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1. The genomes of all lungfish inform on genome expansion and tetrapod evolution

Author: Schartl, Manfred, Woltering, Joost M, Irisarri, Iker, Du, Kang, Kneitz, Susanne, Pippel, Martin, Brown, Thomas, Franchini, Paolo, Li, Jing, Li, Ming, Adolfi, Mateus, Winkler, Sylke, de Freitas Sousa, Josane, Chen, Zhuoxin, Jacinto, Sandra, Kvon, Evgeny Z, Correa de Oliveira, Luis Rogério, Monteiro, Erika, Baia Amaral, Danielson, Burmester, Thorsten, Chalopin, Domitille, Suh, Alexander, Myers, Eugene, Simakov, Oleg, Schneider, Igor, and Meyer, Axel
Subjects: Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Generic health relevance, Animals, Humans, Africa, Animal Fins, Australia, DNA Transposable Elements, DNA, Intergenic, Enhancer Elements, Genetic, Evolution, Molecular, Extinction, Biological, Fishes, Gene Rearrangement, Genome, Genome Size, Hedgehog Proteins, Introns, Karyotype, Phylogeny, Piwi-Interacting RNA, South America, Time Factors, Zinc Fingers, General Science & Technology
Abstract: The genomes of living lungfishes can inform on the molecular-developmental basis of the Devonian sarcopterygian fish-tetrapod transition. We de novo sequenced the genomes of the African (Protopterus annectens) and South American lungfishes (Lepidosiren paradoxa). The Lepidosiren genome (about 91 Gb, roughly 30 times the human genome) is the largest animal genome sequenced so far and more than twice the size of the Australian (Neoceratodus forsteri)1 and African2 lungfishes owing to enlarged intergenic regions and introns with high repeat content (about 90%). All lungfish genomes continue to expand as some transposable elements (TEs) are still active today. In particular, Lepidosiren's genome grew extremely fast during the past 100 million years (Myr), adding the equivalent of one human genome every 10 Myr. This massive genome expansion seems to be related to a reduction of PIWI-interacting RNAs and C2H2 zinc-finger and Krüppel-associated box (KRAB)-domain protein genes that suppress TE expansions. Although TE abundance facilitates chromosomal rearrangements, lungfish chromosomes still conservatively reflect the ur-tetrapod karyotype. Neoceratodus' limb-like fins still resemble those of their extinct relatives and remained phenotypically static for about 100 Myr. We show that the secondary loss of limb-like appendages in the Lepidosiren-Protopterus ancestor was probably due to loss of sonic hedgehog limb-specific enhancers.
Published: 2024

2. Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

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

Author: Ivanković, Mario, Brand, Jeremias N., Pandolfini, Luca, Brown, Thomas, Pippel, Martin, Rozanski, Andrei, Schubert, Til, Grohme, Markus A., Winkler, Sylke, Robledillo, Laura, Zhang, Meng, Codino, Azzurra, Gustincich, Stefano, Vila-Farré, Miquel, Zhang, Shu, Papantonis, Argyris, Marques, André, and Rink, Jochen C.
Published: 2024
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4. Building a Portuguese coalition for biodiversity genomics

Author: Marques, João P., Alves, Paulo C., Amorim, Isabel R., Lopes, Ricardo J., Moura, Monica, Myers, Eugene, Sim-sim, Manuela, Sousa-Santos, Carla, Alves, M. Judite, Borges, Paulo A. V., Brown, Thomas, Carneiro, Miguel, Carrapato, Carlos, Ceríaco, Luís M. P., Ciofi, Claúdio, da Silva, Luís P., Diedericks, Genevieve, Diroma, Maria Angela, Farelo, Liliana, Formenti, Giulio, Gil, Fátima, Grilo, Miguel, Iannucci, Alessio, Leitão, Henrique G., Máguas, Cristina, Mc Cartney, Ann M., Mendes, Sofia L., Moreno, João M., Morselli, Marco, Mouton, Alice, Natali, Chiara, Pereira, Fernando, Rego, Rúben M. C., Resendes, Roberto, Roxo, Guilherme, Svardal, Hannes, Trindade, Helena, Vicente, Sara, Winkler, Sylke, Alvarenga, Marcela, Amaral, Andreia J., Antunes, Agostinho, Campos, Paula F., Canário, Adelino V. M., Castilho, Rita, Castro, L. Filipe C., Crottini, Angelica, Cunha, Mónica V., Espregueira Themudo, Gonçalo, Esteves, Pedro J., Faria, Rui, Rodríguez Fernandes, Carlos, Ledoux, Jean-Baptiste, Louro, Bruno, Magalhaes, Sara, Paulo, Octávio S., Pearson, Gareth, Pimenta, João, Pina-Martins, Francisco, Santos, Teresa L., Serrão, Ester, Melo-Ferreira, José, and Sousa, Vítor C.
Published: 2024
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5. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

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

Author: Sendell-Price, Ashley T., Tulenko, Frank J., Pettersson, Mats, Kang, Du, Montandon, Margo, Winkler, Sylke, Kulb, Kathleen, Naylor, Gavin P., Phillippy, Adam, Fedrigo, Olivier, Mountcastle, Jacquelyn, Balacco, Jennifer R., Dutra, Amalia, Dale, Rebecca E., Haase, Bettina, Jarvis, Erich D., Myers, Gene, Burgess, Shawn M., Currie, Peter D., Andersson, Leif, and Schartl, Manfred
Published: 2023
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7. High-quality haploid genomes corroborate 29 chromosomes and highly conserved synteny of genes in Hyles hawkmoths (Lepidoptera: Sphingidae)

Author: Hundsdoerfer, Anna K., Schell, Tilman, Patzold, Franziska, Wright, Charlotte J., Yoshido, Atsuo, Marec, František, Daneck, Hana, Winkler, Sylke, Greve, Carola, Podsiadlowski, Lars, Hiller, Michael, and Pippel, Martin
Published: 2023
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8. Expanded olfactory system in ray-finned fishes capable of terrestrial exploration

Author: Burguera, Demian, Dionigi, Francesco, Kverková, Kristina, Winkler, Sylke, Brown, Thomas, Pippel, Martin, Zhang, Yicheng, Shafer, Maxwell, Nichols, Annika L. A., Myers, Eugene, Němec, Pavel, and Musilova, Zuzana
Published: 2023
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9. Towards complete and error-free genome assemblies of all vertebrate species

Author: Rhie, Arang, McCarthy, Shane A, Fedrigo, Olivier, Damas, Joana, Formenti, Giulio, Koren, Sergey, Uliano-Silva, Marcela, Chow, William, Fungtammasan, Arkarachai, Kim, Juwan, Lee, Chul, Ko, Byung June, Chaisson, Mark, Gedman, Gregory L, Cantin, Lindsey J, Thibaud-Nissen, Francoise, Haggerty, Leanne, Bista, Iliana, Smith, Michelle, Haase, Bettina, Mountcastle, Jacquelyn, Winkler, Sylke, Paez, Sadye, Howard, Jason, Vernes, Sonja C, Lama, Tanya M, Grutzner, Frank, Warren, Wesley C, Balakrishnan, Christopher N, Burt, Dave, George, Julia M, Biegler, Matthew T, Iorns, David, Digby, Andrew, Eason, Daryl, Robertson, Bruce, Edwards, Taylor, Wilkinson, Mark, Turner, George, Meyer, Axel, Kautt, Andreas F, Franchini, Paolo, Detrich, H William, Svardal, Hannes, Wagner, Maximilian, Naylor, Gavin JP, Pippel, Martin, Malinsky, Milan, Mooney, Mark, Simbirsky, Maria, Hannigan, Brett T, Pesout, Trevor, Houck, Marlys, Misuraca, Ann, Kingan, Sarah B, Hall, Richard, Kronenberg, Zev, Sović, Ivan, Dunn, Christopher, Ning, Zemin, Hastie, Alex, Lee, Joyce, Selvaraj, Siddarth, Green, Richard E, Putnam, Nicholas H, Gut, Ivo, Ghurye, Jay, Garrison, Erik, Sims, Ying, Collins, Joanna, Pelan, Sarah, Torrance, James, Tracey, Alan, Wood, Jonathan, Dagnew, Robel E, Guan, Dengfeng, London, Sarah E, Clayton, David F, Mello, Claudio V, Friedrich, Samantha R, Lovell, Peter V, Osipova, Ekaterina, Al-Ajli, Farooq O, Secomandi, Simona, Kim, Heebal, Theofanopoulou, Constantina, Hiller, Michael, Zhou, Yang, Harris, Robert S, Makova, Kateryna D, Medvedev, Paul, Hoffman, Jinna, Masterson, Patrick, Clark, Karen, Martin, Fergal, Howe, Kevin, Flicek, Paul, Walenz, Brian P, Kwak, Woori, and Clawson, Hiram
Subjects: Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Generic health relevance, Animals, Birds, Gene Library, Genome, Genome Size, Genome, Mitochondrial, Genomics, Haplotypes, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, Sequence Alignment, Sequence Analysis, DNA, Sex Chromosomes, Vertebrates, General Science & Technology
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 species1-4. 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.
Published: 2021

10. Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages

Author: Roscito, Juliana Gusson, Sameith, Katrin, Kirilenko, Bogdan Mikhailovich, Hecker, Nikolai, Winkler, Sylke, Dahl, Andreas, Rodrigues, Miguel Trefaut, and Hiller, Michael
Published: 2022
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11. A Haplotype-resolved reference genome of a long-distance migratory bat, Pipistrellus nathusii (Keyserling & Blasius, 1839)

