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1. An integrated spatio-temporal view of riverine biodiversity using environmental DNA metabarcoding

Author

Perry, William Bernard, Seymour, Mathew, Orsini, Luisa, Jâms, Ifan Bryn, Milner, Nigel, Edwards, François, Harvey, Rachel, de Bruyn, Mark, Bista, Iliana, Walsh, Kerry, Emmett, Bridget, Blackman, Rosetta, Altermatt, Florian, Lawson Handley, Lori, Mächler, Elvira, Deiner, Kristy, Bik, Holly M., Carvalho, Gary, Colbourne, John, Cosby, Bernard Jack, Durance, Isabelle, and Creer, Simon

Published
2024
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2. 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

3. 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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4. A practical guide to DNA-based methods for biodiversity assessment

Author

Bruce, Kat, primary, Blackman, Rosetta, additional, Bourlat, Sarah J., additional, Hellström, Ann Micaela, additional, Bakker, Judith, additional, Bista, Iliana, additional, Bohmann, Kristine, additional, Bouchez, Agnès, additional, Brys, Rein, additional, Clark, Katie, additional, Elbrecht, Vasco, additional, Fazi, Stefano, additional, Fonseca, Vera, additional, Hänfling, Bernd, additional, Leese, Florian, additional, Mächler, Elvira, additional, Mahon, Andrew R., additional, Meissner, Kristian, additional, Panksep, Kristel, additional, Pawlowski, Jan, additional, Schmidt Yáñez, Paul, additional, Seymour, Mathew, additional, Thalinger, Bettina, additional, Valentini, Alice, additional, Woodcock, Paul, additional, Traugott, Michael, additional, Vasselon, Valentin, additional, and Deiner, Kristy, additional

Published
2021
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5. Defining a high throughput sequencing identification framework for freshwater ecosystem biomonitoring

Author

Bista, Iliana-Aglaia and Creer, Simon

Subjects
577.6
Abstract

Freshwater ecosystems are currently amongst the most threatened habitats due to high levels of anthropogenic stress and increasing efforts are required to monitor their status and assess aquatic biodiversity. Biomonitoring, which is the systematic measurement of the responses of aquatic biota to environmental stressors, is used to evaluate ecosystem status. Macroinvertebrates are commonly used organisms for ecosystem assessment, due to their numerous biomonitoring qualities, which qualify them as ecological indicators. Traditional taxonomy-based monitoring is labour intensive, which limits the throughput, and is often inefficient in providing species level identification, which limits the accuracy of detections. The introduction of molecular based methods for biomonitoring, especially when coupled with High Throughput Sequencing (HTS) applications, offers a step change in ecosystem monitoring. Here I tested the utility of DNA based applications for increasing the efficiency of freshwater ecosystem biomonitoring, using benthic macroinvertebrates as a target group. For the first part of this work, I used DNA barcoding of the Cytochrome Oxidase Subunit I (COI), from individual specimens, to populate a barcode reference library for 94 species of Trichoptera, Gastropoda and Chironomidae from the UK. Then, I used High Throughput Sequencing (HTS) methods to characterise diversity from complex environmental samples. First, I used metabarcoding of aqueous environmental DNA (eDNA) and community invertebrate samples (Chironomidae pupal exuviae), collected on regular intervals throughout a year, to identify diversity levels and temporal patterns of community variation on ecosystem-wide and group specific scales. Finally, I used a structured design of mock macroinvertebrate communities, of known biomass content, to perform a comparison between PCR-based metabarcoding of the COI gene and PCR-free shotgun sequencing of mitochondrial genomes (mito-metagenomics), and evaluate their efficiency for accurate characterisation of biomass content of bulk samples. Overall, HTS has demonstrated great potential for advancing biomonitoring efforts, allowing ecosystem scale diversity detection from non-invasive types of samples, such as eDNA, whilst moving into mito-metagenomic work could improve the field even further by improving quantitative abundance results on the community composition level.

