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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. 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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4. 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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5. Evidence of selection in the uncoupling protein 1 gene region suggests local adaptation to solar irradiance in savannah monkeys (Chlorocebus spp.).

Author

Paul Grobler, J, Turner, Trudy, Schmitt, Christopher, Gagnon, Christian, Svardal, Hannes, Jasinska, Anna, Danzy Cramer, Jennifer, and Freimer, Nelson

Subjects
Chlorocebus, cold adaptation, non-shivering thermogenesis, uncoupling protein 1, vervet monkey, Acclimatization, Animals, Chlorocebus aethiops, Phylogeny, South Africa, Thermogenesis, Uncoupling Protein 1
Abstract

In the last 300 thousand years, the genus Chlorocebus expanded from equatorial Africa into the southernmost latitudes of the continent, where colder climate was a probable driver of natural selection. We investigated population-level genetic variation in the mitochondrial uncoupling protein 1 (UCP1) gene region-implicated in non-shivering thermogenesis (NST)-in 73 wild savannah monkeys from three taxa representing this southern expansion (Chlorocebus pygerythrus hilgerti, Chlorocebus cynosuros and Chlorocebus pygerythrus pygerythrus) ranging from Kenya to South Africa. We found 17 single nucleotide polymorphisms with extended haplotype homozygosity consistent with positive selective sweeps, 10 of which show no significant linkage disequilibrium with each other. Phylogenetic generalized least-squares modelling with ecological covariates suggest that most derived allele frequencies are significantly associated with solar irradiance and winter precipitation, rather than overall low temperatures. This selection and association with irradiance is demonstrated by a relatively isolated population in the southern coastal belt of South Africa. We suggest that sunbathing behaviours common to savannah monkeys, in combination with the strength of solar irradiance, may mediate adaptations to thermal stress via NST among savannah monkeys. The variants we discovered all lie in non-coding regions, some with previously documented regulatory functions, calling for further validation and research.

Published
2022

6. 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

7. How genomics can help biodiversity conservation

Author

Aghayan, Sargis A., Alioto, Tyler S., Almudi, Isabel, Alvarez, Nadir, Alves, Paulo C., Amorim do Rosario, Isabel R., Antunes, Agostinho, Arribas, Paula, Baldrian, Petr, Bertorelle, Giorgio, Böhne, Astrid, Bonisoli-Alquati, Andrea, Boštjančić, Ljudevit L., Boussau, Bastien, Breton, Catherine M., Buzan, Elena, Campos, Paula F., Carreras, Carlos, Castro, L. FIlipe C., Chueca, Luis J., Čiampor, Fedor, Conti, Elena, Cook-Deegan, Robert, Croll, Daniel, Cunha, Mónica V., Delsuc, Frédéric, Dennis, Alice B., Dimitrov, Dimitar, Faria, Rui, Favre, Adrien, Fedrigo, Olivier D., Fernández, Rosa, Ficetola, Gentile Francesco, Flot, Jean-François, Gabaldón, Toni, Agius, Dolores R., Giani, Alice M., Gilbert, M. Thomas P., Grebenc, Tine, Guschanski, Katerina, Guyot, Romain, Hausdorf, Bernhard, Hawlitschek, Oliver, Heintzman, Peter D., Heinze, Berthold, Hiller, Michael, Husemann, Martin, Iannucci, Alessio, Irisarri, Iker, Jakobsen, Kjetill S., Klinga, Peter, Kloch, Agnieszka, Kratochwil, Claudius F., Kusche, Henrik, Layton, Kara K.S., Leonard, Jennifer A., Lerat, Emmanuelle, Liti, Gianni, Manousaki, Tereza, Marques-Bonet, Tomas, Matos-Maraví, Pável, Matschiner, Michael, Maumus, Florian, Mc Cartney, Ann M., Meiri, Shai, Melo-Ferreira, José, Mengual, Ximo, Monaghan, Michael T., Montagna, Matteo, Mysłajek, Robert W., Neiber, Marco T., Nicolas, Violaine, Novo, Marta, Ozretić, Petar, Palero, Ferran, Pârvulescu, Lucian, Pascual, Marta, Paulo, Octávio S., Pavlek, Martina, Pegueroles, Cinta, Pellissier, Loïc, Pesole, Graziano, Primmer, Craig R., Riesgo, Ana, Rüber, Lukas, Rubolini, Diego, Salvi, Daniele, Seehausen, Ole, Seidel, Matthias, Studer, Bruno, Theodoridis, Spyros, Thines, Marco, Urban, Lara, Vasemägi, Anti, Vella, Adriana, Vella, Noel, Vernes, Sonja C., Vernesi, Cristiano, Vieites, David R., Wheat, Christopher W., Wörheide, Gert, Wurm, Yannick, Zammit, Gabrielle, Theissinger, Kathrin, Fernandes, Carlos, Formenti, Giulio, Bista, Iliana, Berg, Paul R., Bleidorn, Christoph, Bombarely, Aureliano, Crottini, Angelica, Gallo, Guido R., Godoy, José A., Jentoft, Sissel, Malukiewicz, Joanna, Mouton, Alice, Oomen, Rebekah A., Paez, Sadye, Palsbøll, Per J., Pampoulie, Christophe, Ruiz-López, María J., Secomandi, Simona, Svardal, Hannes, Theofanopoulou, Constantina, de Vries, Jan, Waldvogel, Ann-Marie, Zhang, Guojie, Jarvis, Erich D., Bálint, Miklós, Ciofi, Claudio, Waterhouse, Robert M., Mazzoni, Camila J., and Höglund, Jacob

