Greenaway, Justin O'Grady, Sally Forrest, Andrew Nelson, Monika Pusok, A Lloyd, Edward Barton, James W. Harrison, Sophie Palmer, Amanda Symmonds, James Shepherd, Nazreen F. Hadjirin, Stephen L. Michell, Mohammed O Hassan-Ibrahim, Fiona Ashcroft, Daniel Mair, Richard H. Myers, Dianne Irish-Tavares, Hannah C. Howson-Wells, Jacqui Prieto, Christine Sambles, Andrew Hesketh, Alp Aydin, Sónia Gonçalves, Tabitha Mahungu, Tanzina Haque, Nicholas Ellaby, Karen Oliver, Hannah Paul, Joanne Watts, Claire McMurray, Lisa J Levett, Darren Smith, Simon Cottrell, Joanna Warwick-Dugdale, Pinglawathee Madona, Matthew J. Dorman, Lizzie Meadows, Ali R Awan, Leanne M Kermack, Jennifer Hart, Angie Lackenby, Carol Scott, Michael Spencer Chapman, Lucille Rainbow, Kyriaki Nomikou, Julianne R Brown, Juan Ledesma, Adam P Westhorpe, Giri Shankar, Karlie Fallon, Tim J Sloan, Joanne Watkins, Robert Impey, Sue Edwards, Rebecca C H Brown, Robin J Moll, Karla Spellman, Laura Gifford, Jamie Young, Adrienn Angyal, Graham Phillip Taylor, Robin Manley, Gavin Dabrera, Michelle Wantoch, Rachel Williams, David Heyburn, Mirko Menegazzo, Derrick W. Crook, Gaia Nebbia, Rachel Nelson, Elaine O'Toole, Luke Foulser, Katherine L Harper, Fatima Downing, Hassan Hartman, Nathan Moore, Gemma L. Kay, Matthew Wyles, Thanh Le-Viet, Edith Vamos, John Sillitoe, Lesley Shirley, Nicholas J. Loman, Iona Willingham, Elihu Aranday-Cortes, Ian B Vipond, Jeremy Mirza, Alberto C Cerda, Michelle L Michelsen, Steven Riley, Alison Cox, Igor Siveroni, Nadua Bayzid, Shavanthi Rajatileka, Giselda Bucca, Benjamin J Cogger, Tim Boswell, Matthew J. Bull, Stephen Carmichael, Lisa Berry, Frances Bolt, Kylie E. C. Ainslie, Martyn Guest, Sarojini Pandey, Katherine L. Bellis, Shane A. McCarthy, Christopher Ruis, Fei Sang, David Bonsall, Danni Weldon, Alex Alderton, Lee Graham, Amy Trebes, Sally Corden, Adrian W Signell, Tanya Golubchik, Huw Gulliver, Rocio Martinez Nunez, Dinesh Aggarwal, Tanya Curran, Jonathan K. Ball, Sharif Shaaban, Paul Randell, Jillian Durham, Alec Birchley, Matilde Mori, Joana Dias, Katherine A Twohig, Grant Hall, Antony D Hale, Alan McNally, Jonathan D. Edgeworth, Safiah Afifi, Andrew Rambaut, Katherine Smollett, David N. Lee, Tamyo Mbisa, Shahjahan Miah, Steven Rushton, Grace Taylor-Joyce, Hannah M Pymont, Chloe L Fisher, Cordelia Langford, Alex G. Richter, Jane A. H. Masoli, Michael Gallagher, Vicki M. Fleming, Kathleen A. Williamson, Anna Price, Holli Carden, Khalil Abudahab, Joanne D. Stockton, Meera Unnikrishnan, Jennifer Collins, Emma Moles-Garcia, Michaela John, Christine Kitchen, Tranprit Saluja, Ian Harrison, Lily Tong, Thomas G. Thompson, Thomas Helmer, Amita Patel, Siona Silveira, Deborah Ashby, Claire M Bewshea, Anita Justice, Brendan A I Payne, Alexander J. Trotter, Nikos Manesis, Katie F. Loveson, Cristina V. Ariani, Wendy Chatterton, Robert J. Munn, Julian A. Hiscox, Robert Beer, Judith Breuer, Caroline E. Walters, Liam Crawford, Ara Darzi, Will P. M. Rowe, Cariad Evans, Matthew Parker, Tammy V Merrill, Louise Aigrain, Joshua Quick, Leigh M Jackson, Samuel M. Nicholls, Jonathan W. Moore, John A Hartley, Graham P. Taylor, Cherian Koshy, Shirelle Burton-Fanning, Sheila Waugh, Catherine Moore, Danielle C. Groves, Peijun Zhang, Sahar Eldirdiri, Derek Fairley, Tim E. A. Peto, Jack Cd Lee, Sharon Glaysher, Liam Prestwood, Hannah Dent, Anita Kenyon, Stephen P. Kidd, Nick Levene, Igor Starinskij, Joseph G. Chappell, Steve Paterson, Gary Eltringham, Laia Fina, Angela Marchbank, Daniel Bradshaw, Marina Escalera Zamudio, Scott Goodwin, Andrew D Beggs, Seema Nickbakhsh, Trevor Robinson, Christina Atchison, David K. Jackson, Kathy Li, Rory Gunson, Sunando Roy, Graham S Cooke, Steven Liggett, Yasmin Chaudhry, Anoop Chauhan, Ben Temperton, Mariateresa de Cesare, Paul E Brown, Li Xu-McCrae, Martin P McHugh, Catherine Ludden, Wendy Smith, Danielle Leek, Divya K. Shah, Judith Heaney, Dominic P. Kwiatkowski, Kate M. Johnson, Robin Howe, Malorie Perry, Tetyana I. Vasylyeva, David F. Bibby, Haowei Wang, Steve Palmer, Nicholas W Machin, Charlotte A Williams, Bree Gatica-Wilcox, Angie Green, John A. Todd, Paul Elliott, Noel Craine, Jeffrey K. J. Cheng, Kate Templeton, Jonathan Hubb, Joshua Maksimovic, Christl A. Donnelly, Monique Andersson, Christopher Holmes, Dimitris Grammatopoulos, Christopher B. Williams, David G Partridge, Aminu S Jahun, Alexander Adams, Marius Cotic, Sarah Essex, Christopher J. Moore, Trudy Workman, Nicola Sheriff, Helen L Lowe, Ewan M. Harrison, Dorota Jamrozy, Rachel Jones, Ellen Higginson, Erwan Acheson, Christopher R. Jones, Oliver G. Pybus, Francesc Coll, Sian Morgan, Paul J. Parsons, Patawee Asamaphan, Veena Raviprakash, Andrew R. Bassett, Declan Bradley, Laura Atkinson, Anthony Underwood, Graciela Sluga, Sally Kay, Ellena Brooks, Oliver Eales, Andrew Whitwham, Surendra Parmar, Angela Cowell, Nicole Pacchiarini, Theocharis Tsoleridis, Jason Coombes, Robert Davies, Flavia Flaviani, Benita Percival, Jenna Nichols, Natasha M. Johnson, Salman Goudarzi, Hibo Asad, Amanda Bradley, Hannah Jones, Chrystala Constantinidou, Georgina M McManus, Minal Patel, Steven Leonard, Rebecca Williams Bmbs, Andrew J. Page, Christoph Puethe, Nicola Reynolds, Amy Ash, John Danesh, Corin Yeats, Claudia Wierzbicki, Kordo Saeed, John Boyes, Michael A. Quail, Sharon J. Peacock, Nabil-Fareed Alikhan, Jon-Paul Keatley, Claudio Fronterre, Garry Scarlett, James McKenna, Thushan I de Silva, Malte L Pinckert, Kate B. Cook, Amy Gaskin, Rajiv Shah, Matthew T. G. Holden, Sophie J Prosolek, Nathaniel Storey, Ryan P George, Lindsay Coupland, Jenifer Mason, Matthew Carlile, Thomas D Stanton, Guy Mollett, Siddharth Mookerjee, Mary Ramsay, Steven Platt, Stephen W Attwood, Susanne Stonehouse, Sophie Jones, Venkat Sivaprakasam, Amy Plimmer, Mark Whitehead, Catherine Bresner, Stefanie V Lensing, Louissa R Macfarlane-Smith, Colin P. Smith, Wendy Hogsden, Charlotte Nelson, Ian Johnston, Jeffrey C. Barrett, Joshua B Singer, Samuel Robson, Zoltán Molnár, Emma L. Wise, Sian Ellard, Kim S Smith, Alice Broos, Manjinder Khakh, Kathryn A Jackson, Claire Cormie, Rachel Tucker, Ian Goodfellow, S.E. Moses, Nicola Cumley, Meera Chand, Debra Padgett, Cassandra S Malone, James V. Price, Themoula Charalampous, Ronan A Lyons, Natalie Groves, Stefan Rooke, Rebekah E Wilson, Stephen Bonner, Richard Stark, Sharon Campbell, Michelle Lister, Carlos Balcazar, Ana da Silva Filipe, Ben Warne, Thomas N. Williams, Marta Gallis, Lauren Gilbert, Rose K Davidson, Angela Helen Beckett, Ember Hilvers, Kathryn McCluggage, Eileen Gallagher, Charlotte Beaver, Nick Cortes, Alisha Davies, Yusri Taha, Leah Ensell, Emanuela Pelosi, Elias Allara, Cressida Auckland, Eleanor Drury, Richard Eccles, Adela Alcolea-Medina, William L Hamilton, Rich Livett, Rachel Blacow, Margaret Hughes, Sarah François, Melisa Louise Fenton, Liz Ratcliffe, Verity Hill, Stephanie Hutchings, Kathryn Ann Harris, Emma Betteridge, William D. Fuller, Sophia T Girgis, Louise Berry, Gemma Clark, Nicholas M Redshaw, Richard Hopes, Leonardo de Oliveira Martins, Alexander J Keeley, Beth Blane, Wendy S. Barclay, Victoria Wright, Anita Lucaci, Luke R. Green, Fenella D. Halstead, Sarah Wyllie, Iraad F. Bronner, Áine O'Toole, Ravi Gupta, Leanne Kane, Clare M. McCann, Michael R Chapman, David W Eyre, Kelly Bicknell, Aileen G. Rowan, Sara Rey, Shazaad Ahmad, Diana Rajan, S Taylor, Sarah J. O'Brien, Alessandro M Carabelli, Amelia Joseph, Max Whiteley, Riaz Jannoo, Victoria Blakey, Martin D. Curran, David J. Studholme, Harmeet K Gill, Thomas R. A. Davis, Sushmita Sridhar, Clive Graham, Julian Tang, Clare Pearson, Mark Kristiansen, Miren Iturriza-Gomara, National Institute for Health Research, and UK Research and Innovation
Subjects: Delta, Adult, Male, 2019-20 coronavirus outbreak, COVID-19 Vaccines, Vaccination Coverage, Coronavirus disease 2019 (COVID-19), Adolescent, General Science & Technology, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Vaccine Efficacy, Biology, Young Adult, Exponential growth, Ethnicity, Prevalence, Humans, Child, Aged, Family Characteristics, Multidisciplinary, High prevalence, COVID-19 Genomics UK (COG-UK) Consortium11‡, SARS-CoV-2, Age Factors, COVID-19, Middle Aged, Virology, Hospitalization, England, Socioeconomic Factors, COVID-19 Nucleic Acid Testing, Child, Preschool, Female, Self Report
Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections were rising during early summer 2021 in many countries as a result of the Delta variant. We assessed reverse transcription polymerase chain reaction swab positivity in the Real-time Assessment of Community Transmission–1 (REACT-1) study in England. During June and July 2021, we observed sustained exponential growth with an average doubling time of 25 days, driven by complete replacement of the Alpha variant by Delta and by high prevalence at younger, less-vaccinated ages. Prevalence among unvaccinated people [1.21% (95% credible interval 1.03%, 1.41%)] was three times that among double-vaccinated people [0.40% (95% credible interval 0.34%, 0.48%)]. However, after adjusting for age and other variables, vaccine effectiveness for double-vaccinated people was estimated at between ~50% and ~60% during this period in England. Increased social mixing in the presence of Delta had the potential to generate sustained growth in infections, even at high levels of vaccination.
Published: 2021