Published
2016

8. 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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9. 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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10. Genomics of cold adaptations in the Antarctic notothenioid fish radiation

Author

Bista, Iliana, primary, Wood, Jonathan M. D., additional, Desvignes, Thomas, additional, McCarthy, Shane A., additional, Matschiner, Michael, additional, Ning, Zemin, additional, Tracey, Alan, additional, Torrance, James, additional, Sims, Ying, additional, Chow, William, additional, Smith, Michelle, additional, Oliver, Karen, additional, Haggerty, Leanne, additional, Salzburger, Walter, additional, Postlethwait, John H., additional, Howe, Kerstin, additional, Clark, Melody S., additional, William Detrich, H., additional, Christina Cheng, C.-H., additional, Miska, Eric A., additional, and Durbin, Richard, additional

Published
2023
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11. 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, 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

Subjects
Genetics
Published
2023

12. Building the Molecular Biodiversity Greece Community

Author

Aravanopoulos, Filippos A, Arvanitidis, Christos, Bista, Iliana, Dailianis, Thanos, Galanis, Alex, Ioannidis, Panagiotis, Kapli, Paschalia, Klapa, Maria I., Kolovos, Petros, Kotoulas, Georgios, Magoulas, Antonios N., Manousaki, Tereza, Pafilis, Evangelos, Papageorgiou, Aristotelis C., Papakostas, Spiros, Paragkamian, Savvas, Pavlidis, Pavlos, Pavloudi, Christina, Poulakakis, Nikos, Psomopoulos, Fotis, Reczko, Martin, Sagonas, Kostas, Stamatakis, Alexandros, Theofanopoulou, Constantina, Triantafyllidis, Alexandros, Tsigenopoulos, Costas S., Vasileiadou, Katerina, and Zafeiropoulos, Haris

Subjects
strategy document, molecular biodiversity, Greece, network of networks, community building
Abstract

In the face of the biodiversity crisis, concerted efforts towards understanding the effects of climate change and habitat loss and fragmentation, both locally and globally, are urgently needed. These are often attempted by leveraging the advances of modern genomics and bioinformatics methodologies. Especially in biodiversity hotspots, the need to understand, monitor and mitigate the loss of biodiversity is pivotal. Greece is a country with especially high endemism. A large percentage of its endemic species is threatened by climate change and human activities. To this end, the national academic community in biodiversity genomics has established a corresponding network of scientists from various Greek research institutes and universities covering different disciplines of biodiversity research. The network aims to support and combine individual actions to establish a Task Force that will channel the flow of information amongst researchers, policy makers, stakeholders and the local society. Our overarching goal is to build a sustainable community and infrastructure for the efficient management of the entire molecular biodiversity data cycle (i.e., from production and storage to the analysis and modelling of data, development of computational tools, and knowledge extraction). Using national and European infrastructures, such as ELIXIR and LifeWatch, we envision to set the ground for studying biodiversity through the lens of biodiversity genomics and offer evidence-based knowledge to guide management of the habitats and the biodiversity they host, as well as the implementation of appropriate policies.

Published
2022
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13. Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis

Author

Dallaire, Alexandra, Manley, Bethan F, Wilkens, Maya, Bista, Iliana, Quan, Clement, Evangelisti, Edouard, Bradshaw, Charles R, Ramakrishna, Navin B, Schornack, Sebastian, Butter, Falk, Paszkowski, Uta, Miska, Eric A, Dallaire, Alexandra [0000-0003-1097-7766], Manley, Bethan F [0000-0002-0137-6953], Wilkens, Maya [0000-0003-4631-6177], Bista, Iliana [0000-0002-6155-3093], Evangelisti, Edouard [0000-0002-7218-7850], Bradshaw, Charles R [0000-0002-3528-458X], Ramakrishna, Navin B [0000-0003-2974-9886], Schornack, Sebastian [0000-0002-7836-5881], Butter, Falk [0000-0002-7197-7279], Paszkowski, Uta [0000-0002-7279-7632], Miska, Eric A [0000-0002-4450-576X], and Apollo - University of Cambridge Repository