Published
2023
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8. ACE2 and TMPRSS2 variation in savanna monkeys (Chlorocebus spp.): Potential risk for zoonotic/anthroponotic transmission of SARS-CoV-2 and a potential model for functional studies.

Author

Schmitt, Christopher A, Bergey, Christina M, Jasinska, Anna J, Ramensky, Vasily, Burt, Felicity, Svardal, Hannes, Jorgensen, Matthew J, Freimer, Nelson B, Grobler, J Paul, and Turner, Trudy R

Subjects
Animals, Zoonoses, Pneumonia, Viral, Coronavirus Infections, Primate Diseases, Disease Susceptibility, Serine Endopeptidases, Peptidyl-Dipeptidase A, Pandemics, Spike Glycoprotein, Coronavirus, Whole Genome Sequencing, Betacoronavirus, Chlorocebus aethiops, Pneumonia, Viral, Spike Glycoprotein, Coronavirus, General Science & Technology
Abstract

The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, has devastated health infrastructure around the world. Both ACE2 (an entry receptor) and TMPRSS2 (used by the virus for spike protein priming) are key proteins to SARS-CoV-2 cell entry, enabling progression to COVID-19 in humans. Comparative genomic research into critical ACE2 binding sites, associated with the spike receptor binding domain, has suggested that African and Asian primates may also be susceptible to disease from SARS-CoV-2 infection. Savanna monkeys (Chlorocebus spp.) are a widespread non-human primate with well-established potential as a bi-directional zoonotic/anthroponotic agent due to high levels of human interaction throughout their range in sub-Saharan Africa and the Caribbean. To characterize potential functional variation in savanna monkey ACE2 and TMPRSS2, we inspected recently published genomic data from 245 savanna monkeys, including 163 wild monkeys from Africa and the Caribbean and 82 captive monkeys from the Vervet Research Colony (VRC). We found several missense variants. One missense variant in ACE2 (X:14,077,550; Asp30Gly), common in Ch. sabaeus, causes a change in amino acid residue that has been inferred to reduce binding efficiency of SARS-CoV-2, suggesting potentially reduced susceptibility. The remaining populations appear as susceptible as humans, based on these criteria for receptor usage. All missense variants observed in wild Ch. sabaeus populations are also present in the VRC, along with two splice acceptor variants (at X:14,065,076) not observed in the wild sample that are potentially disruptive to ACE2 function. The presence of these variants in the VRC suggests a promising model for SARS-CoV-2 infection and vaccine and therapy development. In keeping with a One Health approach, characterizing actual susceptibility and potential for bi-directional zoonotic/anthroponotic transfer in savanna monkey populations may be an important consideration for controlling COVID-19 epidemics in communities with frequent human/non-human primate interactions that, in many cases, may have limited health infrastructure.