21. The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

Author: Thushan I. de Silva, Guihai Liu, Benjamin B. Lindsey, Danning Dong, Shona C. Moore, Nienyun Sharon Hsu, Dhruv Shah, Dannielle Wellington, Alexander J. Mentzer, Adrienn Angyal, Rebecca Brown, Matthew D. Parker, Zixi Ying, Xuan Yao, Lance Turtle, Susanna Dunachie, Mala K. Maini, Graham Ogg, Julian C. Knight, Yanchun Peng, Sarah L. Rowland-Jones, Tao Dong, David M. Aanensen, Khalil Abudahab, Helen Adams, Alexander Adams, Safiah Afifi, Dinesh Aggarwal, Shazaad S.Y. Ahmad, Louise Aigrain, Adela Alcolea-Medina, Nabil-Fareed Alikhan, Elias Allara, Roberto Amato, Tara Annett, Stephen Aplin, Cristina V. Ariani, Hibo Asad, Amy Ash, Paula Ashfield, Fiona Ashford, Laura Atkinson, Stephen W. Attwood, Cressida Auckland, Alp Aydin, David J. Baker, Paul Baker, Carlos E. Balcazar, Jonathan Ball, Jeffrey C. Barrett, Magdalena Barrow, Edward Barton, Matthew Bashton, Andrew R. Bassett, Rahul Batra, Chris Baxter, Nadua Bayzid, Charlotte Beaver, Angela H. Beckett, Shaun M. Beckwith, Luke Bedford, Robert Beer, Andrew Beggs, Katherine L. Bellis, Louise Berry, Beatrice Bertolusso, Angus Best, Emma Betteridge, David Bibby, Kelly Bicknell, Debbie Binns, Alec Birchley, Paul W. Bird, Chloe Bishop, Rachel Blacow, Victoria Blakey, Beth Blane, Frances Bolt, James Bonfield, Stephen Bonner, David Bonsall, Tim Boswell, Andrew Bosworth, Yann Bourgeois, Olivia Boyd, Declan T. Bradley, Cassie Breen, Catherine Bresner, Judith Breuer, Stephen Bridgett, Iraad F. Bronner, Ellena Brooks, Alice Broos, Julianne R. Brown, Giselda Bucca, Sarah L. Buchan, David Buck, Matthew Bull, Phillipa J. Burns, Shirelle Burton-Fanning, Timothy Byaruhanga, Matthew Byott, Sharon Campbell, Alessandro M. Carabelli, James S. Cargill, Matthew Carlile, Silvia F. Carvalho, Anna Casey, Anibolina Castigador, Jana Catalan, Vicki Chalker, Nicola J. Chaloner, Meera Chand, Joseph G. Chappell, Themoula Charalampous, Wendy Chatterton, Yasmin Chaudhry, Carol M. Churcher, Gemma Clark, Phillip Clarke, Benjamin J. Cogger, Kevin Cole, Jennifer Collins, Rachel Colquhoun, Thomas R. Connor, Kate F. Cook, Jason Coombes, Sally Corden, Claire Cormie, Nicholas Cortes, Marius Cotic, Seb Cotton, Simon Cottrell, Lindsay Coupland, MacGregor Cox, Alison Cox, Noel Craine, Liam Crawford, Aidan Cross, Matthew R. Crown, Dorian Crudgington, Nicola Cumley, Tanya Curran, Martin D. Curran, Ana da Silva Filipe, Gavin Dabrera, Alistair C. Darby, Rose K. Davidson, Alisha Davies, Robert M. Davies, Thomas Davis, Daniela de Angelis, Elen De Lacy, Leonardo de Oliveira Martins, Johnny Debebe, Rebecca Denton-Smith, Samir Dervisevic, Rebecca Dewar, Jayasree Dey, Joana Dias, Donald Dobie, Matthew J. Dorman, Fatima Downing, Megan Driscoll, Louis du Plessis, Nichola Duckworth, Jillian Durham, Kirstine Eastick, Lisa J. Easton, Richard Eccles, Jonathan Edgeworth, Sue Edwards, Kate El Bouzidi, Sahar Eldirdiri, Nicholas Ellaby, Scott Elliott, Gary Eltringham, Leah Ensell, Michelle J. Erkiert, Marina Escalera Zamudio, Sarah Essex, Johnathan M. Evans, Cariad Evans, William Everson, Derek J. Fairley, Karlie Fallon, Arezou Fanaie, Ben W. Farr, Christopher Fearn, Theresa Feltwell, Lynne Ferguson, Laia Fina, Flavia Flaviani, Vicki M. Fleming, Sally Forrest, Ebenezer Foster-Nyarko, Benjamin H. Foulkes, Luke Foulser, Mireille Fragakis, Dan Frampton, Sarah Francois, Christophe Fraser, Timothy M. Freeman, Helen Fryer, Marc Fuchs, William Fuller, Kavitha Gajee, Katerina Galai, Abbie Gallagher, Eileen Gallagher, Michael D. Gallagher, Marta Gallis, Amy Gaskin, Bree Gatica-Wilcox, Lily Geidelberg, Matthew Gemmell, Iliana Georgana, Ryan P. George, Laura Gifford, Lauren Gilbert, Sophia T. Girgis, Sharon Glaysher, Emily J. Goldstein, Tanya Golubchik, Andrea N. Gomes, Sónia Gonçalves, Ian G. Goodfellow, Scott Goodwin, Salman Goudarzi, Marina Gourtovaia, Clive Graham, Lee Graham, Paul R. Grant, Luke R. Green, Angie Green, Jane Greenaway, Richard Gregory, Martyn Guest, Rory N. Gunson, Ravi K. Gupta, Bernardo Gutierrez, Sam T. Haldenby, William L. Hamilton, Samantha E. Hansford, Tanzina Haque, Kathryn A. Harris, Ian Harrison, Ewan M. Harrison, Jennifer Hart, John A. Hartley, William T. Harvey, Matthew Harvey, Mohammed O. Hassan-Ibrahim, Judith Heaney, Thomas Helmer, John H. Henderson, Andrew R. Hesketh, Jessica Hey, David Heyburn, Ellen E. Higginson, Verity Hill, Jack D. Hill, Rachel A. Hilson, Ember Hilvers, Matthew T.G. Holden, Amy Hollis, Christopher W. Holmes, Nadine Holmes, Alison H. Holmes, Richard Hopes, Hailey R. Hornsby, Myra Hosmillo, Catherine Houlihan, Hannah C. Howson-Wells, Jonathan Hubb, Hannah Huckson, Warwick Hughes, Joseph Hughes, Margaret Hughes, Stephanie Hutchings, Giles Idle, Chris J. Illingworth, Robert Impey, Dianne Irish-Tavares, Miren Iturriza-Gomara, Rhys Izuagbe, Chris Jackson, Ben Jackson, Leigh M. Jackson, Kathryn A. Jackson, David K. Jackson, Aminu S. Jahun, Victoria James, Keith James, Christopher Jeanes, Aaron R. Jeffries, Sarah Jeremiah, Andrew Jermy, Michaela John, Rob Johnson, Kate Johnson, Ian Johnston, Owen Jones, Sophie Jones, Hannah Jones, Christopher R. Jones, Neil Jones, Amelia Joseph, Sarah Judges, Gemma L. Kay, Sally Kay, Jon-Paul Keatley, Alexander J. Keeley, Anita Kenyon, Leanne M. Kermack, Manjinder Khakh, Stephen P. Kidd, Maimuna Kimuli, Stuart Kirk, Christine Kitchen, Katie Kitchman, Bridget A. Knight, Cherian Koshy, Moritz U.G. Kraemer, Sara Kumziene-Summerhayes, Dominic Kwiatkowski, Angie Lackenby, Kenneth G. Laing, Temi Lampejo, Cordelia F. Langford, Deborah Lavin, Andrew I. Lawton, Jack Lee, David Lee, Stefanie V. Lensing, Steven Leonard, Lisa J. Levett, Thanh Le-Viet, Jonathan Lewis, Kevin Lewis, Jennifier Liddle, Steven Liggett, Patrick J. Lillie, Michelle M. Lister, Rich Livett, Stephanie Lo, Nicholas J. Loman, Matthew W. Loose, Stavroula F. Louka, Katie F. Loveson, Sarah Lowdon, Hannah Lowe, Helen L. Lowe, Anita O. Lucaci, Catherine Ludden, Jessica Lynch, Ronan A. Lyons, Katrina Lythgoe, Nicholas W. Machin, George MacIntyre-Cockett, Andrew Mack, Ben Macklin, Alasdair Maclean, Emily Macnaughton, Pinglawathee Madona, Mailis Maes, Laurentiu Maftei, Adhyana I.K. Mahanama, Tabitha W. Mahungu, Daniel Mair, Joshua Maksimovic, Cassandra S. Malone, Daniel Maloney, Nikos Manesis, Robin Manley, Anna Mantzouratou, Angela Marchbank, Arun Mariappan, Inigo Martincorena, Rocio T. Martinez Nunez, Alison E. Mather, Patrick Maxwell, Megan Mayhew, Tamyo Mbisa, Clare M. McCann, Shane A. McCarthy, Kathryn McCluggage, Patrick C. McClure, J.T. McCrone, Martin P. McHugh, James P. McKenna, Caoimhe McKerr, Georgina M. McManus, Claire L. McMurray, Claire McMurray, Alan McNally, Lizzie Meadows, Nathan Medd, Oliver Megram, Mirko Menegazzo, Ian Merrick, Stephen L. Michell, Michelle L. Michelsen, Mariyam Mirfenderesky, Jeremy Mirza, Julia Miskelly, Emma Moles-Garcia, Robin J. Moll, Zoltan Molnar, Irene M. Monahan, Matteo Mondani, Siddharth Mookerjee, Christopher Moore, Jonathan Moore, Nathan Moore, Catherine Moore, Helen Morcrette, Sian Morgan, Mari Morgan, Matilde Mori, Arthur Morriss, Samuel Moses, Craig Mower, Peter Muir, Afrida Mukaddas, Florence Munemo, Robert Munn, Abigail Murray, Leanne J. Murray, Darren R. Murray, Manasa Mutingwende, Richard Myers, Eleni Nastouli, Gaia Nebbia, Andrew Nelson, Charlotte Nelson, Sam Nicholls, Jenna Nichols, Roberto Nicodemi, Kyriaki Nomikou, Justin O’Grady, Sarah O'Brien, Mina Odedra, Natasha Ohemeng-Kumi, Karen Oliver, Richard J. Orton, Husam Osman, null xeine O'Toole, Nicole Pacchiarini, Debra Padgett, Andrew J. Page, Emily J. Park, Naomi R. Park, Surendra Parmar, David G. Partridge, David Pascall, Amita Patel, Bindi Patel, Steve Paterson, Brendan A.I. Payne, Sharon J. Peacock, Clare Pearson, Emanuela Pelosi, Benita Percival, Jon Perkins, Malorie Perry, Malte L. Pinckert, Steven Platt, Olga Podplomyk, Manoj Pohare, Marcus Pond, Cassie F. Pope, Radoslaw Poplawski, Jessica Powell, Jennifer Poyner, Liam Prestwood, Anna Price, James R. Price, Jacqui A. Prieto, David T. Pritchard, Sophie J. Prosolek, Georgia Pugh, Monika Pusok, Oliver G. Pybus, Hannah M. Pymont, Michael A. Quail, Joshua Quick, Clara Radulescu, Jayna Raghwani, Manon Ragonnet-Cronin, Lucille Rainbow, Diana Rajan, Shavanthi Rajatileka, Newara A. Ramadan, Andrew Rambaut, John Ramble, Paul A. Randell, Paul Randell, Liz Ratcliffe, Veena Raviprakash, Mohammad Raza, Nicholas M. Redshaw, Sara Rey, Nicola Reynolds, Alex Richter, David L. Robertson, Esther Robinson, Samuel C. Robson, Fiona Rogan, Stefan Rooke, Will Rowe, Sunando Roy, Steven Rudder, Chris Ruis, Steven Rushton, Felicity Ryan, Kordo Saeed, Buddhini Samaraweera, Christine M. Sambles, Roy Sanderson, Theo Sanderson, Fei Sang, Thea Sass, Emily Scher, Garren Scott, Carol Scott, Jasveen Sehmi, Sharif Shaaban, Divya Shah, Jessica Shaw, Ekaterina Shelest, James G. Shepherd, Liz A. Sheridan, Nicola Sheriff, Lesley Shirley, John Sillitoe, Siona Silviera, David A. Simpson, Aditi Singh, Dawn Singleton, Timofey Skvortsov, Tim J. Sloan, Graciela Sluga, Ken Smith, Kim S. Smith, Perminder