Subjects
3107 Microbiology, 1.1 Normal biological development and functioning, 3103 Ecology, Human Genome, Genetics, 1 Underpinning research, 3105 Genetics, 31 Biological Sciences, Biotechnology
Abstract

Arbuscular mycorrhizal (AM) fungi form mutualistic relationships with most land plant species. AM fungi have long been considered as ancient asexuals. Long-term clonal evolution would be remarkable for a eukaryotic lineage and suggests the importance of alternative mechanisms to promote genetic variability facilitating adaptation. Here, we assessed the potential of transposable elements for generating such genomic diversity. The dynamic expression of TEs during Rhizophagus irregularis spore development suggests ongoing TE activity. We find Mutator-like elements located near genes belonging to highly expanded gene families. Whole-genome epigenomic profiling of R. irregularis provides direct evidence of DNA methylation and small RNA production occurring at TE loci. Our results support a model in which TE activity shapes the genome, while DNA methylation and small RNA-mediated silencing keep their overproliferation in check. We propose that a well-controlled TE activity directly contributes to genome evolution in AM fungi.

Published
2021

14. 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

15. Genomics of cold adaptations in the Antarctic notothenioid fish radiation

Author

Bista, Iliana, primary, Wood, Jonathan M. D., additional, Desvignes, Thomas, additional, McCarthy, Shane A., additional, Matschiner, Michael, additional, Ning, Zemin, additional, Tracey, Alan, additional, Torrance, James, additional, Sims, Ying, additional, Chow, William, additional, Smith, Michelle, additional, Oliver, Karen, additional, Haggerty, Leanne, additional, Salzburger, Walter, additional, Postlethwait, John H., additional, Howe, Kerstin, additional, Clark, Melody S., additional, Detrich, William H., additional, Cheng, C.-H. Christina, additional, Miska, Eric A., additional, and Durbin, Richard, additional

Published
2022
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16. 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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17. 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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18. The genome sequence of the channel bull blenny, Cottoperca gobio (Günther, 1861)

Author

Bista, Iliana, McCarthy, Shane A, Wood, Jonathan, Ning, Zemin, Detrich Iii, H William, Desvignes, Thomas, Postlethwait, John, Chow, William, Howe, Kerstin, Torrance, James, Smith, Michelle, Oliver, Karen, Vertebrate Genomes Project Consortium, Miska, Eric A, Durbin, Richard, Bista, Iliana [0000-0002-6155-3093], McCarthy, Shane A [0000-0002-2715-4187], Wood, Jonathan [0000-0002-7545-2162], Detrich Iii, H William [0000-0002-0783-4505], Desvignes, Thomas [0000-0001-5126-8785], Howe, Kerstin [0000-0003-2237-513X], Torrance, James [0000-0002-6117-8190], and Apollo - University of Cambridge Repository

Subjects
channel bull blenny, genome assembly chromosomal, Cottoperca gobio, Notothenioidei
Abstract

We present a genome assembly for Cottoperca gobio (channel bull blenny, (Günther, 1861)); Chordata; Actinopterygii (ray-finned fishes), a temperate water outgroup for Antarctic Notothenioids. The size of the genome assembly is 609 megabases, with the majority of the assembly scaffolded into 24 chromosomal pseudomolecules. Gene annotation on Ensembl of this assembly has identified 21,662 coding genes.

Published
2020
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19. Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis

Author

Dallaire, Alexandra, primary, Manley, Bethan F., additional, Wilkens, Maya, additional, Bista, Iliana, additional, Quan, Clement, additional, Evangelisti, Edouard, additional, Bradshaw, Charles R., additional, Ramakrishna, Navin B., additional, Schornack, Sebastian, additional, Butter, Falk, additional, Paszkowski, Uta, additional, and Miska, Eric A., additional

Published
2021
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22. Contributors