Published
2020

9. The era of reference genomes in conservation genomics

Author

Formenti, Giulio, Theissinger, Kathrin, Fernandes, Carlos, Bista, Iliana, Bombarely, Aureliano, Bleidorn, Christoph, Čiampor, Fedor, Ciofi, Claudio, Crottini, Angelica, Godoy, José A., Hoglund, Jacob, Malukiewicz, Joanna, Mouton, Alice, Oomen, Rebekah A., Paez, Sadye, Palsbøll, Per, Pampoulie, Christophe, Ruiz-López, María José, Svardal, Hannes, Theofanopoulou, Constantina, de Vries, Jan, Waldvogel, Ann-Marie, Zhang, Goujie, Mazzoni, Camila J., Jarvis, Erich, Bálint, Miklós, Aghayan, Sargis A., Alioto, Tyler S., Almudi, Isabel, Alvarez, Nadir, Alves, Paulo C., Amorim, Isabel R., Antunes, Agostinho, Arribas, Paula, Baldrian, Petr, Berg, Paul R., Bertorelle, Giorgio, Böhne, Astrid, Bonisoli-Alquati, Andrea, Boštjančić, Ljudevit L., Boussau, Bastien, Breton, Catherine M., Buzan, Elena, Campos, Paula F., Carreras, Carlos, Castro, L. FIlipe, Chueca, Luis J., Conti, Elena, Cook-Deegan, Robert, Croll, Daniel, Cunha, Mónica V., Delsuc, Frédéric, Dennis, Alice B., Dimitrov, Dimitar, Faria, Rui, Favre, Adrien, Fedrigo, Olivier D., Fernández, Rosa, Ficetola, Gentile Francesco, Flot, Jean-François, Gabaldón, Toni, Galea Agius, Dolores R., Gallo, Guido R., Giani, Alice M., Gilbert, M. Thomas P., Grebenc, Tine, Guschanski, Katerina, Guyot, Romain, Hausdorf, Bernhard, Hawlitschek, Oliver, Heintzman, Peter D., Heinze, Berthold, Hiller, Michael, Husemann, Martin, Iannucci, Alessio, Irisarri, Iker, Jakobsen, Kjetill S., Jentoft, Sissel, Klinga, Peter, Kloch, Agnieszka, Kratochwil, Claudius F., Kusche, Henrik, Layton, Kara K.S., Leonard, Jennifer A., Lerat, Emmanuelle, Liti, Gianni, Manousaki, Tereza, Marques-Bonet, Tomas, Matos-Maraví, Pável, Matschiner, Michael, Maumus, Florian, Mc Cartney, Ann M., Meiri, Shai, Melo-Ferreira, José, Mengual, Ximo, Monaghan, Michael T., Montagna, Matteo, Mysłajek, Robert W., Neiber, Marco T., Nicolas, Violaine, Novo, Marta, Ozretić, Petar, Palero, Ferran, Pârvulescu, Lucian, Pascual, Marta, Paulo, Octávio S., Pavlek, Martina, Pegueroles, Cinta, Pellissier, Loïc, Pesole, Graziano, Primmer, Craig R., Riesgo, Ana, Rüber, Lukas, Rubolini, Diego, Salvi, Daniele, Seehausen, Ole, Seidel, Matthias, Secomandi, Simona, Studer, Bruno, Theodoridis, Spyros, Thines, Marco, Urban, Lara, Vasemägi, Anti, Vella, Adriana, Vella, Noel, Vernes, Sonja C., Vernesi, Cristiano, Vieites, David R., Waterhouse, Robert M., Wheat, Christopher W., Wörheide, Gert, Wurm, Yannick, Zammit, Gabrielle, Höglund, Jacob, Palsbøll, Per J., Ruiz-López, María J., Zhang, Guojie, and Jarvis, Erich D.

Published
2022
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12. Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate.

Author

Jasinska, Anna J, Zelaya, Ivette, Service, Susan K, Peterson, Christine B, Cantor, Rita M, Choi, Oi-Wa, DeYoung, Joseph, Eskin, Eleazar, Fairbanks, Lynn A, Fears, Scott, Furterer, Allison E, Huang, Yu S, Ramensky, Vasily, Schmitt, Christopher A, Svardal, Hannes, Jorgensen, Matthew J, Kaplan, Jay R, Villar, Diego, Aken, Bronwen L, Flicek, Paul, Nag, Rishi, Wong, Emily S, Blangero, John, Dyer, Thomas D, Bogomolov, Marina, Benjamini, Yoav, Weinstock, George M, Dewar, Ken, Sabatti, Chiara, Wilson, Richard K, Jentsch, J David, Warren, Wesley, Coppola, Giovanni, Woods, Roger P, and Freimer, Nelson B

Subjects
Brain, Animals, Humans, Gene Expression Profiling, Genotype, Phenotype, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Genetic Variation, Genome-Wide Association Study, Chlorocebus aethiops, Genetics, Biotechnology, Human Genome, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

By analyzing multitissue gene expression and genome-wide genetic variation data in samples from a vervet monkey pedigree, we generated a transcriptome resource and produced the first catalog of expression quantitative trait loci (eQTLs) in a nonhuman primate model. This catalog contains more genome-wide significant eQTLs per sample than comparable human resources and identifies sex- and age-related expression patterns. Findings include a master regulatory locus that likely has a role in immune function and a locus regulating hippocampal long noncoding RNAs (lncRNAs), whose expression correlates with hippocampal volume. This resource will facilitate genetic investigation of quantitative traits, including brain and behavioral phenotypes relevant to neuropsychiatric disorders.

Published
2017

13. Ancient hybridization and strong adaptation to viruses across African vervet monkey populations.

Author

Svardal, Hannes, Jasinska, Anna J, Apetrei, Cristian, Coppola, Giovanni, Huang, Yu, Schmitt, Christopher A, Jacquelin, Beatrice, Ramensky, Vasily, Müller-Trutwin, Michaela, Antonio, Martin, Weinstock, George, Grobler, J Paul, Dewar, Ken, Wilson, Richard K, Turner, Trudy R, Warren, Wesley C, Freimer, Nelson B, and Nordborg, Magnus