Author: Driller, Maximilian, primary, Brown, Thomas, additional, Currie, Shannon E, additional, Hiller, Michael, additional, Winkler, Sylke, additional, Pippel, Martin, additional, Voigt, Christian C, additional, Fickel, Jörns, additional, and Mazzoni, Camila J, additional
Published: 2024
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12. Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19

Author: Altmüller, Janine, Angelov, Angel, Aschenbrenner, Anna C., Bals, Robert, Bartholomäus, Alexander, Becker, Anke, Becker, Matthias, Bezdan, Daniela, Bitzer, Michael, Blumert, Conny, Bonifacio, Ezio, Bork, Peer, Boyke, Bunk, Blum, Helmut, Casadei, Nicolas, Clavel, Thomas, Colome-Tatche, Maria, Cornberg, Markus, De La Rosa Velázquez, Inti Alberto, Diefenbach, Andreas, Dilthey, Alexander, Fischer, Nicole, Förstner, Konrad, Franzenburg, Sören, Frick, Julia-Stefanie, Gabernet, Gisela, Gagneur, Julien, Ganzenmueller, Tina, Gauder, Marie, Geißert, Janina, Goesmann, Alexander, Göpel, Siri, Grundhoff, Adam, Grundmann, Hajo, Hain, Torsten, Hanses, Frank, Hehr, Ute, Heimbach, André, Hoeper, Marius, Horn, Friedemann, Hübschmann, Daniel, Hummel, Michael, Iftner, Thomas, Iftner, Angelika, Illig, Thomas, Janssen, Stefan, Kalinowski, Jörn, Kallies, René, Kehr, Birte, Keller, Andreas, Keppler, Oliver T., Kim-Hellmuth, Sarah, Klein, Christoph, Knop, Michael, Kohlbacher, Oliver, Köhrer, Karl, Korbel, Jan, Kremsner, Peter G., Kühnert, Denise, Kurth, Ingo, Landthaler, Markus, Li, Yang, Ludwig, Kerstin U., Makarewicz, Oliwia, Marini, Federico, Marz, Manja, McHardy, Alice C., Mertes, Christian, Münchhoff, Maximilian, Nahnsen, Sven, Nöthen, Markus, Ntoumi, Francine, Nürnberg, Peter, Ossowski, Stephan, Overmann, Jörg, Peter, Silke, Pfeffer, Klaus, Pink, Isabell, Poetsch, Anna R., Protzer, Ulrike, Pühler, Alfred, Rajewsky, Nikolaus, Ralser, Markus, Reiche, Kristin, Rieß, Olaf, Ripke, Stephan, Nunes da Rocha, Ulisses, Rosenstiel, Philip, Saliba, Antoine-Emmanuel, Sander, Leif Erik, Sawitzki, Birgit, Scheithauer, Simone, Schiffer, Philipp, Schmid-Burgk, Jonathan, Schneider, Wulf, Schulte, Eva-Christina, Schultze, Joachim L., Sczyrba, Alexander, Sharaf, Mariam L., Singh, Yogesh, Sonnabend, Michael, Stegle, Oliver, Stoye, Jens, Theis, Fabian, Ulas, Thomas, Vehreschild, Janne, Velavan, Thirumalaisamy P., Vogel, Jörg, Volland, Sonja, von Kleist, Max, Walker, Andreas, Walter, Jörn, Wieczorek, Dagmar, Winkler, Sylke, Ziebuhr, John, Krämer, Benjamin, Knoll, Rainer, Bonaguro, Lorenzo, ToVinh, Michael, Raabe, Jan, Astaburuaga-García, Rosario, Schulte-Schrepping, Jonas, Kaiser, Kim Melanie, Rieke, Gereon J., Bischoff, Jenny, Monin, Malte B., Hoffmeister, Christoph, Schlabe, Stefan, De Domenico, Elena, Reusch, Nico, Händler, Kristian, Reynolds, Gary, Blüthgen, Nils, Hack, Gudrun, Finnemann, Claudia, Nischalke, Hans D., Strassburg, Christian P., Stephenson, Emily, Su, Yapeng, Gardner, Louis, Yuan, Dan, Chen, Daniel, Goldman, Jason, Rosenstiel, Philipp, Schmidt, Susanne V., Latz, Eicke, Hrusovsky, Kevin, Ball, Andrew J., Johnson, Joe M., Koenig, Paul-Albert, Schmidt, Florian I., Haniffa, Muzlifah, Heath, James R., Kümmerer, Beate M., Keitel, Verena, Jensen, Björn, Stubbemann, Paula, Kurth, Florian, Sander, Leif E., and Nattermann, Jacob
Published: 2021
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13. Low Threshold for Cutaneous Allergen Sensitization but No Spontaneous Dermatitis or Atopy in FLG-Deficient Mice

Author: Muhandes, Lina, Chapsa, Maria, Pippel, Martin, Behrendt, Rayk, Ge, Yan, Dahl, Andreas, Yi, Buqing, Dalpke, Alexander, Winkler, Sylke, Hiller, Michael, Boutin, Sebastien, Beissert, Stefan, Jessberger, Rolf, Fallon, Padraic G., and Roers, Axel
Published: 2021
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14. Six reference-quality genomes reveal evolution of bat adaptations

Author: Jebb, David, Huang, Zixia, Pippel, Martin, Hughes, Graham M., Lavrichenko, Ksenia, Devanna, Paolo, and Winkler, Sylke
Subjects: Adaptation (Biology) -- Genetic aspects, Bats -- Natural history -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity and unique immunity. High-quality genomes are crucial for understanding the molecular basis and evolution of these traits. Here we incorporated long-read sequencing and state-of-the-art scaffolding protocols.sup.1 to generate, to our knowledge, the first reference-quality genomes of six bat species (Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pipistrellus kuhlii and Molossus molossus). We integrated gene projections from our 'Tool to infer Orthologs from Genome Alignments' (TOGA) software with de novo and homology gene predictions as well as short- and long-read transcriptomics to generate highly complete gene annotations. To resolve the phylogenetic position of bats within Laurasiatheria, we applied several phylogenetic methods to comprehensive sets of orthologous protein-coding and noncoding regions of the genome, and identified a basal origin for bats within Scrotifera. Our genome-wide screens revealed positive selection on hearing-related genes in the ancestral branch of bats, which is indicative of laryngeal echolocation being an ancestral trait in this clade. We found selection and loss of immunity-related genes (including pro-inflammatory NF-[kappa]B regulators) and expansions of anti-viral APOBEC3 genes, which highlights molecular mechanisms that may contribute to the exceptional immunity of bats. Genomic integrations of diverse viruses provide a genomic record of historical tolerance to viral infection in bats. Finally, we found and experimentally validated bat-specific variation in microRNAs, which may regulate bat-specific gene-expression programs. Our reference-quality bat genomes provide the resources required to uncover and validate the genomic basis of adaptations of bats, and stimulate new avenues of research that are directly relevant to human health and disease.sup.1. Reference-quality genomes for six bat species shed light on the phylogenetic position of Chiroptera, and provide insight into the genetic underpinnings of the unique adaptations of this clade., Author(s): David Jebb [sup.1] [sup.2] [sup.3] , Zixia Huang [sup.4] , Martin Pippel [sup.1] [sup.3] , Graham M. Hughes [sup.4] , Ksenia Lavrichenko [sup.5] , Paolo Devanna [sup.5] , Sylke [...]
Published: 2020
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15. A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence

Author: Ivankovic, Mario, primary, Brand, Jeremias N, additional, Pandolfini, Luca, additional, Brown, Tom, additional, Pippel, Martin, additional, Rozanski, Andrei, additional, Schubert, Til, additional, Grohme, Markus A, additional, Winkler, Sylke, additional, Robledillo, Laura, additional, Zhang, Meng, additional, Codino, Azzurra, additional, Gustincich, Stefano, additional, Vila-Farré, Miquel, additional, Zhang, Shu, additional, Papantonis, Argyris, additional, Marques, André, additional, and Rink, Jochen C, additional
Published: 2023
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16. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author: Mc Cartney, Ann M, primary, Formenti, Giulio, additional, Mouton, Alice, additional, Ciofi, Claudio, additional, Waterhouse, Robert M, additional, Mazzoni, Camila J, additional, De Panis, Diego, additional, Schlude Marins, Luisa S, additional, Leitao, Henrique G, additional, Diedericks, Genevieve, additional, Kirangwa, Joseph, additional, Morselli, Marco, additional, Salces, Judit, additional, Escudero, Nuria, additional, Iannucci, Alessio, additional, Natali, Chiara, additional, Svardal, Hannes, additional, Fernandez, Rosa, additional, De Pooter, Tim, additional, Joris, Geert, additional, Strazisar, Mojca, additional, Wood, Jo, additional, Herron, Katie E, additional, Seehausen, Ole, additional, Watts, Phillip C, additional, Shaw, Felix, additional, Davey, Robert P, additional, Minotto, Alice, additional, Fernandez Gonzalez, Jose Maria, additional, Bohne, Astrid, additional, Alegria, Carla, additional, Alioto, Tyler, additional, Alves, Paulo C, additional, Amorim, Isabel R, additional, Aury, Jean-Marc, additional, Backstrom, Niclas, additional, Baldrian, Petr, additional, Ballarin, Loriano, additional, Baltrunaite, Laima, additional, Barta, Endre, additional, BedHom, Bertrand, additional, Belser, Caroline, additional, Bergsten, Johannes, additional, Bertrand, Laurie, additional, Bilandija, Helena, additional, Binzer-Panchal, Mahesh, additional, Bista, Iliana, additional, Blaxter, Mark, additional, Borges, Paulo AV, additional, Borges Dias, Guilherme, additional, Bosse, Mirte, additional, Brown, Tom, additional, Bruggmann, Remy, additional, Buena-Atienza, Elena, additional, Burgin, Josephine, additional, Buzan, Elena, additional, Casadei, Nicolas, additional, Chiara, Matteo, additional, Chozas, Sergio, additional, Ciampor, Fedor F, additional, Crottini, Angelica, additional, Cruaud, Corinne, additional, Cruz, Fernando, additional, Dalen, Love, additional, De Biase, Alessio, additional, del Campo, Javier, additional, Delic, Teo, additional, Dennis, Alice B, additional, Derks, Martijn FL, additional, Diroma, Maria Angela, additional, Djan, Mihajla, additional, Duprat, Simone, additional, Eleftheriadi, Klara, additional, Feulner, Philine GD, additional, Flot, Jean-Francois, additional, Forni, Giobbe, additional, Fosso, Bruno, additional, Fournier, Pascal, additional, Fournier-Chambrillon, Christine, additional, Gabaldon, Toni, additional, Garg, Shilpa, additional, Gissi, Carmela, additional, Giupponi, Luca, additional, Gomez-Garrido, Jessica, additional, Gonzalez, Josefa, additional, Grilo, Miguel L, additional, Gruening, Bjoern, additional, Guerin, Thomas, additional, Guiglielmoni, Nadege, additional, Gut, Marta, additional, Haesler, Marcel P, additional, Hahn, Christoph, additional, Halpern, Balint, additional, Harrison, Peter, additional, Heintz, Julia, additional, Hindrikson, Maris, additional, Hoglund, Jacob, additional, Howe, Kerstin, additional, Hughes, Graham, additional, Istace, Benjamin, additional, Cock, Mark J., additional, Jancekovic, Franc, additional, Jonsson, Zophonias O, additional, Joye-Dind, Sagane, additional, Koskimaki, Janne J., additional, Krystufek, Boris, additional, Kubacka, Justyna, additional, Kuhl, Heiner, additional, Kusza, Szilvia, additional, Labadie, Karine, additional, Lahteenaro, Meri, additional, Lantz, Henrik, additional, Lavrinienko, Anton, additional, Leclere, Lucas, additional, Lopes, Ricardo Jorge, additional, Madsen, Ole, additional, Magdelenat, Ghislaine, additional, Magoga, Giulia, additional, Manousaki, Tereza, additional, Mappes, Tapio, additional, Marques, Joao Pedro, additional, Martinez Redondo, Gemma I, additional, Maumus, Florian, additional, Megens, Hendrik-Jan, additional, Melo-Ferreira, Jose, additional, Mendes, Sofia L, additional, Montagna, Matteo, additional, Moreno, Joao, additional, Mosbech, Mai-Britt, additional, Moura, Monica, additional, Musilova, Zuzana, additional, Myers, Eugene, additional, Nash, Will J., additional, Nater, Alexander, additional, Nicholson, Pamela, additional, Niell, Manuel, additional, Nijland, Reindert, additional, Noel, Benjamin, additional, Noren, Karin, additional, Oliveira, Pedro H, additional, Olsen, Remi-Andre, additional, Ometto, Lino, additional, Ossowski, Stephan, additional, Palinauskas, Vaidas, additional, Palsson, Snaebjorn, additional, Panibe, Jerome P, additional, Pauperio, Joana, additional, Pavlek, Martina, additional, Payen, Emilie, additional, Pawlowska, Julia, additional, Pellicer, Jaume, additional, Pesole, Graziano, additional, Pimenta, Joao, additional, Pippel, Martin, additional, Pirttila, Anna Maria, additional, Poulakakis, Nikos, additional, Rajan, Jeena, additional, Rego, Ruben MC, additional, Resendes, Roberto, additional, Resl, Philipp, additional, Riesgo, Ana, additional, Rodin-Morch, Patrik, additional, Soares, Andre ER, additional, Rodriguez Fernandes, Carlos, additional, Romeiras, Maria M., additional, Roxo, Guilherme, additional, Ruber, Lukas, additional, Ruiz-Lopez, Maria Jose, additional, Saarma, Urmas, additional, Silva, Luis P, additional, Sim-Sim, Manuela, additional, Soler, Lucile, additional, Sousa, Vitor C, additional, Sousa Santos, Carla, additional, Spada, Alberto, additional, Stefanovic, Milomir, additional, Steger, Viktor, additional, Stiller, Josefin, additional, Stock, Matthias, additional, Struck, Torsten Hugo H, additional, Sudasinghe, Hiranya, additional, Tapanainen, Riikka, additional, Tellgren-Roth, Christian, additional, Trindade, Helena, additional, Tukalenko, Yevhen, additional, Urso, Ilenia, additional, Vacherie, Benoit, additional, Van Belleghem, Steven M, additional, van Oers, Kees, additional, Vargas-Chavez, Carlos, additional, Velickovic, Nevena, additional, Vella, Noel, additional, Vella, Adriana, additional, Vernesi, Cristiano, additional, Vicente, Sara, additional, Villa, Sara, additional, Vinnere Pettersson, Olga, additional, Volckaert, Filip AM, additional, Voros, Judit, additional, Wincker, Patrick, additional, and Winkler, Sylke, additional
Published: 2023
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17. A novel nematode species from the Siberian permafrost shares adaptive mechanisms for cryptobiotic survival with C. elegans dauer larva

Author: Shatilovich, Anastasia, primary, Gade, Vamshidhar R., additional, Pippel, Martin, additional, Hoffmeyer, Tarja T., additional, Tchesunov, Alexei V., additional, Stevens, Lewis, additional, Winkler, Sylke, additional, Hughes, Graham M., additional, Traikov, Sofia, additional, Hiller, Michael, additional, Rivkina, Elizaveta, additional, Schiffer, Philipp H., additional, Myers, Eugene W., additional, and Kurzchalia, Teymuras V., additional
Published: 2023
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18. The round goby genome provides insights into mechanisms that may facilitate biological invasions

Author: Adrian-Kalchhauser, Irene, Blomberg, Anders, Larsson, Tomas, Musilova, Zuzana, Peart, Claire R., Pippel, Martin, Solbakken, Monica Hongroe, Suurväli, Jaanus, Walser, Jean-Claude, Wilson, Joanna Yvonne, Alm Rosenblad, Magnus, Burguera, Demian, Gutnik, Silvia, Michiels, Nico, Töpel, Mats, Pankov, Kirill, Schloissnig, Siegfried, and Winkler, Sylke
Published: 2020
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19. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Author: Bentley, Blair P., Carrasco-Valenzuela, Tomas, Ramos, Elisa K. S., Pawar, Harvinder, Arantes, Larissa Souza, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, V. Todd, Erica, Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Francoise, Nery, Mariana F., Marques-Bonet, Tomas, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., Komoroske, Lisa M., Bentley, Blair P., Carrasco-Valenzuela, Tomas, Ramos, Elisa K. S., Pawar, Harvinder, Arantes, Larissa Souza, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, V. Todd, Erica, Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Francoise, Nery, Mariana F., Marques-Bonet, Tomas, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., and Komoroske, Lisa M.
Abstract: Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of noncollinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared with other reptiles, and harbor a higher genetic load compared with green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage.
Published: 2023
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20. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Author: University of Massachusetts, National Marine Fisheries Service (US), National Science Foundation (US), National Research Council of Canada, Rockefeller University, Howard Hughes Medical Institute, Wellcome Sanger Institute, Max Planck Society, Agencia Nacional de Investigación y Desarrollo (Chile), Fundação de Amparo à Pesquisa do Estado de São Paulo, Federal Ministry of Education and Research (Germany), National Library of Medicine (US), Generalitat de Catalunya, Fundación la Caixa, Vienna Science and Technology Fund, Welsh Government, European Commission, Sea Turtle Conservancy (US), Kuhlwilm, Martin [0000-0002-0115-1797], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Bentley, Blair P., Carrasco-Valenzuela, Tomás, Ramos, Elisa K. S., Pawar, Harvinder, Souza Arantes, Larissa, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, Todd, Erica V., Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Françoise, Nery, Mariana F., Marqués-Bonet, Tomàs, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., Komoroske, Lisa M., University of Massachusetts, National Marine Fisheries Service (US), National Science Foundation (US), National Research Council of Canada, Rockefeller University, Howard Hughes Medical Institute, Wellcome Sanger Institute, Max Planck Society, Agencia Nacional de Investigación y Desarrollo (Chile), Fundação de Amparo à Pesquisa do Estado de São Paulo, Federal Ministry of Education and Research (Germany), National Library of Medicine (US), Generalitat de Catalunya, Fundación la Caixa, Vienna Science and Technology Fund, Welsh Government, European Commission, Sea Turtle Conservancy (US), Kuhlwilm, Martin [0000-0002-0115-1797], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Bentley, Blair P., Carrasco-Valenzuela, Tomás, Ramos, Elisa K. S., Pawar, Harvinder, Souza Arantes, Larissa, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, Todd, Erica V., Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Françoise, Nery, Mariana F., Marqués-Bonet, Tomàs, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., and Komoroske, Lisa M.
Abstract: [Significance] Sea turtle populations have undergone recent global declines. We analyzed de novo assembled genomes for both extant sea turtle families through the Vertebrate Genomes Project to inform their conservation and evolutionary biology. These highly conserved genomes were differentiated by localized gene-rich regions of divergence, particularly within microchromosomes, suggesting that these genomic elements play key functional roles in the evolution of sea turtles and possibly other vertebrates. We further demonstrate that dissimilar evolutionary histories impact standing genomic diversity and genetic load, and are critical to consider when using these metrics to assess adaptive potential and extinction risk. Our results also demonstrate how reference genome quality impacts inferences of comparative and conservation genomics analyses that need to be considered in their application., [Abstract] Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of noncollinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared with other reptiles, and harbor a higher genetic load compared with green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage.
Published: 2023