Smith, Darren L. Smith, Louise Smith, Colin P. Smith, Nikki Smith, Katherine L. Smollett, Luke B. Snell, Thomas Somassa, Joel Southgate, Karla Spellman, Michael H. Spencer Chapman, Lewis G. Spurgin, Moira J. Spyer, Rachael Stanley, William Stanley, Thomas D. Stanton, Igor Starinskij, Joanne Stockton, Susanne Stonehouse, Nathaniel Storey, David J. Studholme, Malur Sudhanva, Emma Swindells, Yusri Taha, Ngee Keong Tan, Julian W. Tang, Miao Tang, Ben E.W. Taylor, Joshua F. Taylor, Sarah Taylor, Ben Temperton, Kate E. Templeton, Claire Thomas, Laura Thomson, Emma C. Thomson, Alicia Thornton, Scott A.J. Thurston, John A. Todd, Rachael Tomb, Lily Tong, Gerry Tonkin-Hill, M. Estee Torok, Jaime M. Tovar-Corona, Amy Trebes, Alexander J. Trotter, Ioulia Tsatsani, Robyn Turnbull, Katherine A. Twohig, Helen Umpleby, Anthony P. Underwood, Edith E. Vamos, Tetyana I. Vasylyeva, Sreenu Vattipally, Gabrielle Vernet, Barry B. Vipond, Erik M. Volz, Sarah Walsh, Dennis Wang, Ben Warne, Joanna Warwick-Dugdale, Elizabeth Wastnedge, Joanne Watkins, Louisa K. Watson, Sheila Waugh, Hermione J. Webster, Danni Weldon, Elaine Westwick, Thomas Whalley, Helen Wheeler, Mark Whitehead, Max Whiteley, Andrew Whitwham, Claudia Wierzbicki, Nicholas J. Willford, Lesley-Anne Williams, Rebecca Williams, Cheryl Williams, Chris Williams, Charlotte A. Williams, Rachel J. Williams, Thomas Williams, Catryn Williams, Kathleen A. Williamson, Eleri Wilson-Davies, Eric Witele, Karen T. Withell, Adam A. Witney, Paige Wolverson, Nick Wong, Trudy Workman, Victoria Wright, Derek W. Wright, Tim Wyatt, Sarah Wyllie, Li Xu-McCrae, Mehmet Yavus, Geraldine Yaze, Corin A. Yeats, Gonzalo Yebra, Wen C. Yew, Gregory R. Young, Jamie Young, Alex E. Zarebski, Peijun Zhang, J. Kenneth Baillie, Malcolm G. Semple, Peter J.M. Openshaw, Gail Carson, Beatrice Alex, Petros Andrikopoulos, Benjamin Bach, Wendy S. Barclay, Debby Bogaert, Kanta Chechi, Graham S. Cooke, Annemarie B. Docherty, Gonçalo dos Santos Correia, Marc-Emmanuel Dumas, Jake Dunning, Tom Fletcher, Christopher A. Green, William Greenhalf, Julian L. Griffin, Rishi K. Gupta, Ewen M. Harrison, Julian A. Hiscox, Antonia Ying Wai Ho, Peter W. Horby, Samreen Ijaz, Saye Khoo, Paul Klenerman, Andrew Law, Matthew R. Lewis, Sonia Liggi, Wei Shen Lim, Lynn Maslen, Laura Merson, Alison M. Meynert, Mahdad Noursadeghi, Michael Olanipekun, Anthonia Osagie, Massimo Palmarini, Carlo Palmieri, William A. Paxton, Georgios Pollakis, Nicholas Price, Clark D. Russell, Vanessa Sancho-Shimizu, Caroline J. Sands, Janet T. Scott, Louise Sigfrid, Tom Solomon, Shiranee Sriskandan, David Stuart, Charlotte Summers, Olivia V. Swann, Zoltan Takats, Panteleimon Takis, Richard S. Tedder, A.A. Roger Thompson, Ryan S. Thwaites, Maria Zambon, Hayley Hardwick, Chloe Donohue, Fiona Griffiths, Wilna Oosthuyzen, Cara Donegan, Rebecca G. Spencer, Jo Dalton, Michelle Girvan, Egle Saviciute, Stephanie Roberts, Janet Harrison, Laura Marsh, Marie Connor, Sophie Halpin, Clare Jackson, Carrol Gamble, Daniel Plotkin, James Lee, Gary Leeming, Murray Wham, Sara Clohisey, Ross Hendry, James Scott-Brown, Victoria Shaw, Sarah E. McDonald, Seán Keating, Katie A. Ahmed, Jane A. Armstrong, Milton Ashworth, Innocent G. Asiimwe, Siddharth Bakshi, Samantha L. Barlow, Laura Booth, Benjamin Brennan, Katie Bullock, Benjamin W.A. Catterall, Jordan J. Clark, Emily A. Clarke, Sarah Cole, Louise Cooper, Helen Cox, Christopher Davis, Oslem Dincarslan, Chris Dunn, Philip Dyer, Angela Elliott, Anthony Evans, Lorna Finch, Lewis W.S. Fisher, Terry Foster, Isabel Garcia-Dorival, Philip Gunning, Catherine Hartley, Rebecca L. Jensen, Christopher B. Jones, Trevor R. Jones, Shadia Khandaker, Katharine King, Robyn T. Kiy, Chrysa Koukorava, Annette Lake, Suzannah Lant, Diane Latawiec, Lara Lavelle-Langham, Daniella Lefteri, Lauren Lett, Lucia A. Livoti, Maria Mancini, Sarah McDonald, Laurence McEvoy, John McLauchlan, Soeren Metelmann, Nahida S. Miah, Joanna Middleton, Joyce Mitchell, Ellen G. Murphy, Rebekah Penrice-Randal, Jack Pilgrim, Tessa Prince, Will Reynolds, P. Matthew Ridley, Debby Sales, Victoria E. Shaw, Rebecca K. Shears, Benjamin Small, Krishanthi S. Subramaniam, Agnieska Szemiel, Aislynn Taggart, Jolanta Tanianis-Hughes, Jordan Thomas, Erwan Trochu, Libby van Tonder, Eve Wilcock, J. Eunice Zhang, Lisa Flaherty, Nicole Maziere, Emily Cass, Alejandra Doce Carracedo, Nicola Carlucci, Anthony Holmes, Hannah Massey, Lee Murphy, Nicola Wrobel, Sarah McCafferty, Kirstie Morrice, Alan MacLean, Kayode Adeniji, Daniel Agranoff, Ken Agwuh, Dhiraj Ail, Erin L. Aldera, Ana Alegria, Sam Allen, Brian Angus, Abdul Ashish, Dougal Atkinson, Shahedal Bari, Gavin Barlow, Stella Barnass, Nicholas Barrett, Christopher Bassford, Sneha Basude, David Baxter, Michael Beadsworth, Jolanta Bernatoniene, John Berridge, Colin Berry, Nicola Best, Pieter Bothma, David Chadwick, Robin Brittain-Long, Naomi Bulteel, Tom Burden, Andrew Burtenshaw, Vikki Caruth, Duncan Chambler, Nigel Chee, Jenny Child, Srikanth Chukkambotla, Tom Clark, Paul Collini, Catherine Cosgrove, Jason Cupitt, Maria-Teresa Cutino-Moguel, Paul Dark, Chris Dawson, Phil Donnison, Sam Douthwaite, Andrew Drummond, Ingrid DuRand, Ahilanadan Dushianthan, Tristan Dyer, Chi Eziefula, Chrisopher Fegan, Adam Finn, Duncan Fullerton, Sanjeev Garg, Atul Garg, Effrossyni Gkrania-Klotsas, Jo Godden, Arthur Goldsmith, Elaine Hardy, Stuart Hartshorn, Daniel Harvey, Peter Havalda, Daniel B. Hawcutt, Maria Hobrok, Luke Hodgson, Anil Hormis, Michael Jacobs, Susan Jain, Paul Jennings, Agilan Kaliappan, Vidya Kasipandian, Stephen Kegg, Michael Kelsey, Jason Kendall, Caroline Kerrison, Ian Kerslake, Oliver Koch, Gouri Koduri, George Koshy, Shondipon Laha, Steven Laird, Susan Larkin, Tamas Leiner, Patrick Lillie, James Limb, Vanessa Linnett, Jeff Little, Mark Lyttle, Michael MacMahon, Emily MacNaughton, Ravish Mankregod, Huw Masson, Elijah Matovu, Katherine McCullough, Ruth McEwen, Manjula Meda, Gary Mills, Jane Minton, Kavya Mohandas, Quen Mok, James Moon, Elinoor Moore, Patrick Morgan, Craig Morris, Katherine Mortimore, Mbiye Mpenge, Rohinton Mulla, Michael Murphy, Megan Nagel, Thapas Nagarajan, Mark Nelson, Lillian Norris, Matthew K. O'Shea, Igor Otahal, Marlies Ostermann, Mark Pais, Selva Panchatsharam, Danai Papakonstantinou, Hassan Paraiso, Brij Patel, Natalie Pattison, Justin Pepperell, Mark Peters, Mandeep Phull, Stefania Pintus, Jagtur Singh Pooni, Tim Planche, Frank Post, David Price, Rachel Prout, Nikolas Rae, Henrik Reschreiter, Tim Reynolds, Neil Richardson, Mark Roberts, Devender Roberts, Alistair Rose, Guy Rousseau, Bobby Ruge, Brendan Ryan, Taranprit Saluja, Matthias L. Schmid, Aarti Shah, Prad Shanmuga, Anil Sharma, Anna Shawcross, Jeremy Sizer, Manu Shankar-Hari, Richard Smith, Catherine Snelson, Nick Spittle, Nikki Staines, Tom Stambach, Richard Stewart, Pradeep Subudhi, Tamas Szakmany, Kate Tatham, Jo Thomas, Chris Thompson, Robert Thompson, Ascanio Tridente, Darell Tupper-Carey, Mary Twagira, Nick Vallotton, Rama Vancheeswaran, Lisa Vincent-Smith, Shico Visuvanathan, Alan Vuylsteke, Sam Waddy, Rachel Wake, Andrew Walden, Ingeborg Welters, Tony Whitehouse, Paul Whittaker, Ashley Whittington, Padmasayee Papineni, Meme Wijesinghe, Martin Williams, Lawrence Wilson, Stephen Winchester, Martin Wiselka, Adam Wolverson, Daniel G. Wootton, Andrew Workman, Bryan Yates, Peter Young, UK Research and Innovation, Division of Computational and Systems Medicine, Imperial College London, London, SW7 2AZ, UK, Imperial College London - National Heart and Lung Institute, Centre National de la Recherche Scientifique (CNRS), and Apollo - University of Cambridge Repository
Subjects: Molecular biology, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Science, Immunology, Biology, Epitope, Article, A900, 03 medical and health sciences, 0302 clinical medicine, Data sequences, Immune system, COVID-19 Genomics UK (COG-UK) Consortium, Virology, Cytotoxic T cell, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Immune response, Receptor, ISARIC4C Investigators, 030304 developmental biology, 0303 health sciences, Multidisciplinary, C100, A300, C900, 3. Good health, Phylogenetics, 030220 oncology & carcinogenesis, Humoral immunity, [SDV.IMM]Life Sciences [q-bio]/Immunology, CD8
Abstract: We identify amino acid variants within dominant SARS-CoV-2 T-cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T-cells assessed by IFN-γ and cytotoxic killing assays. Complete loss of T-cell responsiveness was seen due to Q213K in the A*01:01-restricted CD8+ ORF3a epitope FTSDYYQLY207-215, due to P13L, P13S and P13T in the B*27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF9-17, and due to T362I and P365S in the A*03:01/A*11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK361-369. CD8+ T-cell lines unable to recognise variant epitopes have diverse T-cell receptor repertoires. These data demonstrate the potential for T-cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T-cell as well as humoral immunity., Graphical Abstract
Published: 2021