Subjects
CD4-Positive T-Lymphocytes, Animals, Macaca mulatta, Simian Acquired Immunodeficiency Syndrome, Gene Expression Profiling, Hybridization, Genetic, Adaptation, Physiological, Phylogeny, Species Specificity, Africa, Simian immunodeficiency virus, Gene Regulatory Networks, Host-Pathogen Interactions, Genetic Variation, Gene Ontology, Chlorocebus aethiops, Simian Immunodeficiency Virus, Human Genome, Genetics, Biotechnology, Good Health and Well Being, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Vervet monkeys are among the most widely distributed nonhuman primates, show considerable phenotypic diversity, and have long been an important biomedical model for a variety of human diseases and in vaccine research. Using whole-genome sequencing data from 163 vervets sampled from across Africa and the Caribbean, we find high diversity within and between taxa and clear evidence that taxonomic divergence was reticulate rather than following a simple branching pattern. A scan for diversifying selection across taxa identifies strong and highly polygenic selection signals affecting viral processes. Furthermore, selection scores are elevated in genes whose human orthologs interact with HIV and in genes that show a response to experimental simian immunodeficiency virus (SIV) infection in vervet monkeys but not in rhesus macaques, suggesting that part of the signal reflects taxon-specific adaptation to SIV.

Published
2017

14. A pangenomic perspective of the Lake Malawi cichlid radiation reveals extensive structural variation driven by transposable elements

Author

Quah, Fu Xiang, primary, Almeida, Miguel Vasconcelos, additional, Blumer, Moritz, additional, Yuan, Chengwei Ulrika, additional, Fischer, Bettina, additional, See, Kirsten, additional, Jackson, Ben, additional, Zatta, Richard, additional, Rusuwa, Bosco, additional, Turner, George F., additional, Santos, M. Emília, additional, Svardal, Hannes, additional, Hemberg, Martin, additional, Durbin, Richard, additional, and Miska, Eric, additional

Published
2024
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15. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

Author

Kawakatsu, Taiji, Huang, Shao-shan Carol, Jupe, Florian, Sasaki, Eriko, Schmitz, Robert J, Urich, Mark A, Castanon, Rosa, Nery, Joseph R, Barragan, Cesar, He, Yupeng, Chen, Huaming, Dubin, Manu, Lee, Cheng-Ruei, Wang, Congmao, Bemm, Felix, Becker, Claude, O’Neil, Ryan, O’Malley, Ronan C, Quarless, Danjuma X, Consortium, The 1001 Genomes, Alonso-Blanco, Carlos, Andrade, Jorge, Bergelson, Joy, Borgwardt, Karsten, Chae, Eunyoung, Dezwaan, Todd, Ding, Wei, Ecker, Joseph R, Expósito-Alonso, Moisés, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G, Hancock, Angela, Henz, Stefan R, Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A, Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Chen-Ruei, Meng, Dazhe, Michael, Todd P, Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina, Picó, F Xavier, Platzer, Alexander, Rabanal, Fernando A, Rodriguez, Alex, Rowan, Beth A, Salomé, Patrice A, Schmid, Karl, Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M, Todd, Donald, Volchenboum, Samuel L, Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, Zhou, Xuefeng, and Schork, Nicholas J

Subjects
Human Genome, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Arabidopsis, DNA Methylation, Epigenesis, Genetic, Epigenomics, Gene Expression Regulation, Plant, Genome, Plant, Transcriptome, Genomes Consortium, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant.

Published
2016

16. A general condition for adaptive genetic polymorphism in temporally and spatially heterogeneous environments

Author

Svardal, Hannes, Rueffler, Claus, and Hermisson, Joachim

Subjects
Quantitative Biology - Populations and Evolution, 92Dxx
Abstract

Both evolution and ecology have long been concerned with the impact of variable environmental conditions on observed levels of genetic diversity within and between species. We model the evolution of a quantitative trait under selection that fluctuates in space and time, and derive an analytical condition for when these fluctuations promote genetic diversification. As ecological scenario we use a generalized island model with soft selection within patches in which we incorporate generation overlap. We allow for arbitrary fluctuations in the environment including spatio-temporal correlations and any functional form of selection on the trait. Using the concepts of invasion fitness and evolutionary branching, we derive a simple and transparent condition for the adaptive evolution and maintenance of genetic diversity. This condition relates the strength of selection within patches to expectations and variances in the environmental conditions across space and time. Our results unify, clarify, and extend a number of previous results on the evolution and maintenance of genetic variation under fluctuating selection. Individual-based simulations show that our results are independent of the details of the genetic architecture and on whether reproduction is clonal or sexual. The onset of increased genetic variance is predicted accurately also in small populations in which alleles can go extinct due to environmental stochasticity., Comment: Accepted for publication in Theoretical Population Biology