21. High-molecular-weight DNA extraction for broadleaved and conifer tree species

Author: Krautwurst, Melina, Eikhof, Annika, Winkler, Sylke, Bross, Daniel, Kersten, Birgit, and Müller, Niels A.
Abstract: Plant genome sequencing based on long reads has increasingly been applied also to tree species in recent years. A crucial step in these genome projects is the successful extraction of high-molecular-weight DNA in high quality and sufficient quantity, which is imperative for long-read sequencing. The extraction of high-molecular-weight DNA in trees has been limited and difficult to conduct. To achieve successful extraction, modification of the protocol for tree species is necessary. Here, we present a protocol for high-molecular-weight DNA extraction from the broadleaved tree species Fraxinus excelsiorand from the conifer species Taxus baccata. The protocol is based on nuclei isolation and is divided into two main steps, i.e. nuclei separation based on the nuclei isolation buffer and DNA extraction using the Nanobind® plant nuclei kit by Pacific Biosciences (PacBio). The protocol can be applied to different tree species to obtain high-molecular-weight DNA in high quality, which can be used for Oxford Nanopore Technologies (ONT) and PacBio sequencing. ONT sequencing using four high-molecular-weight DNA preparations from Fraxinus excel-siorresulted in different read length N50 values (12.91-38.19 kb) and total base output (5.81-23.17 Gb), emphasizing the complex nature of the sequencing pipeline of high-molecular-weight DNA. PacBio HiFi sequencing of Taxus baccataproduced circular consensus sequencing reads with an average length of 12.9 kb and an N50 of 13.59 kb. Altogether, this study presents a protocol to obtain high-molecular-weight DNA from different challenging tree species and discusses several important points that can be considered when adapting the protocol to additional species.
Published: 2024
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22. Reference-quality bat genomes illuminate adaptations to viral tolerance and disease resistance

Author: Hiller, Michael, primary, Morales, Ariadna, additional, Ahmed, Alexis, additional, Hilgers, Leon, additional, Kirilenko, Bogdan, additional, Kontopoulos, Dimitrios, additional, Dong, Yue, additional, Li, Xiaomeng, additional, Irving, Aaron, additional, Brown, Thomas, additional, Pippel, Martin, additional, Winkler, Sylke, additional, Baid, Kaushal, additional, Gonzalez, Victoria, additional, Banerjee, Arinjay, additional, Huang, Zixia, additional, Hughes, Graham, additional, Teeling, Emma, additional, Myers, Eugene, additional, Devanna, Paolo, additional, Vernes, Sonja, additional, Lama, Tanya, additional, Dávalos, Liliana, additional, Nissan, Yomiran, additional, Yovel, Yossi, additional, Puechmaille, Sebastien, additional, Rossiter, Stephen, additional, Prescott, Joe, additional, Kurth, Andreas, additional, Ray, David, additional, and Lim, Burton, additional
Published: 2023
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23. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Author: Bentley, Blair P., primary, Carrasco-Valenzuela, Tomás, additional, Ramos, Elisa K. S., additional, Pawar, Harvinder, additional, Souza Arantes, Larissa, additional, Alexander, Alana, additional, Banerjee, Shreya M., additional, Masterson, Patrick, additional, Kuhlwilm, Martin, additional, Pippel, Martin, additional, Mountcastle, Jacquelyn, additional, Haase, Bettina, additional, Uliano-Silva, Marcela, additional, Formenti, Giulio, additional, Howe, Kerstin, additional, Chow, William, additional, Tracey, Alan, additional, Sims, Ying, additional, Pelan, Sarah, additional, Wood, Jonathan, additional, Yetsko, Kelsey, additional, Perrault, Justin R., additional, Stewart, Kelly, additional, Benson, Scott R., additional, Levy, Yaniv, additional, Todd, Erica V., additional, Shaffer, H. Bradley, additional, Scott, Peter, additional, Henen, Brian T., additional, Murphy, Robert W., additional, Mohr, David W., additional, Scott, Alan F., additional, Duffy, David J., additional, Gemmell, Neil J., additional, Suh, Alexander, additional, Winkler, Sylke, additional, Thibaud-Nissen, Françoise, additional, Nery, Mariana F., additional, Marques-Bonet, Tomas, additional, Antunes, Agostinho, additional, Tikochinski, Yaron, additional, Dutton, Peter H., additional, Fedrigo, Olivier, additional, Myers, Eugene W., additional, Jarvis, Erich D., additional, Mazzoni, Camila J., additional, and Komoroske, Lisa M., additional
Published: 2023
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24. Loss of a gluconeogenic muscle enzyme contributed to adaptive metabolic traits in hummingbirds

Author: Osipova, Ekaterina, primary, Barsacchi, Rico, additional, Brown, Tom, additional, Sadanandan, Keren, additional, Gaede, Andrea H., additional, Monte, Amanda, additional, Jarrells, Julia, additional, Moebius, Claudia, additional, Pippel, Martin, additional, Altshuler, Douglas L., additional, Winkler, Sylke, additional, Bickle, Marc, additional, Baldwin, Maude W., additional, and Hiller, Michael, additional
Published: 2023
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25. Expanded olfactory system in fishes capable of terrestrial exploration

Author: Burguera, Demian, primary, Dionigi, Francesco, additional, Kverková, Kristina, additional, Winkler, Sylke, additional, Brown, Thomas, additional, Pippel, Martin, additional, Zhang, Yicheng, additional, Shafer, Maxwell, additional, Nichols, Annika L.A., additional, Myers, Eugene, additional, Němec, Pavel, additional, and Musilova, Zuzana, additional
Published: 2022
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26. Investigating the cause of a 2021 winter wave of COVID-19 in a border region in Eastern Germany: a mixed-methods study, August to November 2021

Author: Yi, Buqing, primary, Laubner, Alexa, additional, Stadtmüller, Marlena, additional, Patrasová, Eva, additional, Šimůnková, Lenka, additional, Rost, Fabian, additional, Winkler, Sylke, additional, Reinhardt, Susanne, additional, Dahl, Andreas, additional, and Dalpke, Alexander H., additional
Published: 2022
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27. CRISPR/Cas9‐induced disruption of gene expression in mouse embryonic brain and single neural stem cells in vivo

Author: Kalebic, Nereo, Taverna, Elena, Tavano, Stefania, Wong, Fong Kuan, Suchold, Dana, Winkler, Sylke, Huttner, Wieland B, and Sarov, Mihail
Published: 2016
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28. Longer metaphase and fewer chromosome segregation errors in modern human than Neanderthal brain development

Author: Mora-Bermúdez, Felipe, primary, Kanis, Philipp, additional, Macak, Dominik, additional, Peters, Jula, additional, Naumann, Ronald, additional, Xing, Lei, additional, Sarov, Mihail, additional, Winkler, Sylke, additional, Oegema, Christina Eugster, additional, Haffner, Christiane, additional, Wimberger, Pauline, additional, Riesenberg, Stephan, additional, Maricic, Tomislav, additional, Huttner, Wieland B., additional, and Pääbo, Svante, additional
Published: 2022
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29. Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Author: Dahn, Hollis A, Mountcastle, Jacquelyn, Balacco, Jennifer, Winkler, Sylke, Bista, Iliana, Schmitt, Anthony D, Pettersson, Olga Vinnere, Formenti, Giulio, Oliver, Karen, Smith, Michelle, Tan, Wenhua, Kraus, Anne, Mac, Stephen, Komoroske, Lisa M, Lama, Tanya, Crawford, Andrew J, Murphy, Robert W, Brown, Samara, Scott, Alan F, Morin, Phillip A, Jarvis, Erich D, Fedrigo, Olivier, Dahn, Hollis A [0000-0001-9777-2303], Mountcastle, Jacquelyn [0000-0003-1078-4905], Balacco, Jennifer [0000-0001-7102-1632], Winkler, Sylke [0000-0002-0915-3316], Bista, Iliana [0000-0002-6155-3093], Pettersson, Olga Vinnere [0000-0002-5597-1870], Formenti, Giulio [0000-0002-7554-5991], Smith, Michelle [0000-0001-5288-0001], Tan, Wenhua [0000-0002-5208-8126], Komoroske, Lisa M [0000-0003-0676-7053], Lama, Tanya [0000-0002-7372-8081], Crawford, Andrew J [0000-0003-3153-6898], Murphy, Robert W [0000-0001-8555-2338], Brown, Samara [0000-0003-0391-2016], Scott, Alan F [0000-0002-9706-7839], Morin, Phillip A [0000-0002-3279-1519], Jarvis, Erich D [0000-0001-8931-5049], Fedrigo, Olivier [0000-0002-6450-7551], and Apollo - University of Cambridge Repository
Subjects: High-Throughput Nucleotide Sequencing, Health Informatics, DNA, Sequence Analysis, DNA, HMW DNA extraction, Computer Science Applications, Molecular Weight, Benchmarking, long-read sequencing, Genetics, genome assembly, Animals, Dimethyl Sulfoxide, Genetik, tissue preservation, Edetic Acid
Abstract: Background Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. Results We find that storage temperature was the strongest predictor of uHMW fragment lengths. While immediate flash-freezing remains the sample preservation gold standard, samples preserved in 95% EtOH or 20–25% DMSO-EDTA showed little fragment length degradation when stored at 4°C for 6 hours. Samples in 95% EtOH or 20–25% DMSO-EDTA kept at 4°C for 1 week after dissection still yielded adequate amounts of uHMW DNA for most applications. Tissue type was a significant predictor of total DNA yield but not fragment length. Preservation solution had a smaller but significant influence on both fragment length and DNA yield. Conclusion We provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for phase 1 of the Vertebrate Genomes Project, whose ultimate mission is to generate chromosome-level reference genome assemblies of all ∼70,000 extant vertebrate species.
Published: 2021

30. Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Author: Dahn, Hollis A., Mountcastle, Jacquelyn, Balacco, Jennifer, Winkler, Sylke, Bista, Iliana, Schmitt, Anthony D., Vinnere, Olga, Formenti, Giulio, Oliver, Karen, Smith, Michelle, Tan, Wenhua, Kraus, Anne, Mac, Stephen, Komoroske, Lisa M., Lama, Tanya, Crawford, Andrew J., Murphy, Robert W., Brown, Samara, Scott, Alan F., Morin, Phillip A., Jarvis, Erich D., Fedrigo, Olivier, Dahn, Hollis A., Mountcastle, Jacquelyn, Balacco, Jennifer, Winkler, Sylke, Bista, Iliana, Schmitt, Anthony D., Vinnere, Olga, Formenti, Giulio, Oliver, Karen, Smith, Michelle, Tan, Wenhua, Kraus, Anne, Mac, Stephen, Komoroske, Lisa M., Lama, Tanya, Crawford, Andrew J., Murphy, Robert W., Brown, Samara, Scott, Alan F., Morin, Phillip A., Jarvis, Erich D., and Fedrigo, Olivier
Abstract: Background: Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. Results: We find that storage temperature was the strongest predictor of uHMW fragment lengths. While immediate flash-freezing remains the sample preservation gold standard, samples preserved in 95% EtOH or 20-25% DMSO-EDTA showed little fragment length degradation when stored at 4 degrees C for 6 hours. Samples in 95% EtOH or 20-25% DMSO-EDTA kept at 4 degrees C for 1 week after dissection still yielded adequate amounts of uHMW DNA for most applications. Tissue type was a significant predictor of total DNA yield but not fragment length. Preservation solution had a smaller but significant influence on both fragment length and DNA yield. Conclusion: We provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for phase 1 of the Vertebrate Genomes Project, whose ultimate mission is to generate chromosome-level reference genome assemblies of all similar to 70,000 extant vertebrate species.
Published: 2022
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31. High quality genomes corroborate 29 chromosomes of the haploid Hyles (Lepidoptera: Sphingidae) karyotype

Author: Hundsdoerfer, Anna K., primary, Schell, Tilman, additional, Patzold, Franziska, additional, Yoshido, Atsuo, additional, Marec, František, additional, Daneck, Hana, additional, Winkler, Sylke, additional, Greve, Carola, additional, Hiller, Michael, additional, and Pippel, Martin, additional
Published: 2022
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32. A novel nematode species from the Siberian permafrost shares adaptive mechanisms for cryptobiotic survival withC. elegansdauer larva

Author: Shatilovich, Anastasia, primary, Gade, Vamshidhar R., additional, Pippel, Martin, additional, Hoffmeyer, Tarja T., additional, Tchesunov, Alexei V., additional, Stevens, Lewis, additional, Winkler, Sylke, additional, Hughes, Graham M., additional, Traikov, Sofia, additional, Hiller, Michael, additional, Rivkina, Elizaveta, additional, Schiffer, Philipp H., additional, Myers, Eugene W, additional, and Kurzchalia, Teymuras V., additional
Published: 2022
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33. Genome biology of the darkedged splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentation

Author: Du, Kang, primary, Pippel, Martin, additional, Kneitz, Susanne, additional, Feron, Romain, additional, da Cruz, Irene, additional, Winkler, Sylke, additional, Wilde, Brigitta, additional, Avila Luna, Edgar G., additional, Myers, Gene, additional, Guiguen, Yann, additional, Macias Garcia, Constantino, additional, and Schartl, Manfred, additional
Published: 2022
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34. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Author: Bentley, Blair P., primary, Carrasco-Valenzuela, Tomás, additional, Ramos, Elisa K. S., additional, Pawar, Harvinder, additional, Arantes, Larissa Souza, additional, Alexander, Alana, additional, Banerjee, Shreya M., additional, Masterson, Patrick, additional, Kuhlwilm, Martin, additional, Pippel, Martin, additional, Mountcastle, Jacquelyn, additional, Haase, Bettina, additional, Uliano-Silva, Marcela, additional, Formenti, Giulio, additional, Howe, Kerstin, additional, Chow, William, additional, Tracey, Alan, additional, Sims, Ying, additional, Pelan, Sarah, additional, Wood, Jonathan, additional, Yetsko, Kelsey, additional, Perrault, Justin R., additional, Stewart, Kelly, additional, Benson, Scott R., additional, Levy, Yaniv, additional, Todd, Erica V., additional, Shaffer, H. Bradley, additional, Scott, Peter, additional, Henen, Brian T., additional, Murphy, Robert W., additional, Mohr, David W., additional, Scott, Alan F., additional, Duffy, David J., additional, Gemmell, Neil J., additional, Suh, Alexander, additional, Winkler, Sylke, additional, Thibaud-Nissen, Françoise, additional, Nery, Mariana F., additional, Marques-Bonet, Tomas, additional, Antunes, Agostinho, additional, Tikochinski, Yaron, additional, Dutton, Peter H., additional, Fedrigo, Olivier, additional, Myers, Eugene W., additional, Jarvis, Erich D., additional, Mazzoni, Camila J., additional, and Komoroske, Lisa M., additional
Published: 2022
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35. Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Author: Dahn, Hollis A, primary, Mountcastle, Jacquelyn, additional, Balacco, Jennifer, additional, Winkler, Sylke, additional, Bista, Iliana, additional, Schmitt, Anthony D, additional, Pettersson, Olga Vinnere, additional, Formenti, Giulio, additional, Oliver, Karen, additional, Smith, Michelle, additional, Tan, Wenhua, additional, Kraus, Anne, additional, Mac, Stephen, additional, Komoroske, Lisa M, additional, Lama, Tanya, additional, Crawford, Andrew J, additional, Murphy, Robert W, additional, Brown, Samara, additional, Scott, Alan F, additional, Morin, Phillip A, additional, Jarvis, Erich D, additional, and Fedrigo, Olivier, additional
Published: 2022
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36. Emergence and spread of a sub-lineage of SARS-CoV-2 Alpha variant B.1.1.7 in Europe, and with further evolution of spike mutation accumulations shared with the Beta and Gamma variants

Author: Stadtmüller, Marlena, primary, Laubner, Alexa, additional, Rost, Fabian, additional, Winkler, Sylke, additional, Patrasová, Eva, additional, Šimůnková, Lenka, additional, Reinhardt, Susanne, additional, Beil, Johanna, additional, Dalpke, Alexander H, additional, and Yi, Buqing, additional
Published: 2022
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37. Emergence and spread of a sub-lineage of SARS-CoV-2 Alpha variant B.1.1.7 in Europe, and with further evolution of spike mutation accumulations shared with the Beta and Gamma variants

Author: Stadtmüller, Marlena, primary, Laubner, Alexa, additional, Rost, Fabian, additional, Winkler, Sylke, additional, Patrasová, Eva, additional, Šimůnková, Lenka, additional, Reinhardt, Susanne, additional, Beil, Johanna, additional, Dalpke, Alexander H., additional, and Yi, Buqing, additional
Published: 2021
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38. Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19