22. Correction to: A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

Author: Chris D. Jiggins, Johanna Mappes, Joana I. Meier, Ian A. Warren, Eugenie C Yen, Tomas N Generalovic, Sarah Pelan, Richard Durbin, Juan A. Galarza, Petr Nguyen, and Shane A. McCarthy
Subjects: Arctia plantaginis, Tiger, Evolutionary biology, Haplotype, Sequence assembly, Health Informatics, Biology, Computer Science Applications
Published: 2021

23. The complete genome sequence of Eimeria tenella (Tyzzer 1929), a common gut parasite of chickens [version 1; peer review: 2 approved]

Author: Eerik Aunin, Ulrike Böhme, Damer Blake, Alexander Dove, Michelle Smith, Craig Corton, Karen Oliver, Emma Betteridge, Michael A. Quail, Shane A. McCarthy, Jonathan Wood, Alan Tracey, James Torrance, Ying Sims, Kerstin Howe, Richard Challis, Matthew Berriman, and Adam Reid
Subjects: Science, parasitic diseases, food and beverages, Medicine
Abstract: We present a genome assembly from a clonal population of Eimeria tenella Houghton parasites (Apicomplexa; Conoidasida; Eucoccidiorida; Eimeriidae). The genome sequence is 53.25 megabases in span. The entire assembly is scaffolded into 15 chromosomal pseudomolecules, with complete mitochondrion and apicoplast organellar genomes also present.
Published: 2021

24. Differential use of multiple genetic sex determination systems in divergent ecomorphs of an African crater lake cichlid

Author: Bettina Fischer, Benjamin P. Ngatunga, Shane A. McCarthy, George F. Turner, Iliana Bista, Alexandra M. Tyers, Asilatu Shechonge, M. Emília Santos, Eric A. Miska, Richard Durbin, Hubert Denise, Mingliu Du, Tyler Linderoth, Grégoire Vernaz, Hannah Munby, and Martin J. Genner
Subjects: Haplochromine, Speciation, Evolutionary biology, Cichlid, media_common.quotation_subject, Crater lake, Gene duplication, Tandem exon duplication, Biology, Allele, biology.organism_classification, Genome, media_common
Abstract: African cichlid fishes not only exhibit remarkably high rates of speciation but also have some of the fastest evolving sex determination systems in vertebrates. However, little is known empirically in cichlids about the genetic mechanisms generating new sex-determining variants, what forces dictate their fate, the demographic scales at which they evolve, and whether they are related to speciation. To address these questions, we looked for sex-associated loci in full genome data from 647 individuals of Astatotilapia calliptera from Lake Masoko, a small isolated crater lake in Tanzania, which contains two distinct ecomorphs of the species. We identified three separate XY systems on recombining chromosomes. Two Y alleles derive from mutations that increase expression of the gonadal soma-derived factor gene (gsdf) on chromosome 7; the first is a tandem duplication of the entire gene observed throughout much of the Lake Malawi haplochromine cichlid radiation to which A. calliptera belongs, and the second is a 5 kb insertion directly upstream of gsdf. Both the latter variant and another 700 bp insertion on chromosome 19 responsible for the third Y allele arose from transposable element insertions. Males belonging to the Masoko deep-water benthic ecomorph are determined exclusively by the gsdf duplication, whereas all three Y alleles are used in the Masoko littoral ecomorph, in which they appear to act antagonistically among males with different amounts of benthic admixture. This antagonism in the face of ongoing admixture may be important for sustaining multifactorial sex determination in Lake Masoko. In addition to identifying the molecular basis of three coexisting sex determining alleles, these results demonstrate that genetic interactions between Y alleles and genetic background can potentially affect fitness and adaptive evolution.
Published: 2021

25. The genome sequence of the European turtle dove, Streptopelia turtur Linnaeus 1758

Author: Karen Oliver, Craig Corton, Jonathan Threlfall, Keith C. Hamer, Richard Challis, Michelle Smith, Jale Dolucan, Jason Skelton, Michael A. Quail, James Torrance, Daniel Mead, Sarah Pelan, William Chow, Kerstin Howe, Shane A. McCarthy, Mark Blaxter, Ying Sims, Marcela Uliano-Silva, Jenny C. Dunn, Philip V. Grice, Antony J. Morris, and Emma Betteridge
Subjects: Whole genome sequencing, 0303 health sciences, Medicine (miscellaneous), Sequence assembly, Biology, biology.organism_classification, General Biochemistry, Genetics and Molecular Biology, Streptopelia turtur, law.invention, 03 medical and health sciences, 0302 clinical medicine, Evolutionary biology, law, 030220 oncology & carcinogenesis, C400 Genetics, Columbidae, Turtle (robot), Dove, 030304 developmental biology
Abstract: We present a genome assembly from an individual female Streptopelia turtur (the European turtle dove; Chordata; Aves; Columbidae). The genome sequence is 1.18 gigabases in span. The majority of the assembly is scaffolded into 35 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled.
Published: 2021