Published
2014

17. The genome of the vervet (Chlorocebus aethiops sabaeus)

Author

Warren, Wesley C, Jasinska, Anna J, García-Pérez, Raquel, Svardal, Hannes, Tomlinson, Chad, Rocchi, Mariano, Archidiacono, Nicoletta, Capozzi, Oronzo, Minx, Patrick, Montague, Michael J, Kyung, Kim, Hillier, LaDeana W, Kremitzki, Milinn, Graves, Tina, Chiang, Colby, Hughes, Jennifer, Tran, Nam, Huang, Yu, Ramensky, Vasily, Choi, Oi-wa, Jung, Yoon J, Schmitt, Christopher A, Juretic, Nikoleta, Wasserscheid, Jessica, Turner, Trudy R, Wiseman, Roger W, Tuscher, Jennifer J, Karl, Julie A, Schmitz, Jörn E, Zahn, Roland, O'Connor, David H, Redmond, Eugene, Nisbett, Alex, Jacquelin, Béatrice, Müller-Trutwin, Michaela C, Brenchley, Jason M, Dione, Michel, Antonio, Martin, Schroth, Gary P, Kaplan, Jay R, Jorgensen, Matthew J, Thomas, Gregg WC, Hahn, Matthew W, Raney, Brian J, Aken, Bronwen, Nag, Rishi, Schmitz, Juergen, Churakov, Gennady, Noll, Angela, Stanyon, Roscoe, Webb, David, Thibaud-Nissen, Francoise, Nordborg, Magnus, Marques-Bonet, Tomas, Dewar, Ken, Weinstock, George M, Wilson, Richard K, and Freimer, Nelson B

Subjects
Human Genome, Biotechnology, Genetics, Infection, Animals, Chlorocebus aethiops, Chromosome Painting, Computational Biology, Evolution, Molecular, Gene Rearrangement, Genetic Variation, Genome, Genomics, Karyotype, Major Histocompatibility Complex, Molecular Sequence Annotation, Phylogeny, Phylogeography, Biological Sciences, Medical and Health Sciences, Bioinformatics
Abstract

We describe a genome reference of the African green monkey or vervet (Chlorocebus aethiops). This member of the Old World monkey (OWM) superfamily is uniquely valuable for genetic investigations of simian immunodeficiency virus (SIV), for which it is the most abundant natural host species, and of a wide range of health-related phenotypes assessed in Caribbean vervets (C. a. sabaeus), whose numbers have expanded dramatically since Europeans introduced small numbers of their ancestors from West Africa during the colonial era. We use the reference to characterize the genomic relationship between vervets and other primates, the intra-generic phylogeny of vervet subspecies, and genome-wide structural variations of a pedigreed C. a. sabaeus population. Through comparative analyses with human and rhesus macaque, we characterize at high resolution the unique chromosomal fission events that differentiate the vervets and their close relatives from most other catarrhine primates, in whom karyotype is highly conserved. We also provide a summary of transposable elements and contrast these with the rhesus macaque and human. Analysis of sequenced genomes representing each of the main vervet subspecies supports previously hypothesized relationships between these populations, which range across most of sub-Saharan Africa, while uncovering high levels of genetic diversity within each. Sequence-based analyses of major histocompatibility complex (MHC) polymorphisms reveal extremely low diversity in Caribbean C. a. sabaeus vervets, compared to vervets from putatively ancestral West African regions. In the C. a. sabaeus research population, we discover the first structural variations that are, in some cases, predicted to have a deleterious effect; future studies will determine the phenotypic impact of these variations.

Published
2015

20. 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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22. How genomics can help biodiversity conservation