Author: Krämer, Benjamin, primary, Knoll, Rainer, additional, Bonaguro, Lorenzo, additional, ToVinh, Michael, additional, Raabe, Jan, additional, Astaburuaga-García, Rosario, additional, Schulte-Schrepping, Jonas, additional, Kaiser, Kim Melanie, additional, Rieke, Gereon J., additional, Bischoff, Jenny, additional, Monin, Malte B., additional, Hoffmeister, Christoph, additional, Schlabe, Stefan, additional, De Domenico, Elena, additional, Reusch, Nico, additional, Händler, Kristian, additional, Reynolds, Gary, additional, Blüthgen, Nils, additional, Hack, Gudrun, additional, Finnemann, Claudia, additional, Nischalke, Hans D., additional, Strassburg, Christian P., additional, Stephenson, Emily, additional, Su, Yapeng, additional, Gardner, Louis, additional, Yuan, Dan, additional, Chen, Daniel, additional, Goldman, Jason, additional, Rosenstiel, Philipp, additional, Schmidt, Susanne V., additional, Latz, Eicke, additional, Hrusovsky, Kevin, additional, Ball, Andrew J., additional, Johnson, Joe M., additional, Koenig, Paul-Albert, additional, Schmidt, Florian I., additional, Haniffa, Muzlifah, additional, Heath, James R., additional, Kümmerer, Beate M., additional, Keitel, Verena, additional, Jensen, Björn, additional, Stubbemann, Paula, additional, Kurth, Florian, additional, Sander, Leif E., additional, Sawitzki, Birgit, additional, Aschenbrenner, Anna C., additional, Schultze, Joachim L., additional, Nattermann, Jacob, additional, Altmüller, Janine, additional, Angelov, Angel, additional, Bals, Robert, additional, Bartholomäus, Alexander, additional, Becker, Anke, additional, Becker, Matthias, additional, Bezdan, Daniela, additional, Bitzer, Michael, additional, Blumert, Conny, additional, Bonifacio, Ezio, additional, Bork, Peer, additional, Boyke, Bunk, additional, Blum, Helmut, additional, Casadei, Nicolas, additional, Clavel, Thomas, additional, Colome-Tatche, Maria, additional, Cornberg, Markus, additional, De La Rosa Velázquez, Inti Alberto, additional, Diefenbach, Andreas, additional, Dilthey, Alexander, additional, Fischer, Nicole, additional, Förstner, Konrad, additional, Franzenburg, Sören, additional, Frick, Julia-Stefanie, additional, Gabernet, Gisela, additional, Gagneur, Julien, additional, Ganzenmueller, Tina, additional, Gauder, Marie, additional, Geißert, Janina, additional, Goesmann, Alexander, additional, Göpel, Siri, additional, Grundhoff, Adam, additional, Grundmann, Hajo, additional, Hain, Torsten, additional, Hanses, Frank, additional, Hehr, Ute, additional, Heimbach, André, additional, Hoeper, Marius, additional, Horn, Friedemann, additional, Hübschmann, Daniel, additional, Hummel, Michael, additional, Iftner, Thomas, additional, Iftner, Angelika, additional, Illig, Thomas, additional, Janssen, Stefan, additional, Kalinowski, Jörn, additional, Kallies, René, additional, Kehr, Birte, additional, Keller, Andreas, additional, Keppler, Oliver T., additional, Kim-Hellmuth, Sarah, additional, Klein, Christoph, additional, Knop, Michael, additional, Kohlbacher, Oliver, additional, Köhrer, Karl, additional, Korbel, Jan, additional, Kremsner, Peter G., additional, Kühnert, Denise, additional, Kurth, Ingo, additional, Landthaler, Markus, additional, Li, Yang, additional, Ludwig, Kerstin U., additional, Makarewicz, Oliwia, additional, Marini, Federico, additional, Marz, Manja, additional, McHardy, Alice C., additional, Mertes, Christian, additional, Münchhoff, Maximilian, additional, Nahnsen, Sven, additional, Nöthen, Markus, additional, Ntoumi, Francine, additional, Nürnberg, Peter, additional, Ossowski, Stephan, additional, Overmann, Jörg, additional, Peter, Silke, additional, Pfeffer, Klaus, additional, Pink, Isabell, additional, Poetsch, Anna R., additional, Protzer, Ulrike, additional, Pühler, Alfred, additional, Rajewsky, Nikolaus, additional, Ralser, Markus, additional, Reiche, Kristin, additional, Rieß, Olaf, additional, Ripke, Stephan, additional, Nunes da Rocha, Ulisses, additional, Rosenstiel, Philip, additional, Saliba, Antoine-Emmanuel, additional, Sander, Leif Erik, additional, Scheithauer, Simone, additional, Schiffer, Philipp, additional, Schmid-Burgk, Jonathan, additional, Schneider, Wulf, additional, Schulte, Eva-Christina, additional, Sczyrba, Alexander, additional, Sharaf, Mariam L., additional, Singh, Yogesh, additional, Sonnabend, Michael, additional, Stegle, Oliver, additional, Stoye, Jens, additional, Theis, Fabian, additional, Ulas, Thomas, additional, Vehreschild, Janne, additional, Velavan, Thirumalaisamy P., additional, Vogel, Jörg, additional, Volland, Sonja, additional, von Kleist, Max, additional, Walker, Andreas, additional, Walter, Jörn, additional, Wieczorek, Dagmar, additional, Winkler, Sylke, additional, and Ziebuhr, John, additional
Published: 2021
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39. The genome of Schmidtea mediterranea and the evolution of core cellular mechanisms

Author: Grohme, Markus Alexander, Schloissnig, Siegfried, Rozanski, Andrei, Pippel, Martin, Young, George Robert, Winkler, Sylke, Brandl, Holger, Henry, Ian, Dahl, Andreas, Powell, Sean, Hiller, Michael, Myers, Eugene, and Rink, Jochen Christian
Subjects: Regeneration (Biology) -- Genetic aspects -- Observations, Freshwater planarian -- Genetic aspects -- Observations, Genomes -- Observations, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: The planarian Schmidtea mediterranea is an important model for stem cell research and regeneration, but adequate genome resources for this species have been lacking. Here we report a highly contiguous genome assembly of S. mediterranea, using long-read sequencing and a de novo assembler (MARVEL) enhanced for low-complexity reads. The S. mediterranea genome is highly polymorphic and repetitive, and harbours a novel class of giant retroelements. Furthermore, the genome assembly lacks a number of highly conserved genes, including critical components of the mitotic spindle assembly checkpoint, but planarians maintain checkpoint function. Our genome assembly provides a key model system resource that will be useful for studying regeneration and the evolutionary plasticity of core cell biological mechanisms., Author(s): Markus Alexander Grohme [1]; Siegfried Schloissnig (corresponding author) [2]; Andrei Rozanski [1]; Martin Pippel [2]; George Robert Young [3]; Sylke Winkler [1]; Holger Brandl [1]; Ian Henry [1]; Andreas [...]
Published: 2018
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40. The axolotl genome and the evolution of key tissue formation regulators

Author: Nowoshilow, Sergej, Schloissnig, Siegfried, Fei, Ji-Feng, Dahl, Andreas, Pang, Andy W. C., Pippel, Martin, Winkler, Sylke, Hastie, Alex R., Young, George, Roscito, Juliana G., Falcon, Francisco, Knapp, Dunja, Powell, Sean, Cruz, Alfredo, Cao, Han, Habermann, Bianca, Hiller, Michael, Tanaka, Elly M., and Myers, Eugene W.
Subjects: Regeneration (Biology) -- Genetic aspects -- Observations, Genome-wide association studies -- Methods, Mexican axolotl -- Genetic aspects -- Observations, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Salamanders serve as important tetrapod models for developmental, regeneration and evolutionary studies. An extensive molecular toolkit makes the Mexican axolotl (Ambystoma mexicanum) a key representative salamander for molecular investigations. Here we report the sequencing and assembly of the 32-gigabase-pair axolotl genome using an approach that combined long-read sequencing, optical mapping and development of a new genome assembler (MARVEL). We observed a size expansion of introns and intergenic regions, largely attributable to multiplication of long terminal repeat retroelements. We provide evidence that intron size in developmental genes is under constraint and that species-restricted genes may contribute to limb regeneration. The axolotl genome assembly does not contain the essential developmental gene Pax3. However, mutation of the axolotl Pax3 paralogue Pax7 resulted in an axolotl phenotype that was similar to those seen in Pax3[sup./] and Pax7[sup./] mutant mice. The axolotl genome provides a rich biological resource for developmental and evolutionary studies., Author(s): Sergej Nowoshilow [1, 2, 3]; Siegfried Schloissnig (corresponding author) [4]; Ji-Feng Fei [5]; Andreas Dahl [3, 6]; Andy W. C. Pang [7]; Martin Pippel [4]; Sylke Winkler [1]; Alex [...]
Published: 2018
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41. Author Correction: The axolotl genome and the evolution of key tissue formation regulators

Author: Nowoshilow, Sergej, Schloissnig, Siegfried, Fei, Ji-Feng, Dahl, Andreas, Pang, Andy W. C., Pippel, Martin, Winkler, Sylke, Hastie, Alex R., Young, George, Roscito, Juliana G., Falcon, Francisco, Knapp, Dunja, Powell, Sean, Cruz, Alfredo, Cao, Han, Habermann, Bianca, Hiller, Michael, Tanaka, Elly M., and Myers, Eugene W.
Published: 2018
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42. Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

Author: Formenti, Giulio, Rhie, Arang, Balacco, Jennifer, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Brown, Samara, Capodiferro, Marco Rosario, Al-Ajli, Farooq O., Ambrosini, Roberto, Houde, Peter, Koren, Sergey, Oliver, Karen, Smith, Michelle, Skelton, Jason, Betteridge, Emma, Dolucan, Jale, Corton, Craig, Bista, Iliana, Torrance, James, Tracey, Alan, Wood, Jonathan, Uliano-Silva, Marcela, Howe, Kerstin, McCarthy, Shane, Winkler, Sylke, Kwak, Woori, Korlach, Jonas, Fungtammasan, Arkarachai, Fordham, Daniel, Costa, Vania, Mayes, Simon, Chiara, Matteo, Horner, David S., Myers, Eugene, Durbin, Richard, Achilli, Alessandro, Braun, Edward L., Phillippy, Adam M., Jarvis, Erich D., Kirschel, Alexander N. G., Digby, Andrew, Veale, Andrew, Bronikowski, Anne, Murphy, Bob, Robertson, Bruce, Baker, Clare, Mazzoni, Camila, Balakrishnan, Christopher, Lee, Chul, Mead, Daniel, Teeling, Emma, Aiden, Erez Lieberman, Todd, Erica, Eichler, Evan, Naylor, Gavin J. P., Zhang, Guojie, Smith, Jeramiah, Wolf, Jochen, Touchon, Justin, Delmore, Kira, Jakobsen, Kjetill, Komoroske, Lisa, Wilkinson, Mark, Genner, Martin, Pšenička, Martin, Fuxjager, Matthew, Stratton, Mike, Liedvogel, Miriam, Gemmell, Neil, Minias, Piotr, Dunn, Peter O., Sudmant, Peter, Morin, Phil, Ayub, Qasim, Kraus, Robert, Vernes, Sonja, Smith, Steve, Lama, Tanya, Edwards, Taylor, Smith, Tim, Gilbert, Tom, Marques-Bonet, Tomas, Einfeldt, Tony, Venkatesh, Byrappa, Johnson, Warren, Warren, Wes, Bukhman, Yury, Formenti, Giulio [0000-0002-7554-5991], and Apollo - University of Cambridge Repository
Subjects: Vertebrate, Research, Assembly, Sequencing, Duplications, Long reads, Repeats, Mitochondrial DNA
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