26. The genome sequence of the European water vole, Arvicola amphibius Linnaeus 1758

Author: Ying Sims, Francesca Floriana Tricomi, Marcela Uliano Da Silva, Angus I. Carpenter, Jonathan Wood, Emma Betteridge, James Torrance, Sarah Pelan, Shane A. McCarthy, Kerstin Howe, Jale Doulcan, Craig Corton, Richard Challis, Michelle Smith, Daniel Mead, Jonathan Threlfall, Karen Oliver, Mark Blaxter, Michael A. Quail, and Jason Skelton
Subjects: Whole genome sequencing, 0303 health sciences, biology, Medicine (miscellaneous), Sequence assembly, European water vole, Gene Annotation, biology.organism_classification, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Evolutionary biology, Arvicola, Ensembl, Gene, Z601, 030217 neurology & neurosurgery, 030304 developmental biology, Cricetidae
Abstract: We present a genome assembly from an individual male Arvicola amphibius (the European water vole; Chordata; Mammalia; Rodentia; Cricetidae). The genome sequence is 2.30 gigabases in span. The majority of the assembly is scaffolded into 18 chromosomal pseudomolecules, including the X sex chromosome. Gene annotation of this assembly on Ensembl has identified 21,394 protein coding genes.
Published: 2021

27. The genome sequence of the European water vole

Author: Angus I, Carpenter, Michelle, Smith, Craig, Corton, Karen, Oliver, Jason, Skelton, Emma, Betteridge, Jale, Doulcan, Michael A, Quail, Shane A, McCarthy, Marcela, Uliano Da Silva, Kerstin, Howe, James, Torrance, Jonathan, Wood, Sarah, Pelan, Ying, Sims, Francesca Floriana, Tricomi, Richard, Challis, Jonathan, Threlfall, Daniel, Mead, and Mark, Blaxter
Abstract: We present a genome assembly from an individual male
Published: 2021

28. The genome sequence of the brown trout

Author: Tom, Hansen, Per Gunnar, Fjelldal, Sigbjørn, Lien, Michelle, Smith, Craig, Corton, Karen, Oliver, Jason, Skelton, Emma, Betteridge, Jale, Doulcan, Olivier, Fedrigo, Jacquelyn, Mountcastle, Erich, Jarvis, Shane A, McCarthy, William, Chow, Kerstin, Howe, James, Torrance, Jonathan, Wood, Ying, Sims, Leanne, Haggerty, Richard, Challis, Jonathan, Threlfall, Daniel, Mead, Richard, Durbin, and Mark, Blaxter
Subjects: brown trout, animal diseases, genome sequence, Salmo trutta, Articles, Data Note, chromosomal
Abstract: We present a genome assembly from an individual female Salmo trutta (the brown trout; Chordata; Actinopteri; Salmoniformes; Salmonidae). The genome sequence is 2.37 gigabases in span. The majority of the assembly is scaffolded into 40 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl has identified 43,935 protein coding genes.
Published: 2021

29. The genome sequence of the European golden eagle, Aquila chrysaetos chrysaetos Linnaeus 1758

Author: Michael A. Quail, William Chow, Matthew Loose, Emma Betteridge, Dan Mead, Craig Corton, Shane A. McCarthy, Rob Ogden, Nadine Holmes, Jason Skelton, Anna Meredith, Karen Oliver, Victoria Wright, Joanna Collins, Richard Durbin, Gabriela Peniche, James Torrance, Richard Challis, Michelle Smith, Mark Blaxter, Jale Doulcan, and Kerstin Howe
Subjects: 0106 biological sciences, Whole genome sequencing, Eagle, 0303 health sciences, biology, Aquila chrysaetos, genome sequence, Medicine (miscellaneous), Sequence assembly, European golden eagle, Articles, biology.organism_classification, Data Note, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Evolutionary biology, biology.animal, Accipitridae, chromosomal, 030304 developmental biology
Abstract: We present a genome assembly from an individual female Aquila chrysaetos chrysaetos (the European golden eagle; Chordata; Aves; Accipitridae). The genome sequence is 1.23 gigabases in span. The majority of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the W and Z sex chromosomes.
Published: 2021

30. The genome sequence of the Norway rat, Rattus norvegicus Berkenhout 1769 [version 1; peer review: 2 approved]

Author: Kerstin Howe, Melinda Dwinell, Mary Shimoyama, Craig Corton, Emma Betteridge, Alexander Dove, Michael A. Quail, Michelle Smith, Laura Saba, Robert W. Williams, Hao Chen, Anne E. Kwitek, Shane A. McCarthy, Marcela Uliano-Silva, William Chow, Alan Tracey, James Torrance, Ying Sims, Richard Challis, Jonathan Threlfall, and Mark Blaxter
Subjects: Science, Medicine
Abstract: We present a genome assembly from an individual male Rattus norvegicus (the Norway rat; Chordata; Mammalia; Rodentia; Muridae). The genome sequence is 2.44 gigabases in span. The majority of the assembly is scaffolded into 20 chromosomal pseudomolecules, with both X and Y sex chromosomes assembled. This genome assembly, mRatBN7.2, represents the new reference genome for R. norvegicus and has been adopted by the Genome Reference Consortium.
Published: 2021

31. The genome sequence of the European golden eagle, Aquila chrysaetos chrysaetos Linnaeus 1758 [version 1; peer review: 2 approved]

Author: Dan Mead, Rob Ogden, Anna Meredith, Gabriela Peniche, Michelle Smith, Craig Corton, Karen Oliver, Jason Skelton, Emma Betteridge, Jale Doulcan, Nadine Holmes, Victoria Wright, Matt Loose, Michael A. Quail, Shane A. McCarthy, Kerstin Howe, William Chow, James Torrance, Joanna Collins, Richard Challis, Richard Durbin, and Mark Blaxter
Subjects: Science, Medicine
Abstract: We present a genome assembly from an individual female Aquila chrysaetos chrysaetos (the European golden eagle; Chordata; Aves; Accipitridae). The genome sequence is 1.23 gigabases in span. The majority of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the W and Z sex chromosomes.
Published: 2021

32. The genome sequence of the Norway rat, Rattus norvegicus Berkenhout 1769

Author: Emma Betteridge, Laura Saba, Anne E. Kwitek, William Chow, Mary Shimoyama, Shane A. McCarthy, Marcela Uliano-Silva, Alan Tracey, Robert W. Williams, Michael A. Quail, James Torrance, Kerstin Howe, Richard Challis, Michelle Smith, Hao Chen, Mark Blaxter, Craig Corton, Alexander Dove, Ying Sims, Jonathan Threlfall, and Melinda R. Dwinell
Subjects: viruses, genome sequence, Medicine (miscellaneous), Sequence assembly, Data Note, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Genome Reference Consortium, chromosomal, reference genome, 030304 developmental biology, Muridae, Genetics, Whole genome sequencing, 0303 health sciences, biology, virus diseases, Articles, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Rattus norvegicus, digestive system diseases, 030217 neurology & neurosurgery, Reference genome, Norway rat
Abstract: We present a genome assembly from an individual male Rattus norvegicus (the Norway rat; Chordata; Mammalia; Rodentia; Muridae). The genome sequence is 2.44 gigabases in span. The majority of the assembly is scaffolded into 20 chromosomal pseudomolecules, with both X and Y sex chromosomes assembled. This genome assembly, mRatBN7.2, represents the new reference genome for R. norvegicus and has been adopted by the Genome Reference Consortium.
Published: 2021

33. Genomic consequences of domestication of the Siamese fighting fish

Author: Lichak Mr, Vranken N, Hoge C, von Lintig J, Iliana Bista, Shane A. McCarthy, Jonathan Wood, Kwon Y, Bandara S, Hannes Svardal, Kerstin Howe, Heok Hui Tan, Camacho-Garcia J, Lukas Rüber, Richard Durbin, William Chow, Andres Bendesky, and Francis Kx
Subjects: Species complex, Betta, Directional selection, Evolutionary biology, Human evolutionary genetics, Locus (genetics), Biology, Domestication, Betta splendens, biology.organism_classification, Genome
Abstract: Siamese fighting fish, commonly known as betta, are among the world’s most popular and morphologically diverse pet fish, but the genetic processes leading to their domestication and phenotypic diversification are largely unknown. We assembled de novo the genome of a wildBetta splendensand whole-genome sequenced multiple individuals across five species within theB. splendensspecies complex, including wild populations and domesticated ornamental betta. Given our estimate of the mutation rate from pedigrees, our analyses suggest that betta were domesticated at least 1,000 years ago, centuries earlier than previously thought. Ornamental betta individuals have variable contributions from otherBettaspecies and have also introgressed into wild populations of those species. We identifydmrt1as the main sex determination gene in ornamental betta but not in wildB. splendens, and find evidence for recent directional selection at the X-allele of the locus. Furthermore, we find genes with signatures of recent, strong selection that have large effects on color in specific parts of the body, or the shape of individual fins, and are almost all unlinked. Our results demonstrate how simple genetic architectures paired with anatomical modularity can lead to vast phenotypic diversity generated during animal domestication, and set the stage for using betta as a modern system for evolutionary genetics.One-Sentence SummaryGenomic analyses reveal betta fish were domesticated more than 1,000 years ago and the genes that changed in the process.
Published: 2021