Author

Theissinger, Kathrin, primary, Fernandes, Carlos, additional, Formenti, Giulio, additional, Bista, Iliana, additional, Berg, Paul R., additional, Bleidorn, Christoph, additional, Bombarely, Aureliano, additional, Crottini, Angelica, additional, Gallo, Guido R., additional, Godoy, José A., additional, Jentoft, Sissel, additional, Malukiewicz, Joanna, additional, Mouton, Alice, additional, Oomen, Rebekah A., additional, Paez, Sadye, additional, Palsbøll, Per J., additional, Pampoulie, Christophe, additional, Ruiz-López, María J., additional, Secomandi, Simona, additional, Svardal, Hannes, additional, Theofanopoulou, Constantina, additional, de Vries, Jan, additional, Waldvogel, Ann-Marie, additional, Zhang, Guojie, additional, Jarvis, Erich D., additional, Bálint, Miklós, additional, Ciofi, Claudio, additional, Waterhouse, Robert M., additional, Mazzoni, Camila J., additional, Höglund, Jacob, additional, Aghayan, Sargis A., additional, Alioto, Tyler S., additional, Almudi, Isabel, additional, Alvarez, Nadir, additional, Alves, Paulo C., additional, Amorim do Rosario, Isabel R., additional, Antunes, Agostinho, additional, Arribas, Paula, additional, Baldrian, Petr, additional, Bertorelle, Giorgio, additional, Böhne, Astrid, additional, Bonisoli-Alquati, Andrea, additional, Boštjančić, Ljudevit L., additional, Boussau, Bastien, additional, Breton, Catherine M., additional, Buzan, Elena, additional, Campos, Paula F., additional, Carreras, Carlos, additional, Castro, L. FIlipe C., additional, Chueca, Luis J., additional, Čiampor, Fedor, additional, Conti, Elena, additional, Cook-Deegan, Robert, additional, Croll, Daniel, additional, Cunha, Mónica V., additional, Delsuc, Frédéric, additional, Dennis, Alice B., additional, Dimitrov, Dimitar, additional, Faria, Rui, additional, Favre, Adrien, additional, Fedrigo, Olivier D., additional, Fernández, Rosa, additional, Ficetola, Gentile Francesco, additional, Flot, Jean-François, additional, Gabaldón, Toni, additional, Agius, Dolores R., additional, Giani, Alice M., additional, Gilbert, M. Thomas P., additional, Grebenc, Tine, additional, Guschanski, Katerina, additional, Guyot, Romain, additional, Hausdorf, Bernhard, additional, Hawlitschek, Oliver, additional, Heintzman, Peter D., additional, Heinze, Berthold, additional, Hiller, Michael, additional, Husemann, Martin, additional, Iannucci, Alessio, additional, Irisarri, Iker, additional, Jakobsen, Kjetill S., additional, Klinga, Peter, additional, Kloch, Agnieszka, additional, Kratochwil, Claudius F., additional, Kusche, Henrik, additional, Layton, Kara K.S., additional, Leonard, Jennifer A., additional, Lerat, Emmanuelle, additional, Liti, Gianni, additional, Manousaki, Tereza, additional, Marques-Bonet, Tomas, additional, Matos-Maraví, Pável, additional, Matschiner, Michael, additional, Maumus, Florian, additional, Mc Cartney, Ann M., additional, Meiri, Shai, additional, Melo-Ferreira, José, additional, Mengual, Ximo, additional, Monaghan, Michael T., additional, Montagna, Matteo, additional, Mysłajek, Robert W., additional, Neiber, Marco T., additional, Nicolas, Violaine, additional, Novo, Marta, additional, Ozretić, Petar, additional, Palero, Ferran, additional, Pârvulescu, Lucian, additional, Pascual, Marta, additional, Paulo, Octávio S., additional, Pavlek, Martina, additional, Pegueroles, Cinta, additional, Pellissier, Loïc, additional, Pesole, Graziano, additional, Primmer, Craig R., additional, Riesgo, Ana, additional, Rüber, Lukas, additional, Rubolini, Diego, additional, Salvi, Daniele, additional, Seehausen, Ole, additional, Seidel, Matthias, additional, Studer, Bruno, additional, Theodoridis, Spyros, additional, Thines, Marco, additional, Urban, Lara, additional, Vasemägi, Anti, additional, Vella, Adriana, additional, Vella, Noel, additional, Vernes, Sonja C., additional, Vernesi, Cristiano, additional, Vieites, David R., additional, Wheat, Christopher W., additional, Wörheide, Gert, additional, Wurm, Yannick, additional, and Zammit, Gabrielle, additional

Published
2023
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24. How genomics can help biodiversity conservation

Author

Theissinger, Kathrin, Fernandes, Carlos, Formenti, Giulio, Bista, Iliana, Berg, Paul R., Bleidorn, Christoph, Bombarely, Aureliano, Crottini, Angelica, Gallo, Guido R., Godoy, Jose A., Jentoft, Sissel, Malukiewicz, Joanna, Mouton, Alice, Oomen, Rebekah A., Paez, Sadye, Palsboll, Per J., Pampoulie, Christophe, Ruiz-Lopez, Maria J., Secomandi, Simona, Svardal, Hannes, Theofanopoulou, Constantina, de Vries, Jan, Waldvogel, Ann-Marie, Zhang, Guojie, Jarvis, Erich D., Balint, Miklos, Ciofi, Claudio, Waterhouse, Robert M., Mazzoni, Camila J., Höglund, Jacob, Guschanski, Katerina, Theissinger, Kathrin, Fernandes, Carlos, Formenti, Giulio, Bista, Iliana, Berg, Paul R., Bleidorn, Christoph, Bombarely, Aureliano, Crottini, Angelica, Gallo, Guido R., Godoy, Jose A., Jentoft, Sissel, Malukiewicz, Joanna, Mouton, Alice, Oomen, Rebekah A., Paez, Sadye, Palsboll, Per J., Pampoulie, Christophe, Ruiz-Lopez, Maria J., Secomandi, Simona, Svardal, Hannes, Theofanopoulou, Constantina, de Vries, Jan, Waldvogel, Ann-Marie, Zhang, Guojie, Jarvis, Erich D., Balint, Miklos, Ciofi, Claudio, Waterhouse, Robert M., Mazzoni, Camila J., Höglund, Jacob, and Guschanski, Katerina

Abstract

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics., Katerina Guschanski är bidragsgivare till forskningsöversikten och ingår i gruppen The European Reference Genome Atlas Consortium