Author

Arim, Matías, primary, Belgrano, Andrea, additional, Berazategui, Mauro, additional, Berg, Sofia, additional, Bista, Iliana, additional, Borthagaray, Ana Inés, additional, Brey, Thomas, additional, Claudet, Joachim, additional, Creer, Simon, additional, Dell, Anthony I., additional, Demars, Benoit O.L., additional, Eklöf, Anna, additional, Falciani, Francesco, additional, Fisher, Jonathan A.D., additional, Fowler, Charles W., additional, Frank, Kenneth T., additional, Fryxell, David C., additional, Gray, Clare, additional, Jacob, Ute, additional, Jonsson, Tomas, additional, Leenhardt, Pierre, additional, Low, Natalie, additional, Messinger, Susanna M., additional, Micheli, Fiorenza, additional, Mintenbeck, Katja, additional, Möllmann, Christian, additional, Monteith, Don T., additional, Mora, Camilo, additional, Morissette, Lyne, additional, Palkovacs, Eric P., additional, Pascal, Nicolas, additional, Pawar, Samraat, additional, Perkins, Daniel M., additional, Petchey, Owen, additional, Pinelli, Verónica, additional, Post, David M., additional, Raffaelli, David, additional, Rau, Andrea, additional, Rodríguez-Tricot, Lucía, additional, Savage, Van M., additional, Sun, Xiaoliang, additional, Turley, Nash E., additional, Vasseur, David A., additional, and Woodward, Guy, additional

Published
2015
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23. 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

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

Author

Munby, Hannah, primary, Linderoth, Tyler, additional, Fischer, Bettina, additional, Du, Mingliu, additional, Vernaz, Grégoire, additional, Tyers, Alexandra M., additional, Ngatunga, Benjamin P., additional, Shechonge, Asilatu, additional, Denise, Hubert, additional, McCarthy, Shane A., additional, Bista, Iliana, additional, Miska, Eric A., additional, Santos, M. Emília, additional, Genner, Martin J., additional, Turner, George F., additional, and Durbin, Richard, additional

Published
2021
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25. 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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26. A practical guide to DNA-based methods for biodiversity assessment

Author

Bruce, Kat, Blackman, Rosetta C., Bourlat, Sarah J., Hellström, Micaela, Bakker, Judith, Bista, Iliana, Bohmann, Kristine, Bouchez, Agnès, Brys, Rein, Clark, Katie, Elbrecht, Vasco, Fazi, Stefano, Fonseca, Vera G., Hänfling, Bernd, Leese, Florian, Mächler, Elvira, Mahon, Andrew R., Meissner, Kristian, Panksep, Kristel, Pawlowski, Jan, Schmidt Yáñez, Paul Luis, Seymour, Mathew, Thalinger, Bettina, Valentini, Alice, Woodcock, Paul, Traugott, Michael, Vasselon, Valentin, and Deiner, Kristy

Subjects
Data processing, DNA based methods, Biodiversity, Biota composition, Species identification
Abstract