34. A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia illucens L.)

Author: Chris D. Jiggins, Miha Pipan, Tomas N Generalovic, James Torrance, Kerstin Howe, Shane A. McCarthy, Ian A. Warren, Jonathan Wood, Michael A. Quail, Richard Durbin, Ying Sims, Generalovic, Tomas N [0000-0002-8983-1024], Durbin, Richard [0000-0002-9130-1006], and Apollo - University of Cambridge Repository
Subjects: AcademicSubjects/SCI01140, Hermetia illucens, genome annotation, AcademicSubjects/SCI00010, Population, Sequence assembly, inbreeding, Genomics, Computational biology, Biology, Runs of Homozygosity, QH426-470, Hi-C assembly, AcademicSubjects/SCI01180, Genome, Chromosomes, Population genomics, 03 medical and health sciences, domestication, 0302 clinical medicine, BRAKER2, Genetics, Animals, education, Molecular Biology, Genetics (clinical), 030304 developmental biology, Repetitive Sequences, Nucleic Acid, PacBio, 0303 health sciences, education.field_of_study, Contig, Diptera, Genome project, biology.organism_classification, Genome Report, genome assembly, AcademicSubjects/SCI00960, 030217 neurology & neurosurgery, Reference genome, Black Soldier Fly
Abstract: BackgroundHermetia illucens L. (Diptera: Stratiomyidae), the Black Soldier Fly (BSF) is an increasingly important mass reared entomological resource for bioconversion of organic material into animal feed.ResultsWe generated a high-quality chromosome-scale genome assembly of the BSF using Pacific Bioscience, 10X Genomics linked read and high-throughput chromosome conformation capture sequencing technology. Scaffolding the final assembly with Hi-C data produced a highly contiguous 1.01 Gb genome with 99.75% of scaffolds assembled into pseudo-chromosomes representing seven chromosomes with 16.01 Mb contig and 180.46 Mb scaffold N50 values. The highly complete genome obtained a BUSCO completeness of 98.6%. We masked 67.32% of the genome as repetitive sequences and annotated a total of 17,664 protein-coding genes using the BRAKER2 pipeline. We analysed an established lab population to investigate the genomic variation and architecture of the BSF revealing six autosomes and the identification of an X chromosome. Additionally, we estimated the inbreeding coefficient (1.9%) of a lab population by assessing runs of homozygosity. This revealed a plethora of inbreeding events including recent long runs of homozygosity on chromosome five.ConclusionsRelease of this novel chromosome-scale BSF genome assembly will provide an improved platform for further genomic studies and functional characterisation of candidate regions of artificial selection. This reference sequence will provide an essential tool for future genetic modifications, functional and population genomics.
Published: 2021
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35. The genome sequence of the brown trout, Salmo trutta Linnaeus 1758

Author: Erich D. Jarvis, Jonathan Threlfall, James Torrance, Jacquelyn Mountcastle, Jale Doulcan, Karen Oliver, Emma Betteridge, Richard Durbin, William Chow, Craig Corton, Richard Challis, Michelle Smith, Ying Sims, Kerstin Howe, Jason Skelton, Leanne Haggerty, Shane A. McCarthy, Daniel Mead, Mark Blaxter, Jonathan Wood, Olivier Fedrigo, Sigbjørn Lien, Per Gunnar Fjelldal, and Tom Hansen
Subjects: 0106 biological sciences, Whole genome sequencing, 0303 health sciences, biology, viruses, Salmoniformes, animal diseases, virus diseases, Medicine (miscellaneous), Sequence assembly, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, digestive system diseases, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Brown trout, Evolutionary biology, Ensembl, Salmo, Gene, Salmonidae, 030304 developmental biology
Abstract: We present a genome assembly from an individual female Salmo trutta (the brown trout; Chordata; Actinopteri; Salmoniformes; Salmonidae). The genome sequence is 2.37 gigabases in span. The majority of the assembly is scaffolded into 40 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl has identified 43,935 protein coding genes.
Published: 2021

36. Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

Author: Jennifer Balacco, Sylke Winkler, Jason Skelton, Jacquelyn Mountcastle, Roberto Ambrosini, Giulio Formenti, Olivier Fedrigo, Karen Oliver, Iliana Bista, Marco Rosario Capodiferro, Simon Mayes, David S. Horner, Alessandro Achilli, Samara Brown, Emma Betteridge, Sergey Koren, Alan Tracey, Shane A. McCarthy, Jonas Korlach, Craig Corton, Edward L. Braun, Bettina Haase, Adam M. Phillippy, Marcela Uliano-Silva, Jonathan Wood, Erich D. Jarvis, Eugene W. Myers, Woori Kwak, Matteo Chiara, Vania Costa, Daniel Fordham, Arkarachai Fungtammasan, Farooq O. Al-Ajli, Peter Houde, Michelle Smith, Jale Dolucan, Kerstin Howe, James Torrance, Arang Rhie, Richard Durbin, Formenti, Giulio [0000-0002-7554-5991], and Apollo - University of Cambridge Repository
Subjects: Mitochondrial DNA, QH301-705.5, Assembly, Sequence assembly, QH426-470, Long reads, Genome, Novel gene, Evolution, Molecular, 03 medical and health sciences, biology.animal, Gene Duplication, Genetics, Animals, Sequencing, Biology (General), Gene, 030304 developmental biology, Repetitive Sequences, Nucleic Acid, 0303 health sciences, biology, Vertebrate, Research, 030302 biochemistry & molecular biology, Computational Biology, High-Throughput Nucleotide Sequencing, Duplications, Repetitive Regions, Genomics, Repeats, Human genetics, Evolutionary biology, Genome, Mitochondrial, Vertebrates
Abstract: Background Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. Results As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100–300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization. Conclusions Our results indicate that even in the “simple” case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.
Published: 2021

37. Author response: Population-scale proteome variation in human induced pluripotent stem cells

Author: Helena Kilpinen, Rachel Denton, Francesco Paolo Casale, Ewan Birney, Laura Clarke, Christopher M. Kirton, Natalie Moens, Daniel D Seaton, Alex Alderton, Alejandro Brenes, Petr Danecek, Angus I. Lamond, Oliver Stegle, Dalila Bensaddek, Chukwuma A. Agu, Minal Patel, Angela Goncalves, Ian Streeter, Anja Kolb-Kokocinski, Peter W. Harrison, Marc Jan Bonder, Shane A. McCarthy, Philip L. Beales, Reena Halai, Bogdan Mirauta, Davide Denovi, Willem H. Ouwehand, Ruta Meleckyte, Sarah Harper, Andreas Leha, Richard Durbin, Fiona M. Watt, Yasin Memari, and Daniel J. Gaffney
Subjects: education.field_of_study, Variation (linguistics), Scale (ratio), Population, Proteome, Computational biology, Human Induced Pluripotent Stem Cells, Biology, education
Published: 2020

38. Complete vertebrate mitogenomes reveal widespread gene duplications and repeats

Author: Sylke Winkler, Daniel Fordham, Marcela Uliano-Silva, Samara Brown, Emma Betteridge, James Torrance, David S. Horner, Shane A. McCarthy, Jennifer Balacco, Alan Tracey, Simon Mayes, Farooq O. Al-Ajli, Matteo Chiara, Sergey Koren, Edward L. Braun, Michelle Smith, Jason Skelton, Arang Rhie, Richard Durbin, Alessandro Achilli, Craig Corton, Vania Costa, Iliana Bista, Bettina Haase, Peter Houde, Olivier Fedrigo, Marco Rosario Capodiferro, Erich D. Jarvis, Woori Kwak, Jonas Korlach, Jacquelyn Mountcastle, Giulio Formenti, Karen Oliver, Jonathan Wood, Kerstin Howe, Jale Dolucan, Eugene W. Myers, Roberto Ambrosini, Arkarachai Fungtammasan, and Adam M. Phillippy
Subjects: Novel gene, Mitochondrial DNA, Fully automated, biology, biology.animal, Sequence assembly, Vertebrate, Tissue type, Computational biology, Genome, Gene
Abstract: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. As part of the Vertebrate Genomes Project (VGP) we have developed mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (>10 kbp, PacBio or Nanopore) and short (100-300 bp, Illumina) reads. Our pipeline led to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We have observed that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we have identified errors, missing sequences, and incomplete genes in those references, particularly in repeat regions. Our assemblies have also identified novel gene region duplications, shedding new light on mitochondrial genome evolution and organization.
Published: 2020

39. The genome sequence of the channel bull blenny, Cottoperca gobio (Günther, 1861)

Author: Eric A. Miska, William Chow, John H. Postlethwait, Iliana Bista, Zemin Ning, Michelle Smith, Jonathan Wood, Thomas Desvignes, James Torrance, Karen Oliver, Shane A. McCarthy, H. William Detrich, Kerstin Howe, and Richard Durbin
Subjects: 0106 biological sciences, Cottoperca gobio, Medicine (miscellaneous), Sequence assembly, Notothenioidei, Data Note, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, channel bull blenny, Ensembl, 14. Life underwater, Gene, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, biology, genome assembly chromosomal, Actinopterygii, Gene Annotation, Articles, biology.organism_classification, Evolutionary biology
Abstract: We present a genome assembly for Cottoperca gobio (channel bull blenny, (Günther, 1861)); Chordata; Actinopterygii (ray-finned fishes), a temperate water outgroup for Antarctic Notothenioids. The size of the genome assembly is 609 megabases, with the majority of the assembly scaffolded into 24 chromosomal pseudomolecules. Gene annotation on Ensembl of this assembly has identified 21,662 coding genes.
Published: 2020

40. The genome sequence of the channel bull blenny, Cottoperca gobio (Günther, 1861) [version 1; peer review: 2 approved]

Author: Iliana Bista, Shane A. McCarthy, Jonathan Wood, Zemin Ning, H. William Detrich III, Thomas Desvignes, John Postlethwait, William Chow, Kerstin Howe, James Torrance, Michelle Smith, Karen Oliver, Vertebrate Genomes Project Consortium, Eric A. Miska, and Richard Durbin
Subjects: lcsh:R, lcsh:Medicine, lcsh:Q, lcsh:Science
Abstract: We present a genome assembly for Cottoperca gobio (channel bull blenny, (Günther, 1861)); Chordata; Actinopterygii (ray-finned fishes), a temperate water outgroup for Antarctic Notothenioids. The size of the genome assembly is 609 megabases, with the majority of the assembly scaffolded into 24 chromosomal pseudomolecules. Gene annotation on Ensembl of this assembly has identified 21,662 coding genes.
Published: 2020