Published
2023
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25. The European Reference Genome Atlas:piloting a decentralised approach to equitable biodiversity genomics

Author

Mc Cartney, Ann M, Formenti, Giulio, Mouton, Alice, Panis, Diego De, Marins, Luisa S, Leitão, Henrique G, Diedericks, Genevieve, Kirangwa, Joseph, Morselli, Marco, Salces-Ortiz, Judit, Escudero, Nuria, Iannucci, Alessio, Natali, Chiara, Svardal, Hannes, Fernández, Rosa, Pooter, Tim De, Joris, Geert, Strazisar, Mojca, Wood, Jo, 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, Bed’Hom, Bertrand, Belser, Caroline, Bergsten, Johannes, Bertrand, Laurie, Bilandžija, Helena, Binzer-Panchal, Mahesh, Bista, Iliana, Blaxter, Mark, Borges, Paulo AV, Dias, Guilherme Borges, Bosse, Mirte, Garg, Shilpa, Madsen, Ole, Stiller, Josefin, Mc Cartney, Ann M, Formenti, Giulio, Mouton, Alice, Panis, Diego De, Marins, Luisa S, Leitão, Henrique G, Diedericks, Genevieve, Kirangwa, Joseph, Morselli, Marco, Salces-Ortiz, Judit, Escudero, Nuria, Iannucci, Alessio, Natali, Chiara, Svardal, Hannes, Fernández, Rosa, Pooter, Tim De, Joris, Geert, Strazisar, Mojca, Wood, Jo, 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, Bed’Hom, Bertrand, Belser, Caroline, Bergsten, Johannes, Bertrand, Laurie, Bilandžija, Helena, Binzer-Panchal, Mahesh, Bista, Iliana, Blaxter, Mark, Borges, Paulo AV, Dias, Guilherme Borges, Bosse, Mirte, Garg, Shilpa, Madsen, Ole, and Stiller, Josefin

Abstract

A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all 1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.Competing Interest StatementThe authors have declared no competing interest.Biodiversity genomicsThe application of genomic methods to research biodiversity.BUSCOA bioinformatic method (Benchmarking Universal Single-Copy Orthologues) used to e

Published
2023

26. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

Author

Alonso-Blanco, Carlos, Andrade, Jorge, Becker, Claude, Bemm, Felix, Bergelson, Joy, Borgwardt, Karsten, Chae, Eunyoung, Dezwaan, Todd, Ding, Wei, Ecker, Joseph R., Expósito-Alonso, Moisés, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela, Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Chen-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina, Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl, Schmitz, Robert J., Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, Congmao, Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, Zhou, Xuefeng, Kawakatsu, Taiji, Huang, Shao-shan Carol, Jupe, Florian, Sasaki, Eriko, Urich, Mark A., Castanon, Rosa, Nery, Joseph R., Barragan, Cesar, He, Yupeng, Chen, Huaming, Dubin, Manu, Lee, Cheng-Ruei, O’Neil, Ryan, O’Malley, Ronan C., Quarless, Danjuma X., and Schork, Nicholas J.

Published
2016
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27. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

Author

Alonso-Blanco, Carlos, Andrade, Jorge, Becker, Claude, Bemm, Felix, Bergelson, Joy, Borgwardt, Karsten M., Cao, Jun, Chae, Eunyoung, Dezwaan, Todd M., Ding, Wei, Ecker, Joseph R., Exposito-Alonso, Moises, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela M., Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Cheng-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina Yu., Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl J., Schmitz, Robert J., Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, Congmao, Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, and Zhou, Xuefeng

Published
2016
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32. Phylogenomics of trophically diverse cichlids disentangles processes driving adaptive radiation and repeated trophic transitions

Author

Singh, Pooja, primary, Irisarri, Iker, additional, Torres‐Dowdall, Julián, additional, Thallinger, Gerhard G., additional, Svardal, Hannes, additional, Lemmon, Emily Moriarty, additional, Lemmon, Alan R., additional, Koblmüller, Stephan, additional, Meyer, Axel, additional, and Sturmbauer, Christian, additional

Published
2022
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39. Genomic consequences of domestication of the Siamese fighting fish

Author

Kwon, Young Mi, primary, Vranken, Nathan, additional, Hoge, Carla, additional, Lichak, Madison R., additional, Norovich, Amy L., additional, Francis, Kerel X., additional, Camacho-Garcia, Julia, additional, Bista, Iliana, additional, Wood, Jonathan, additional, McCarthy, Shane, additional, Chow, William, additional, Tan, Heok Hui, additional, Howe, Kerstin, additional, Bandara, Sepalika, additional, von Lintig, Johannes, additional, Rüber, Lukas, additional, Durbin, Richard, additional, Svardal, Hannes, additional, and Bendesky, Andres, additional

Published
2022
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40. Publisher Correction: Ancient hybridization and strong adaptation to viruses across African vervet monkey populations