This book represents a synthesis of knowledge and best practice in the field of DNA-based biomonitoring at the time of writing. It has been written with end-users of molecular tools in mind, as well as those who are new to the field in research settings and are looking to gain an overall grounding in the subject area. For each of the main types of sample (water, soil / sediment, bulk invertebrates and diatoms), and for each stage of the field and laboratory processes, we outline key considerations, decisions that need to be made, factors that might influence those decisions, and trade-offs inherent in the choices made. We hope that this will help users, practitioners, and those commissioning DNA-based monitoring programmes to navigate this large field and critically evaluate the strengths and weaknesses of different analysis workflows based on context, project aims and available resources. DNA-based methods for species detection and identification have revolutionised our ability to assess biodiversity in terrestrial, freshwater and marine ecosystems. Starting from the seminal study that used eDNA to detect invasive american bullfrogs in France (Ficetola et al. 2008), research conducted over the last decade has demonstrated the power of these approaches for surveying a wide range of species and groups. Early applications included the use of eDNA to monitor Asian Carp in the USA (Jerde et al. 2013). Following heavy scrutiny, the method was eventually adopted, and is still employed today by the United States Geological Survey (USGS). A flurry of research followed, with tests designed for many threatened and invasive species including New zealand mudsnails (Goldberg et al. 2013), american crayfish (Geerts et al. 2018), gammarids (Blackman et al. 2017), and great crested newts (Biggs et al. 2015). The great crested newt eDNA test has been employed for regulatory monitoring in the UK since 2014. During the same time period, there was a proliferation of research studies that used high-throughput sequencing approaches to describe whole communities of organisms from mixed species and environmental samples, using an approach termed DNA metabarcoding (Taberlet et al. 2012c). As the field developed fast and the approaches were applied to a wide range of research and monitoring objectives, a high level of methodological variation was introduced at all stages of the workflow (Seymour 2019). Thus, while a significant level of consensus on scientific best-practice now exists in many areas, this may not be readily discerned from the now-extensive body of research literature. As environmental practitioners and policy makers are now increasingly starting to integrate DNAbased methods into routine monitoring applications including protected species licensing1, statutory monitoring2 (Hänfling et al. 2016) and environmental impact assessment3, various national and international efforts have been undertaken to standardise methods and integrate them into monitoring frameworks (Pilliod et al. 2019, Loeza-Quintana et al. 2020, Minamoto et al. 2021, Pawlowski et al. 2020a4). In Europe, the EU COST Action DNAqua-Net (Leese et al. 2018) has been working towards incorporating molecular monitoring tools for Biological Quality Elements (BQEs, e.g., fish, macroinvertebrates and phytoplankton- benthos) into the Water Framework Directive (WFD, 2000/60/EC)5 and the Marine Strategy Framework Directive (MSFD, 2008/56/EC)6. Thus, emphasis now shifts from fundamental research to robust and efficient application of DNAbased methods for operational use at large scales. This requires that scientific robustness is balanced with consideration of the practical realities faced by environmental managers. Moreover, there is increased need for strong quality assurance in a setting where non-expert field samplers and commercial laboratories are involved with the generation of data that non-specialist decision-makers then rely on to inform potentially costly action (or non-action). This places increased emphasis on robustness, replicability, traceability and ease-of-use, which may not always be the central focus of studies carried out in the academic research environment. This document aims to summarise the scientific consensus relating to every step of the field and laboratory workflows involved in the most common types of samples and analyses. We do not go into great detail regarding bioinformatics (computational processing of sequence data) and data analysis since these are extensive topics in their own right. We uniquely set the field and lab steps in the context of the practical and logistical constraints faced by environmental managers in terms of cost, logistics, safety, ease-of-use, and quality assurance, highlighting key decisions to be made and the inherent trade-offs associated with the various options. We hope that this will support non-experts, and those new to the field, to navigate the key considerations associated with planning or evaluating monitoring programmes using DNA-based monitoring methods. Additionally, it will aid decision-makers in writing and evaluating tenders and proposals, ensuring that the methods used for a given project are fit-for-purpose and that results are correctly interpreted. Alongside the many areas of emerging consensus, there remain some areas where further research is still required to balance scientific best-practice with the constraints and priorities of end-users. We hope that by shining a light on the importance of these issues, the research community will be encouraged to address them. More generally, we hope to inspire researchers in this now highly-applied scientific field to consider end-user constraints when designing and implementing research projects. This will help to accelerate uptake by users and maximise the impact of research. DNA-based bioassessment methods continue to evolve, and there are several emerging technologies that show exciting promise to move beyond even what is possible today. Examples include in-field sequencing using the MinION device from Oxford Nanopore Technologies (Pomerantz et al. 2018, Davidov et al. 2020, Hatfield et al. 2020), PCR-free metagenomic approaches (Bista et al. 2018, Giebner et al. 2020) and CRISPR for rapid detection of species, which is particularly relevant for invasive an non-native species monitoring (Williams et al. 2019, 2020). We recognise the potential of these methods, but do not consider them in detail here, since they are not yet far enough developed for routine application. EU COST Action DNAqua-Net (CA 15219 a COST (European Cooperation in Science and Technology). DNAqua-Net, European Union Horizon 2020 Published Refereed Current 14.a Mature Multi-organisational International Genetic differentiation Species distributions Method

Published
2021

27. 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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28. 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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29. 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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30. 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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31. Strategies for sample labelling and library preparation in DNA metabarcoding studies.