43. Deletion of lrrk2 causes early developmental abnormalities and age-dependent increase of monoamine catabolism in the zebrafish brain

Author: Suzzi, Stefano, primary, Ahrendt, Reiner, additional, Hans, Stefan, additional, Semenova, Svetlana A., additional, Chekuru, Avinash, additional, Wirsching, Paul, additional, Kroehne, Volker, additional, Bilican, Saygın, additional, Sayed, Shady, additional, Winkler, Sylke, additional, Spieß, Sandra, additional, Machate, Anja, additional, Kaslin, Jan, additional, Panula, Pertti, additional, and Brand, Michael, additional
Published: 2021
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44. Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Author: Dahn, Hollis A., primary, Mountcastle, Jacquelyn, additional, Balacco, Jennifer, additional, Winkler, Sylke, additional, Bista, Iliana, additional, Schmitt, Anthony D., additional, Pettersson, Olga Vinnere, additional, Formenti, Giulio, additional, Oliver, Karen, additional, Smith, Michelle, additional, Tan, Wenhua, additional, Kraus, Anne, additional, Mac, Stephen, additional, Komoroske, Lisa M., additional, Lama, Tanya, additional, Crawford, Andrew J., additional, Murphy, Robert W., additional, Brown, Samara, additional, Scott, Alan F., additional, Morin, Phillip A., additional, Jarvis, Erich D., additional, and Fedrigo, Olivier, additional
Published: 2021
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45. Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients

Author: Aschenbrenner, Anna C, Mouktaroudi, Maria, Saridaki, Maria, McHardy, Alice, Mertes, Christian, Nöthen, Markus, Nürnberg, Peter, Ohler, Uwe, Ossowski, Stephan, Overmann, Jörg, Pfeffer, Klaus, Poetsch, Anna R, Pühler, Alfred, Knoll, Rainer, Rajewsky, Nikolaus, Ralser, Markus, Rieß, Olaf, Ripke, Stephan, Nunes da Rocha, Ulisses, Rosenstiel, Philip, Saliba, Antoine-Emmanuel, Sander, Leif Erik, Sawitzki, Birgit, Schiffer, Philipp, Pecht, Tal, Schneider, Wulf, Schulte, Eva-Christina, Schultze, Joachim L, Sczyrba, Alexander, Singh, Yogesh, Sonnabend, Michael, Stegle, Oliver, Stoye, Jens, Theis, Fabian, Vehreschild, Janne, Kapellos, Theodore S, Vogel, Jörg, von Kleist, Max, Walker, Andreas, Walter, Jörn, Wieczorek, Dagmar, Winkler, Sylke, Ziebuhr, John, Doulou, Sarandia, Kröger, Charlotte, Herbert, Miriam, Holsten, Lisa, Horne, Arik, Gemünd, Ioanna D, Krämer, Benjamin, Rovina, Nikoletta, Agrawal, Shobhit, Dahm, Kilian, van Uelft, Martina, Drews, Anna, Lenkeit, Lena, Bruse, Niklas, Gerretsen, Jelle, Gierlich, Jannik, Becker, Matthias, Oestreich, Marie, Händler, Kristian, Kraut, Michael, Theis, Heidi, Mengiste, Simachew, De Domenico, Elena, Schulte-Schrepping, Jonas, Seep, Lea, Raabe, Jan, Hoffmeister, Christoph, ToVinh, Michael, Antonakos, Nikolaos, Keitel, Verena, Rieke, Gereon, Talevi, Valentina, Skowasch, Dirk, Aziz, N. Ahmad, Pickkers, Peter, van de Veerdonk, Frank L, Netea, Mihai G, Kox, Matthijs, Nuesch-Germano, Melanie, Breteler, Monique M B, Nattermann, Jacob, Koutsoukou, Antonia, Giamarellos-Bourboulis, Evangelos J, Ulas, Thomas, Initiative, German COVID-19 Omics, Altmüller, Janine, Angelov, Angel, Bals, Robert, Bartholomäus, Alexander, Gkizeli, Konstantina, Becker, Anke, Bitzer, Michael, Bonifacio, Ezio, Bork, Peer, Casadei, Nicolas, Clavel, Thomas, Colome-Tatche, Maria, Diefenbach, Andreas, Dilthey, Alexander, Fischer, Nicole, Bonaguro, Lorenzo, Förstner, Konrad, Franzenburg, Sören, Frick, Julia-Stefanie, Gabernet, Gisela, Gagneur, Julien, Ganzenmüller, Tina, Göpel, Siri, Goesmann, Alexander, Hain, Torsten, Heimbach, André, Reusch, Nico, Hummel, Michael, Iftner, Angelika, Iftner, Thomas, Janssen, Stefan, Kalinowski, Jörn, Kallies, René, Kehr, Birte, Keller, Andreas, Kim-Hellmuth, Sarah, Klein, Christoph, Baßler, Kevin, Kohlbacher, Oliver, Köhrer, Karl, Korbel, Jan, Kühnert, Denise, Kurth, Ingo, Landthaler, Markus, Li, Yang, Ludwig, Kerstin, Makarewicz, Oliwia, and Marz, Manja
Subjects: Cancer Research, Neutrophils, virology [COVID-19], cytology [Neutrophils], Drug repurposing, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], lcsh:Medicine, chemistry [RNA], Severity of Illness Index, pathology [COVID-19], Transcriptome, 0302 clinical medicine, Genetics (clinical), Whole blood, immunology [Neutrophils], Principal Component Analysis, 0303 health sciences, metabolism [Neutrophils], Up-Regulation, 3. Good health, Co-expression analysis, Phenotype, medicine.anatomical_structure, metabolism [RNA], 030220 oncology & carcinogenesis, Molecular disease phenotypes, Molecular Medicine, Technology Platforms, lcsh:QH426-470, blood [RNA], Down-Regulation, drug therapy [COVID-19], Granulocyte, Antiviral Agents, 03 medical and health sciences, Immune system, All institutes and research themes of the Radboud University Medical Center, Severity of illness, Genetics, medicine, Humans, ddc:610, Molecular Biology, 030304 developmental biology, Sequence Analysis, RNA, business.industry, Research, lcsh:R, Drug Repositioning, Case-control study, Blood transcriptomics, COVID-19, Human genetics, COVID-19 Drug Treatment, therapeutic use [Antiviral Agents], lcsh:Genetics, Respiratory failure, Cardiovascular and Metabolic Diseases, Case-Control Studies, Immunology, RNA, Stratification, business, Granulocytes
Abstract: Background The SARS-CoV-2 pandemic is currently leading to increasing numbers of COVID-19 patients all over the world. Clinical presentations range from asymptomatic, mild respiratory tract infection, to severe cases with acute respiratory distress syndrome, respiratory failure, and death. Reports on a dysregulated immune system in the severe cases call for a better characterization and understanding of the changes in the immune system. Methods In order to dissect COVID-19-driven immune host responses, we performed RNA-seq of whole blood cell transcriptomes and granulocyte preparations from mild and severe COVID-19 patients and analyzed the data using a combination of conventional and data-driven co-expression analysis. Additionally, publicly available data was used to show the distinction from COVID-19 to other diseases. Reverse drug target prediction was used to identify known or novel drug candidates based on finding from data-driven findings. Results Here, we profiled whole blood transcriptomes of 39 COVID-19 patients and 10 control donors enabling a data-driven stratification based on molecular phenotype. Neutrophil activation-associated signatures were prominently enriched in severe patient groups, which was corroborated in whole blood transcriptomes from an independent second cohort of 30 as well as in granulocyte samples from a third cohort of 16 COVID-19 patients (44 samples). Comparison of COVID-19 blood transcriptomes with those of a collection of over 3100 samples derived from 12 different viral infections, inflammatory diseases, and independent control samples revealed highly specific transcriptome signatures for COVID-19. Further, stratified transcriptomes predicted patient subgroup-specific drug candidates targeting the dysregulated systemic immune response of the host. Conclusions Our study provides novel insights in the distinct molecular subgroups or phenotypes that are not simply explained by clinical parameters. We show that whole blood transcriptomes are extremely informative for COVID-19 since they capture granulocytes which are major drivers of disease severity.
Published: 2021
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46. Additional file 8 of Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