Author

Svardal, Hannes, Jasinska, Anna J, Apetrei, Cristian, Coppola, Giovanni, Huang, Yu, Schmitt, Christopher A, Jacquelin, Beatrice, Ramensky, Vasily, Müller-Trutwin, Michaela, Antonio, Martin, Weinstock, George, Grobler, J Paul, Dewar, Ken, Wilson, Richard K, Turner, Trudy R, Warren, Wesley C, Freimer, Nelson B, and Nordborg, Magnus

Published
2018
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42. Genomic consequences of domestication of the Siamese fighting fish

Author

Kwon, Young Mi, Vranken, Nathan, Hoge, Carla, Lichak, Madison R, Francis, Kerel X, Camacho-Garcia, Julia, Bista, Iliana, Wood, Jonathan, McCarthy, Shane, Chow, William, Tan, Heok Hui, Howe, Kerstin, Bandara, Sepalika, von Lintig, Johannes, Rüber, Lukas, Durbin, Richard, Svardal, Hannes, and Bendesky, Andres

Subjects
570 Life sciences, biology
Abstract

Siamese fighting fish, commonly known as betta, are among the world’s most popular and morphologically diverse pet fish, but the genetic processes leading to their domestication and phenotypic diversification are largely unknown. We assembled de novo the genome of a wild Betta splendens and whole-genome sequenced multiple individuals across five species within the B. splendens species complex, including wild populations and domesticated ornamental betta. Given our estimate of the mutation rate from pedigrees, our analyses suggest that betta were domesticated at least 1,000 years ago, centuries earlier than previously thought. Ornamental betta individuals have variable contributions from other Betta species and have also introgressed into wild populations of those species. We identify dmrt1 as the main sex determination gene in ornamental betta but not in wild B. splendens, and find evidence for recent directional selection at the X-allele of the locus. Furthermore, we find genes with signatures of recent, strong selection that have large effects on color in specific parts of the body, or the shape of individual fins, and are almost all unlinked. Our results demonstrate how simple genetic architectures paired with anatomical modularity can lead to vast phenotypic diversity generated during animal domestication, and set the stage for using betta as a modern system for evolutionary genetics.

Published
2021
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43. 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

44. Genomic consequences of domestication of the Siamese fighting fish

Author

Kwon, Young Mi, primary, Vranken, Nathan, additional, Hoge, Carla, additional, Lichak, Madison R, additional, Francis, Kerel X, additional, Camacho-Garcia, Julia, additional, Bista, Iliana, additional, Wood, Jonathan, additional, McCarthy, Shane, additional, Chow, William, additional, Tan, Heok Hui, additional, Howe, Kerstin, additional, Bandara, Sepalika, additional, von Lintig, Johannes, additional, Rüber, Lukas, additional, Durbin, Richard, additional, Svardal, Hannes, additional, and Bendesky, Andres, additional

Published
2021
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45. Evolutionary Genomics at the Human–Environment Interface in Africa

Author

Kamng’ona, Arox, Svardal, Hannes, Rusuwa, Bosco, Linderoth, Tyler, Kiran, Anmol, Charmantier, A., Lattorff, H Michael G, Cagan, Alex, Ommeh, Sheila, Kamng'ona, Arox, Katongo, Cyprian, Santos, M Emília, Durbin, Richard, Kumwenda, Benjamin, Visscher, Peter, von der Heyden, Sophie, Malawi, Smbe, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), SMBE Malawi, Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, 0303 health sciences, Human environment, human impact, Interface (Java), evolutionary genomics, Genomics, challenges, Biology, 010603 evolutionary biology, 01 natural sciences, Data science, 03 medical and health sciences, Chemistry, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Africa, Genetics, Human medicine, SMBE regional meeting, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Evolutionary genomics, meeting report
Abstract

We report on the first meeting of SMBE in Africa. SMBE Malawi was initiated to bring together African and international researchers who use genetics or genomics to study natural systems impacted by human activities. The goals of this conference were 1) to reach a world-class standard of science with a large number of contributions from Africa, 2) to initiate exchange between African and international researchers, and 3) to identify challenges and opportunities for evolutionary genomics research in Africa. As repored, we think that we have achieved these goals and make suggestions on the way forward for African evolutionary genomics research.

Published
2020
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49. Towards complete and error-free genome assemblies of all vertebrate species

Author

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

Published
2020
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50. ACE2 and TMPRSS2 variation in savanna monkeys (Chlorocebus spp.): Potential risk for zoonotic/anthroponotic transmission of SARS-CoV-2 and a potential model for functional studies

Author

Schmitt, Christopher A., primary, Bergey, Christina M., additional, Jasinska, Anna J., additional, Ramensky, Vasily, additional, Burt, Felicity, additional, Svardal, Hannes, additional, Jorgensen, Matthew J., additional, Freimer, Nelson B., additional, Grobler, J. Paul, additional, and Turner, Trudy R., additional

Published
2020
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