Author

Bohmann, Kristine, Elbrecht, Vasco, Carøe, Christian, Bista, Iliana, Leese, Florian, Bunce, Michael, Yu, Douglas W., Seymour, Mathew, Dumbrell, Alex J., and Creer, Simon

Subjects
GENETIC barcoding, DNA primers, GENETIC markers, DNA
Abstract

Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to profile biota in basic and applied biodiversity research because of its targeted nature that allows sequencing of genetic markers from many samples in parallel. To achieve this, PCR amplification is carried out with primers designed to target a taxonomically informative marker within a taxonomic group, and sample‐specific nucleotide identifiers are added to the amplicons prior to sequencing. The latter enables assignment of the sequences back to the samples they originated from. Nucleotide identifiers can be added during the metabarcoding PCR and during "library preparation", that is, when amplicons are prepared for sequencing. Different strategies to achieve this labelling exist. All have advantages, challenges and limitations, some of which can lead to misleading results, and in the worst case compromise the fidelity of the metabarcoding data. Given the range of questions addressed using metabarcoding, ensuring that data generation is robust and fit for the chosen purpose is critically important for practitioners seeking to employ metabarcoding for biodiversity assessments. Here, we present an overview of the three main workflows for sample‐specific labelling and library preparation in metabarcoding studies on Illumina sequencing platforms; one‐step PCR, two‐step PCR, and tagged PCR. Further, we distill the key considerations for researchers seeking to select an appropriate metabarcoding strategy for their specific study. Ultimately, by gaining insights into the consequences of different metabarcoding workflows, we hope to further consolidate the power of metabarcoding as a tool to assess biodiversity across a range of applications. [ABSTRACT FROM AUTHOR]

Published
2022
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32. Environmental DNA provides greater insight to biodiversity and ecosystem function compared to traditional approaches, via spatio-temporal nestedness and turnover partitioning

Author

Seymour, Mathew, primary, Edwards, Francois, additional, Cosby, Jack, additional, Scarlet, Pete, additional, Bista, Iliana, additional, Brailsford, Francesca, additional, Glanville, Helen, additional, de Bruyn, Mark, additional, Carvalho, Gary, additional, and Creer, Simon, additional

Published
2021
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34. 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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36. Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

Author

Deiner, Kristy, Bik, Holly M, Mächler, Elvira, Seymour, Mathew, Lacoursière-Roussel, Anaïs, Altermatt, Florian, Creer, Simon, Bista, Iliana, Lodge, David M, de Vere, Natasha, Pfrender, Michael E, Bernatchez, Louis, University of Zurich, and Deiner, Kristy

Subjects
bioinformatic pipeline, conservation, invasive species, 10127 Institute of Evolutionary Biology and Environmental Studies, 1105 Ecology, Evolution, Behavior and Systematics, 1311 Genetics, biomonitoring, citizen science, 570 Life sciences, biology, 590 Animals (Zoology), macro, ecology, eDNA, species richness, organism
Abstract

The genomic revolution has fundamentally changed how we survey biodiversity on earth. High‐throughput sequencing (“HTS”) platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed “environmental DNA” or “eDNA”). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called “eDNA metabarcoding” and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education. ISSN:0962-1083 ISSN:1365-294X

Published
2017

37. Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples

Author

Bista, Iliana, primary, Carvalho, Gary R., additional, Tang, Min, additional, Walsh, Kerry, additional, Zhou, Xin, additional, Hajibabaei, Mehrdad, additional, Shokralla, Shadi, additional, Seymour, Mathew, additional, Bradley, David, additional, Liu, Shanlin, additional, Christmas, Martin, additional, and Creer, Simon, additional

Published
2018
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39. Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples.