41. Towards complete and error-free genome assemblies of all vertebrate species

Author: Claudio V. Mello, H. William Detrich, Oliver A. Ryder, George F. Turner, Robert H. S. Kraus, Daryl Eason, Sergey Koren, Stephen J. O'Brien, Ivan Sović, Tandy Warnow, Dave W Burt, Martin Pippel, Mark Diekhans, Jonathan Wood, Sylke Winkler, Joana Damas, Benedict Paten, Shane A. McCarthy, Gregory Gedman, M. Thomas P. Gilbert, David F. Clayton, Erich D. Jarvis, Frank Grützner, Richard E. Green, Andrew J. Crawford, Federica Di Palma, Jason T. Howard, Fergal J. Martin, Brett T. Hannigan, Samantha R. Friedrich, Emma C. Teeling, David Iorns, Woori Kwak, Maximilian Wagner, Iliana Bista, Hiram Clawson, Milan Malinsky, Peter V. Lovell, Gavin J. P. Naylor, Robert S. Harris, Ekaterina Osipova, Sadye Paez, Christopher N. Balakrishnan, Eugene W. Myers, Byrappa Venkatesh, Brian P. Walenz, Warren E. Johnson, Nicholas H. Putnam, Harris A. Lewin, Hannes Svardal, Leanne Haggerty, Andreas F. Kautt, Tomas Marques-Bonet, Luis R Nassar, Maria Simbirsky, Christopher Dunn, William Chow, Marlys L. Houck, Paolo Franchini, Joanna Collins, Jinna Hoffman, Sonja C. Vernes, Alan Tracey, Siddarth Selvaraj, Sarah E. London, Ann C Misuraca, Heebal Kim, Byung June Ko, Trevor Pesout, Françoise Thibaud-Nissen, Jimin George, Jennifer A. Marshall Graves, Arang Rhie, Ying Sims, Mark Wilkinson, Robert W. Murphy, Dengfeng Guan, Axel Meyer, Richard Durbin, Arkarachai Fungtammasan, Sarah Pelan, Lindsey J. Cantin, Erik Garrison, Kerstin Howe, Farooq O. Al-Ajli, Zev N. Kronenberg, Michelle Smith, Paul Flicek, James Torrance, Guojie Zhang, J. H. Kim, Richard Hall, Tanya M. Lama, David Haussler, Matthew T. Biegler, Klaus-Peter Koepfli, Beth Shapiro, Bettina Haase, Andrew Digby, Wesley C. Warren, Alex Hastie, Adam M. Phillippy, Paul Medvedev, Marcela Uliano-Silva, Mark Mooney, Constantina Theofanopoulou, Karen Clark, Chul Hee Lee, Zemin Ning, Olivier Fedrigo, Taylor Edwards, Simona Secomandi, Joyce V. Lee, Jonas Korlach, Patrick Masterson, Jay Ghurye, Jacquelyn Mountcastle, Giulio Formenti, Yang Zhou, Kevin L. Howe, Sarah B. Kingan, and Kateryna D. Makova
Subjects: Biodiversity conservation, Extant taxon, biology, Evolutionary biology, biology.animal, Vertebrate, Genomics, Sources of error, Genome, Reference genome
Abstract: High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are only available for a few non-microbial species1–4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling the most accurate and complete reference genomes to date. Here we summarize these developments, introduce a set of quality standards, and present lessons learned from sequencing and assembling 16 species representing major vertebrate lineages (mammals, birds, reptiles, amphibians, teleost fishes and cartilaginous fishes). We confirm that long-read sequencing technologies are essential for maximizing genome quality and that unresolved complex repeats and haplotype heterozygosity are major sources of error in assemblies. Our new assemblies identify and correct substantial errors in some of the best historical reference genomes. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an effort to generate high-quality, complete reference genomes for all ~70,000 extant vertebrate species and help enable a new era of discovery across the life sciences.
Published: 2020

42. The genome sequence of the Eurasian river otter, Lutra lutra Linnaeus 1758

Author: Arina D. Omer, Olga Dudchenko, Shane A. McCarthy, Emma Betteridge, Ying Sims, Karen Oliver, Jason Skelton, Craig Corton, Kerstin Howe, Erez Lieberman Aiden, Roberto Portela Miguez, Jale Doulcan, Frank Hailer, David Weisz, Dan Mead, Elisabeth A Chadwick, Richard Durbin, James Torrance, Richard Challis, Michelle Smith, Mark Blaxter, Alan Tracey, Hailer, Frank [0000-0002-2340-1726], Portela Miguez, Roberto [0000-0003-3094-9949], Doulcan, Jale Doulcan [0000-0002-3551-1770], McCarthy, Shane [0000-0002-2715-4187], Howe, Kerstin [0000-0003-2237-513X], Tracey, Alan [0000-0002-4805-9058], Challis, Richard [0000-0002-3502-1122], Durbin, Richard [0000-0002-9130-1006], Blaxter, Mark [0000-0003-2861-949X], and Apollo - University of Cambridge Repository
Subjects: River otter, geography.river, Whole genome sequencing, 0303 health sciences, geography, biology, Mustelidae, Medicine (miscellaneous), Sequence assembly, Articles, Data Note, biology.organism_classification, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Eutheria, Evolutionary biology, Lutra lutra river otter genome sequence chromosomal, Lutra, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: We present a genome assembly from an individual male Lutra lutra (the Eurasian river otter; Vertebrata; Mammalia; Eutheria; Carnivora; Mustelidae). The genome sequence is 2.44 gigabases in span. The majority of the assembly is scaffolded into 20 chromosomal pseudomolecules, with both X and Y sex chromosomes assembled.
Published: 2020
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43. Insights into human genetic variation and population history from 929 diverse genomes

Author: Howard M. Cann, Shane A. McCarthy, Chris Tyler-Smith, David Reich, Aylwyn Scally, Qasim Ayub, Pontus Skoglund, Petr Danecek, Jean-François Deleuze, Manjinder S. Sandhu, Pille Hallast, Ruoyun Hui, Yuan Chen, Swapan Mallick, Yali Xue, Sabine Felkel, Anders Bergström, Hélène Blanché, Mohamed A. Almarri, Jack Kamm, Richard Durbin, Bergström, Anders [0000-0002-4096-9268], McCarthy, Shane A [0000-0002-2715-4187], Hui, Ruoyun [0000-0002-5689-7131], Almarri, Mohamed A [0000-0003-1255-0918], Ayub, Qasim [0000-0003-3291-0917], Danecek, Petr [0000-0002-4159-1666], Felkel, Sabine [0000-0001-8935-8305], Hallast, Pille [0000-0002-0588-3987], Kamm, Jack [0000-0003-2412-756X], Blanché, Hélène [0000-0003-2115-575X], Deleuze, Jean-François [0000-0002-5358-4463], Mallick, Swapan [0000-0002-4531-4439], Reich, David [0000-0002-7037-5292], Skoglund, Pontus [0000-0002-3021-5913], Scally, Aylwyn [0000-0002-0807-1167], Durbin, Richard [0000-0002-9130-1006], Tyler-Smith, Chris [0000-0002-6492-5403], and Apollo - University of Cambridge Repository
Subjects: Neanderthal, Population structure, Human genetic variation, Genome, 0302 clinical medicine, INDEL Mutation, Genetics (clinical), health care economics and organizations, Phylogeny, Neanderthals, 0303 health sciences, education.field_of_study, Multidisciplinary, Population size, 030305 genetics & heredity, Hominidae, 3. Good health, Asia, DNA Copy Number Variations, Population, education, Oceania, Genome, Viral, Biology, Polymorphism, Single Nucleotide, DNA sequencing, Article, 03 medical and health sciences, biology.animal, Genetic variation, Genetics, Population growth, Animals, Humans, Molecular Biology, Denisovan, 030304 developmental biology, Whole genome sequencing, Population Density, Whole Genome Sequencing, Genome, Human, Racial Groups, Central africa, Genetic Variation, 15. Life on land, biology.organism_classification, Genetics, Population, Haplotypes, Evolutionary biology, Africa, Human genome, Americas, Genome, Bacterial, 030217 neurology & neurosurgery
Abstract: INTRODUCTION: Large-scale human genome sequencing studies to date have been limited to large, metropolitan populations or to small numbers of genomes from each group. Much remains to be understood about the extent and structure of genetic variation in our species and how it was shaped by past population separations, admixture, adaptation, size changes, and gene flow from archaic human groups. Larger numbers of genome sequences from more diverse populations are needed to illuminate these questions. RATIONALE: We sequence 929 genomes from 54 geographically, linguistically and culturally diverse human populations to an average of 35x coverage, and analyze the variation among them. We also physically resolve the haplotype phase of 26 of these genomes using linked-read sequencing. RESULTS: We identify 67.3 million single-nucleotide polymorphisms (SNPs), 8.8 million small insertions or deletions (indels) and 40,736 copy number variants (CNVs). This includes hundreds of thousands of variants that had not been discovered by previous sequencing efforts but which are common in one or more population. We demonstrate benefits to the study of population relationships of genome sequences over ascertained array genotypes, particularly when involving African populations. Populations in central and southern Africa, the Americas and Oceania each harbour tens to hundreds of thousands of private, common genetic variants. The majority of these variants arose as novel mutations rather than through archaic introgression, except in Oceanian populations where many private variants derive from Denisovan admixture. While some reach high frequencies, no variants are fixed between major geographical regions. We estimate that the genetic separation between present-day human populations occurred mostly within the last 250,000 years. However, these early separations were gradual in nature and shaped by protracted gene flow. All populations thus still had some genetic contact more recently than this, but there is also evidence that a small fraction of present-day structure might be hundreds of thousands of years older. Most populations expanded in size over the last 10,000 years, but hunter-gatherer groups did not. The low diversity among the Neanderthal haplotypes segregating in present-day populations indicates that, while more than one Neanderthal individual must have contributed genetic material to modern humans, there was likely only one major episode of admixture. In contrast, Denisovan haplotype diversity reflects a more complex history involving more than one episode of admixture. We find small amounts of Neanderthal ancestry in West African genomes, most likely reflecting Eurasian admixture. Despite their very low levels or absence of archaic ancestry, African populations share many Neanderthal and Denisovan variants that are absent from Eurasia, reflecting how a larger proportion of the ancestral human variation has been maintained in Africa. CONCLUSION: The discovery of substantial amounts of common genetic variation that was previously undocumented, and is geographically restricted, highlights the continued value of anthropologically informed study designs for understanding human diversity. The genome sequences presented here are a freely available resource with relevance to population history, medical genetics, anthropology and linguistics. [Figure: see text]
Published: 2020