Author: Formenti, Giulio, Arang Rhie, Balacco, Jennifer, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Brown, Samara, Capodiferro, Marco Rosario, Al-Ajli, Farooq O., Ambrosini, Roberto, Houde, Peter, Koren, Sergey, Oliver, Karen, Smith, Michelle, Skelton, Jason, Betteridge, Emma, Dolucan, Jale, Corton, Craig, Bista, Iliana, Torrance, James, Tracey, Alan, Wood, Jonathan, Uliano-Silva, Marcela, Howe, Kerstin, McCarthy, Shane, Winkler, Sylke, Woori Kwak, Korlach, Jonas, Arkarachai Fungtammasan, Fordham, Daniel, Costa, Vania, Mayes, Simon, Chiara, Matteo, Horner, David S., Myers, Eugene, Durbin, Richard, Achilli, Alessandro, Braun, Edward L., Phillippy, Adam M., and Jarvis, Erich D.
Abstract: Additional file 8: Supplementary Note 1. Relationship between mtDNA sequencing, coverage and genome size.
Published: 2021
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47. Additional file 12 of Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

Author: Formenti, Giulio, Arang Rhie, Balacco, Jennifer, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Brown, Samara, Capodiferro, Marco Rosario, Al-Ajli, Farooq O., Ambrosini, Roberto, Houde, Peter, Koren, Sergey, Oliver, Karen, Smith, Michelle, Skelton, Jason, Betteridge, Emma, Dolucan, Jale, Corton, Craig, Bista, Iliana, Torrance, James, Tracey, Alan, Wood, Jonathan, Uliano-Silva, Marcela, Howe, Kerstin, McCarthy, Shane, Winkler, Sylke, Woori Kwak, Korlach, Jonas, Arkarachai Fungtammasan, Fordham, Daniel, Costa, Vania, Mayes, Simon, Chiara, Matteo, Horner, David S., Myers, Eugene, Durbin, Richard, Achilli, Alessandro, Braun, Edward L., Phillippy, Adam M., and Jarvis, Erich D.
Abstract: Additional file 12. Review history.
Published: 2021
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48. Towards complete and error-free genome assemblies of all vertebrate species

Author: 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, Rhie, Arang, McCarthy, Shane A., Fedrigo, Olivier, Damas, Joana, Formenti, Giulio, Koren, Sergey, Uliano-Silva, Marcela, Chow, William, Fungtammasan, Arkarachai, Kim, Juwan, Lee, Chul, Haase, Bettina, Mountcastle, Jacquelyn, Winkler, Sylke, Paez, Sadye, Howard, Jason, Vernes, Sonja C, Lama, Tanya M, Grützner, Frank, Warren, Wesley C., Balakrishnan, Christopher N., Pippel, Martin, Burt, Dave, George, Julia M., Biegler, Matthew T., Iorns, David, Digby, Andrew, Eason, Daryl, Robertson, Bruce, Edwards, Taylor, Wilkinson, Mark, Turner, George, Malinsky, Milan, Meyer, Axel, Kautt, Andreas F., Franchini, Paolo, Detrich III, H. William, Svardal, Hannes, Wagner, Maximilian, Naylor, Gavin J. P., Mooney, Mark, Simbirsky, Maria, Hannigan, Brett T., Pesout, Trevor, Houck, Marlys L., Misuraca, Ann, Kingan, Sarah B., Hall, Richard, Wood, Jonathan, Kronenberg, Zev, Sović, Ivan, Dunn, Christopher, Ning, Zemin, Hastie, Alex, Lee, Joyce, Selvaraj, Siddarth, Green, Richard E., Putnam, Nicholas H., Gut, Ivo, Dagnew, Robel E., Ghurye, Jay, Garrison, Erik, Sims, Ying, Collins, Joanna, Pelan, Sarah, Torrance, James, Tracey, Alan, Guan, Dengfeng, London, Sarah E., Clayton, David F., Mello, Claudio V., Friedrich, Samantha R., Lovell, Peter V., Osipova, Ekaterina, Al-Ajli, Farooq O., Diekhans, Mark, Secomandi, Simona, Kim, Heebal, Theofanopoulou, Constantina, Hiller, Michael, Zhou, Yang, Harris, Robert S., Makova, Kateryna D., Medvedev, Paul, Hoffman, Jinna, Masterson, Patrick, Nassar, Luis, Clark, Karen, Martin, Fergal, Howe, Kevin, Flicek, Paul, Walenz, Brian P., Kwak, Woori, Clawson, Hiram, Paten, Benedict, Kraus, Robert H. S., Crawford, Andrew J., Gilbert, M. Thomas P., Zhang, Guojie, Venkatesh, Byrappa, Murphy, Robert W., Koepfli, Klaus-Peter, Ko, Byung June, Shapiro, Beth, Johnson, Warren E., Di Palma, Federica, Marqués-Bonet, Tomàs, Teeling, Emma C., Warnow, Tandy, Marshall Graves, Jennifer, Ryder, Oliver A., Haussler, David, O’Brien, Stephen J., Chaisson, Mark, Korlach, Jonas, Lewin, Harris A., Howe, Kerstin, Myers, Eugene W., Durbin, Richard, Phillippy, Adam M., Jarvis, Erich D., Gedman, Gregory L., Cantin, Lindsey J., Thibaud-Nissen, Francoise, Haggerty, Leanne, Bista, Iliana, Smith, Michelle, 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, Rhie, Arang, McCarthy, Shane A., Fedrigo, Olivier, Damas, Joana, Formenti, Giulio, Koren, Sergey, Uliano-Silva, Marcela, Chow, William, Fungtammasan, Arkarachai, Kim, Juwan, Lee, Chul, Haase, Bettina, Mountcastle, Jacquelyn, Winkler, Sylke, Paez, Sadye, Howard, Jason, Vernes, Sonja C, Lama, Tanya M, Grützner, Frank, Warren, Wesley C., Balakrishnan, Christopher N., Pippel, Martin, Burt, Dave, George, Julia M., Biegler, Matthew T., Iorns, David, Digby, Andrew, Eason, Daryl, Robertson, Bruce, Edwards, Taylor, Wilkinson, Mark, Turner, George, Malinsky, Milan, Meyer, Axel, Kautt, Andreas F., Franchini, Paolo, Detrich III, H. William, Svardal, Hannes, Wagner, Maximilian, Naylor, Gavin J. P., Mooney, Mark, Simbirsky, Maria, Hannigan, Brett T., Pesout, Trevor, Houck, Marlys L., Misuraca, Ann, Kingan, Sarah B., Hall, Richard, Wood, Jonathan, Kronenberg, Zev, Sović, Ivan, Dunn, Christopher, Ning, Zemin, Hastie, Alex, Lee, Joyce, Selvaraj, Siddarth, Green, Richard E., Putnam, Nicholas H., Gut, Ivo, Dagnew, Robel E., Ghurye, Jay, Garrison, Erik, Sims, Ying, Collins, Joanna, Pelan, Sarah, Torrance, James, Tracey, Alan, Guan, Dengfeng, London, Sarah E., Clayton, David F., Mello, Claudio V., Friedrich, Samantha R., Lovell, Peter V., Osipova, Ekaterina, Al-Ajli, Farooq O., Diekhans, Mark, Secomandi, Simona, Kim, Heebal, Theofanopoulou, Constantina, Hiller, Michael, Zhou, Yang, Harris, Robert S., Makova, Kateryna D., Medvedev, Paul, Hoffman, Jinna, Masterson, Patrick, Nassar, Luis, Clark, Karen, Martin, Fergal, Howe, Kevin, Flicek, Paul, Walenz, Brian P., Kwak, Woori, Clawson, Hiram, Paten, Benedict, Kraus, Robert H. S., Crawford, Andrew J., Gilbert, M. Thomas P., Zhang, Guojie, Venkatesh, Byrappa, Murphy, Robert W., Koepfli, Klaus-Peter, Ko, Byung June, Shapiro, Beth, Johnson, Warren E., Di Palma, Federica, Marqués-Bonet, Tomàs, Teeling, Emma C., Warnow, Tandy, Marshall Graves, Jennifer, Ryder, Oliver A., Haussler, David, O’Brien, Stephen J., Chaisson, Mark, Korlach, Jonas, Lewin, Harris A., Howe, Kerstin, Myers, Eugene W., Durbin, Richard, Phillippy, Adam M., Jarvis, Erich D., Gedman, Gregory L., Cantin, Lindsey J., Thibaud-Nissen, Francoise, Haggerty, Leanne, Bista, Iliana, and Smith, Michelle
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.
Published: 2021

49. Phylogenetic analysis of SARS-CoV-2 lineage development across the first and second waves in Eastern Germany, 2020

Author: Yi, Buqing, primary, Poetsch, Anna R., additional, Stadtmüller, Marlena, additional, Rost, Fabian, additional, Winkler, Sylke, additional, and Dalpke, Alexander H., additional
Published: 2021
Full Text: View/download PDF

50. Additional file 16 of The round goby genome provides insights into mechanisms that may facilitate biological invasions

Author: Adrian-Kalchhauser, Irene, Blomberg, Anders, Larsson, Tomas, Musilova, Zuzana, Peart, Claire, Pippel, Martin, Solbakken, Monica, Suurväli, Jaanus, Walser, Jean-Claude, Wilson, Joanna, Rosenblad, Magnus Alm, Demian Burguera, Gutnik, Silvia, Michiels, Nico, Töpel, Mats, Pankov, Kirill, Schloissnig, Siegfried, and Winkler, Sylke
Abstract: Figure S9. Schematic of the immunoglobulin locus.
Published: 2020
Full Text: View/download PDF

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