44. A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

Author: Petr Nguyen, Joana I. Meier, Eugenie C Yen, Johanna Mappes, Chris D. Jiggins, Ian A. Warren, Sarah Pelan, Juan A. Galarza, Richard Durbin, Tomas N Generalovic, Shane A. McCarthy, McCarthy, Shane [0000-0002-2715-4187], Generalovic, Tomas [0000-0002-8983-1024], Meier, Joana [0000-0001-7726-2875], Durbin, Richard [0000-0002-9130-1006], Jiggins, Chris [0000-0002-7809-062X], and Apollo - University of Cambridge Repository
Subjects: 0106 biological sciences, haplotype, population genomics, AcademicSubjects/SCI02254, Population, Sequence assembly, Health Informatics, wood tiger moth, Arctia plantaginis, Moths, Biology, Data Note, genotyyppi, 010603 evolutionary biology, 01 natural sciences, Genome, täpläsiilikäs, Population genomics, Loss of heterozygosity, 03 medical and health sciences, Consensus sequence, Animals, Humans, education, 030304 developmental biology, 0303 health sciences, education.field_of_study, Genetic diversity, trio binning, Haplotype, Karyotype, genomiikka, Genomics, Wood, Computer Science Applications, Lepidoptera, Haplotypes, annotation, populaatiogenetiikka, Evolutionary biology, perimä, genome assembly, AcademicSubjects/SCI00960, Corrigendum
Abstract: Background Diploid genome assembly is typically impeded by heterozygosity because it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an innovative solution that exploits heterozygosity for assembly. Short, parental reads are used to assign parental origin to long reads from their F1 offspring before assembly, enabling complete haplotype resolution. Trio binning could therefore provide an effective strategy for assembling highly heterozygous genomes, which are traditionally problematic, such as insect genomes. This includes the wood tiger moth (Arctia plantaginis), which is an evolutionary study system for warning colour polymorphism. Findings We produced a high-quality, haplotype-resolved assembly for Arctia plantaginis through trio binning. We sequenced a same-species family (F1 heterozygosity ∼1.9%) and used parental Illumina reads to bin 99.98% of offspring Pacific Biosciences reads by parental origin, before assembling each haplotype separately and scaffolding with 10X linked reads. Both assemblies are contiguous (mean scaffold N50: 8.2 Mb) and complete (mean BUSCO completeness: 97.3%), with annotations and 31 chromosomes identified through karyotyping. We used the assembly to analyse genome-wide population structure and relationships between 40 wild resequenced individuals from 5 populations across Europe, revealing the Georgian population as the most genetically differentiated with the lowest genetic diversity. Conclusions We present the first invertebrate genome to be assembled via trio binning. This assembly is one of the highest quality genomes available for Lepidoptera, supporting trio binning as a potent strategy for assembling heterozygous genomes. Using our assembly, we provide genomic insights into the geographic population structure of A. plantaginis.
Published: 2020
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45. The genome sequence of the eastern grey squirrel

Author: Dan, Mead, Kathryn, Fingland, Rachel, Cripps, Roberto, Portela Miguez, Michelle, Smith, Craig, Corton, Karen, Oliver, Jason, Skelton, Emma, Betteridge, Jale, Doulcan, Michael A, Quail, Shane A, McCarthy, Kerstin, Howe, Ying, Sims, James, Torrance, Alan, Tracey, Richard, Challis, Richard, Durbin, and Mark, Blaxter
Subjects: genome sequence, Articles, Data Note, Sciurus carolinensis, chromosomal, grey squirrel
Abstract: We present a genome assembly from an individual male Sciurus carolinensis (the eastern grey squirrel; Vertebrata; Mammalia; Eutheria; Rodentia; Sciuridae). The genome sequence is 2.82 gigabases in span. The majority of the assembly (92.3%) is scaffolded into 21 chromosomal-level scaffolds, with both X and Y sex chromosomes assembled.
Published: 2020

46. The genome sequence of the Eurasian red squirrel, Sciurus vulgaris Linnaeus 1758

Author: Roberto Portela Miguez, Olga Dudchenko, Jason Skelton, Shane A. McCarthy, Alan Tracey, Erich D. Jarvis, Jale Dolucan, David Weisz, Rachel Cripps, Emma Betteridge, Richard Challis, Michelle Smith, Erez Lieberman Aiden, Olivier Fedrigo, Kathryn Fingland, Jacquelyn Mountcastle, Kerstin Howe, Craig Corton, Richard Durbin, Arina D. Omer, Karen Oliver, James Torrance, Mark Blaxter, Ying Sims, and Daniel Mead
Subjects: 0106 biological sciences, Whole genome sequencing, Sciurus vulgaris, 0303 health sciences, Eurasian red squirrel, biology, red squirrel, genome sequence, Medicine (miscellaneous), Sequence assembly, Articles, biology.organism_classification, Data Note, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Eutheria, Evolutionary biology, chromosomal, 030304 developmental biology, Sciurus
Abstract: We present a genome assembly from an individual male Sciurus vulgaris (the Eurasian red squirrel; Vertebrata; Mammalia; Eutheria; Rodentia; Sciuridae). The genome sequence is 2.88 gigabases in span. The majority of the assembly is scaffolded into 21 chromosomal-level scaffolds, with both X and Y sex chromosomes assembled.
Published: 2020

47. The genome sequence of the Eurasian red squirrel, Sciurus vulgaris Linnaeus 1758 [version 1; peer review: 2 approved]

Author: Daniel Mead, Kathryn Fingland, Rachel Cripps, Roberto Portela Miguez, Michelle Smith, Craig Corton, Karen Oliver, Jason Skelton, Emma Betteridge, Jale Dolucan, Olga Dudchenko, Arina D. Omer, David Weisz, Erez Lieberman Aiden, Olivier Fedrigo, Jacquelyn Mountcastle, Erich Jarvis, Shane A. McCarthy, Ying Sims, James Torrance, Alan Tracey, Kerstin Howe, Richard Challis, Richard Durbin, and Mark Blaxter
Subjects: lcsh:R, lcsh:Medicine, lcsh:Q, lcsh:Science
Abstract: We present a genome assembly from an individual male Sciurus vulgaris (the Eurasian red squirrel; Vertebrata; Mammalia; Eutheria; Rodentia; Sciuridae). The genome sequence is 2.88 gigabases in span. The majority of the assembly is scaffolded into 21 chromosomal-level scaffolds, with both X and Y sex chromosomes assembled.
Published: 2020

48. The Gene-Rich Genome of the Scallop Pecten maximus

Author: Emma Betteridge, David Weisz, Sarah Pelan, Olga Dudchenko, Karen Oliver, Nathan J. Kenny, Yan Ryan, Shane A. McCarthy, Suzanne T. Williams, Erez Lieberman Aiden, Jason Skelton, Kerstin Howe, Ying Sims, Anil Wipat, Michelle Smith, Katherine James, Arina D. Omer, Dan Mead, James Torrance, Jale Dolucan, Craig Corton, McCarthy, Shane [0000-0002-2715-4187], and Apollo - University of Cambridge Repository
Subjects: 0106 biological sciences, Range (biology), AcademicSubjects/SCI02254, Sequence assembly, Health Informatics, Biology, Data Note, 010603 evolutionary biology, 01 natural sciences, Genome, DNA sequencing, bivalve, 03 medical and health sciences, chemistry.chemical_compound, mollusc, Animals, Pecten maximus, 14. Life underwater, domoic, Gene, Genetic Association Studies, Phylogeny, 030304 developmental biology, Saxitoxin, Pecten, 0303 health sciences, Computational Biology, Domoic acid, Genomics, neurotoxin, Gene Annotation, C700, biology.organism_classification, Computer Science Applications, scallop, Phenotype, chemistry, Evolutionary biology, Scallop, AcademicSubjects/SCI00960
Abstract: BackgroundThe King Scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and its ubiquity means that it plays a key role in coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which it has evolved some immunity. The molecular origins of this immunity are of interest to evolutionary biologists, pharmaceutical companies and fisheries management.FindingsHere we report the genome sequencing of this species, conducted as part of the Wellcome Sanger 25 Genomes Project. This genome was assembled from PacBio reads and scaffolded with 10x Chromium and Hi-C data, and its 3,983 scaffolds have an N50 of 44.8 Mb (longest scaffold 60.1 Mb), with 92% of the assembly sequence contained in 19 scaffolds, corresponding to the 19 chromosomes found in this species. The total assembly spans 918.3 Mb, and is the best-scaffolded marine bivalve genome published to date, exhibiting 95.5% recovery of the metazoan BUSCO set. Gene annotation resulted in 67,741 gene models. Analysis of gene content revealed large numbers of gene duplicates, as previously seen in bivalves, with little gene loss, in comparison with the sequenced genomes of other marine bivalve species.ConclusionsThe genome assembly of Pecten maximus and its annotated gene set provide a high-quality platform for a wide range of investigations, including studies on such disparate topics as shell biomineralization, pigmentation, vision and resistance to algal toxins. As a result of our findings we highlight the sodium channel gene Nav1, known as a gene conferring resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid.
Published: 2020
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49. The complete genome sequence of Eimeria tenella (Tyzzer 1929), a common gut parasite of chickens

Author: Jonathan Wood, James Torrance, Richard Challis, Michelle Smith, Alexander Dove, Ying Sims, Craig Corton, Matthew Berriman, Shane A. McCarthy, Ulrike Böhme, Kerstin Howe, Michael A. Quail, Adam J. Reid, Emma Betteridge, Alan Tracey, Damer P. Blake, Eerik Aunin, and Karen Oliver
Subjects: Eimeriidae, Whole genome sequencing, Genetics, Apicoplast, biology, genome sequence, food and beverages, Medicine (miscellaneous), Sequence assembly, Articles, Data Note, biology.organism_classification, Eucoccidiorida, Genome, General Biochemistry, Genetics and Molecular Biology, Eimeria, Apicomplexa, parasitic diseases, parasite, chromosomal, protist, Eimeria tenella
Abstract: We present a genome assembly from a clonal population of Eimeria tenella Houghton parasites (Apicomplexa; Conoidasida; Eucoccidiorida; Eimeriidae). The genome sequence is 53.25 megabases in span. The entire assembly is scaffolded into 15 chromosomal pseudomolecules, with complete mitochondrion and apicoplast organellar genomes also present.
Published: 2021

50. The genome sequence of the European robin, Erithacus rubecula Linnaeus 1758

Author: Karen Oliver, Miriam Liedvogel, Emma Betteridge, Kerstin Howe, Sarah Pelan, Craig Corton, James Torrance, Jenny C. Dunn, Ying Sims, Daniel Mead, Jale Dolucan, Michael A. Quail, Shane A. McCarthy, Jason Skelton, Jonathan Wood, Jonathan Threlfall, Richard Challis, Michelle Smith, Mark Blaxter, and Marcela Uliano-Silva
Subjects: Whole genome sequencing, 0303 health sciences, Erithacus, biology, Medicine (miscellaneous), Sequence assembly, biology.organism_classification, European robin, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Evolutionary biology, 030220 oncology & carcinogenesis, biology.animal, C400 Genetics, 030304 developmental biology
Abstract: We present a genome assembly from an individual female Erithacus rubecula (the European robin; Chordata; Aves; Passeriformes; Turdidae). The genome sequence is 1.09 gigabases in span. The majority of the assembly is scaffolded into 36 chromosomal pseudomolecules, with both W and Z sex chromosomes assembled.
Published: 2021

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