Author

Carvalho, Gary R., Seymour, Mathew, Creer, Simon, Bista, Iliana, Tang, Min, Zhou, Xin, Walsh, Kerry, Christmas, Martin, Hajibabaei, Mehrdad, Shokralla, Shadi, Bradley, David, and Liu, Shanlin

Subjects
BIOMASS, BIODIVERSITY, SHOTGUN sequencing, GENOMES, WORKFLOW
Abstract

Abstract: New applications of DNA and RNA sequencing are expanding the field of biodiversity discovery and ecological monitoring, yet questions remain regarding precision and efficiency. Due to primer bias, the ability of metabarcoding to accurately depict biomass of different taxa from bulk communities remains unclear, while PCR‐free whole mitochondrial genome (mitogenome) sequencing may provide a more reliable alternative. Here, we used a set of documented mock communities comprising 13 species of freshwater macroinvertebrates of estimated individual biomass, to compare the detection efficiency of COI metabarcoding (three different amplicons) and shotgun mitogenome sequencing. Additionally, we used individual COI barcoding and de novo mitochondrial genome sequencing, to provide reference sequences for OTU assignment and metagenome mapping (mitogenome skimming), respectively. We found that, even though both methods occasionally failed to recover very low abundance species, metabarcoding was less consistent, by failing to recover some species with higher abundances, probably due to primer bias. Shotgun sequencing results provided highly significant correlations between read number and biomass in all but one species. Conversely, the read–biomass relationships obtained from metabarcoding varied across amplicons. Specifically, we found significant relationships for eight of 13 (amplicons B1FR‐450 bp, FF130R‐130 bp) or four of 13 (amplicon FFFR, 658 bp) species. Combining the results of all three COI amplicons (multiamplicon approach) improved the read–biomass correlations for some of the species. Overall, mitogenomic sequencing yielded more informative predictions of biomass content from bulk macroinvertebrate communities than metabarcoding. However, for large‐scale ecological studies, metabarcoding currently remains the most commonly used approach for diversity assessment. [ABSTRACT FROM AUTHOR]

Published
2018
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41. 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, Clawson, Hiram, Diekhans, Mark, Nassar, Luis, Paten, Benedict, Kraus, Robert HS, Crawford, Andrew J, Gilbert, M Thomas P, Zhang, Guojie, Venkatesh, Byrappa, Murphy, Robert W, Koepfli, Klaus-Peter, Shapiro, Beth, Johnson, Warren E, Di Palma, Federica, Marques-Bonet, Tomas, Teeling, Emma C, Warnow, Tandy, Graves, Jennifer Marshall, Ryder, Oliver A, Haussler, David, O'Brien, Stephen J, Korlach, Jonas, Lewin, Harris A, Howe, Kerstin, Myers, Eugene W, Durbin, Richard, Phillippy, Adam M, and Jarvis, Erich D

Subjects
Genome, Sex Chromosomes, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, Genomics, Sequence Analysis, DNA, Birds, Genome Size, Haplotypes, Genome, Mitochondrial, Vertebrates, Animals, 14. Life underwater, Sequence Alignment, Gene Library
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.

42. Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis

Author

Dallaire, Alexandra, Manley, Bethan F, Wilkens, Maya, Bista, Iliana, Quan, Clement, Evangelisti, Edouard, Bradshaw, Charles R, Ramakrishna, Navin B, Schornack, Sebastian, Butter, Falk, Paszkowski, Uta, and Miska, Eric A

Subjects
3107 Microbiology, FOS: Biological sciences, 1.1 Normal biological development and functioning, 3103 Ecology, Human Genome, Genetics, 1 Underpinning research, 15. Life on land, 3105 Genetics, 3. Good health, 31 Biological Sciences, Biotechnology
Abstract

Arbuscular mycorrhizal (AM) fungi form mutualistic relationships with most land plant species. AM fungi have long been considered as ancient asexuals. Long-term clonal evolution would be remarkable for a eukaryotic lineage and suggests the importance of alternative mechanisms to promote genetic variability facilitating adaptation. Here, we assessed the potential of transposable elements for generating such genomic diversity. The dynamic expression of TEs during Rhizophagus irregularis spore development suggests ongoing TE activity. We find Mutator-like elements located near genes belonging to highly expanded gene families. Whole-genome epigenomic profiling of R. irregularis provides direct evidence of DNA methylation and small RNA production occurring at TE loci. Our results support a model in which TE activity shapes the genome, while DNA methylation and small RNA-mediated silencing keep their overproliferation in check. We propose that a well-controlled TE activity directly contributes to genome evolution in AM fungi.

43. Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

Author

Deiner, Kristy, Bik, Holly M., Mächler, Elvira, Seymour, Mathew, Lacoursière‐Roussel, Anaïs, Altermatt, Florian, Creer, Simon, Bista, Iliana, Lodge, David M., de Vere, Natasha, Pfrender, Michael E., and Bernatchez, Louis

Subjects
15. Life on land
Abstract

The genomic revolution has fundamentally changed how we survey biodiversity on earth. High‐throughput sequencing (“HTS”) platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed “environmental DNA” or “eDNA”). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called “eDNA metabarcoding” and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education., Molecular Ecology, 26 (21), ISSN:0962-1083, ISSN:1365-294X

44. 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 J. P., 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, Clawson, Hiram, Diekhans, Mark, Nassar, Luis, Paten, Benedict, Kraus, Robert H. S., Crawford, Andrew J., Gilbert, M. Thomas P., Zhang, Guojie, Venkatesh, Byrappa, Murphy, Robert W., Koepfli, Klaus-Peter, Shapiro, Beth, Johnson, Warren E., Di Palma, Federica, Marques-Bonet, Tomas, Teeling, Emma C., Warnow, Tandy, Graves, Jennifer Marshall, Ryder, Oliver A., Haussler, David, O’Brien, Stephen J., Korlach, Jonas, Lewin, Harris A., Howe, Kerstin, Myers, Eugene W., Durbin, Richard, Phillippy, Adam M., and Jarvis, Erich D.

Subjects
45/91, 64, 631/61/212/2302, 706/648/697, 631/181/2474, 45, article, 45/23, 14. Life underwater, 631/181/735, 38
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.

45. Genomic consequences of domestication of the Siamese fighting fish

Author

Young Mi Kwon, Nathan Vranken, Carla Hoge, Madison R. Lichak, Amy L. Norovich, Kerel X. Francis, Julia Camacho-Garcia, Iliana Bista, Jonathan Wood, Shane McCarthy, William Chow, Heok Hui Tan, Kerstin Howe, Sepalika Bandara, Johannes von Lintig, Lukas Rüber, Richard Durbin, Hannes Svardal, Andres Bendesky, Kwon, Young Mi [0000-0002-0436-603X], Vranken, Nathan [0000-0003-0728-4715], Hoge, Carla [0000-0001-9798-9684], Norovich, Amy L [0000-0002-8074-2842], Francis, Kerel X [0000-0003-3768-439X], Camacho-Garcia, Julia [0000-0002-4828-1492], Bista, Iliana - Aglaia [0000-0002-6155-3093], Wood, Jonathan [0000-0002-7545-2162], McCarthy, Shane [0000-0002-2715-4187], Chow, William [0000-0002-9056-201X], Tan, Heok Hui [0000-0003-2227-8866], Howe, Kerstin [0000-0003-2237-513X], von Lintig, Johannes [0000-0002-2079-2143], Rüber, Lukas [0000-0003-0125-008X], Durbin, Richard [0000-0002-9130-1006], Svardal, Hannes [0000-0001-7866-7313], Bendesky, Andres [0000-0002-4220-3653], Apollo - University of Cambridge Repository, and Bista, Iliana [0000-0002-6155-3093]

Subjects
SEX DETERMINATION, Multidisciplinary, Science & Technology, Genome, NEURAL CREST, ZEBRAFISH, Fishes, ASSOCIATION, Genomics, GENE, DMRT1, Multidisciplinary Sciences, Domestication, REVEALS, Animal Fins, Science & Technology - Other Topics, Animals, BETTA-SPLENDENS, MEDAKA, SPECIFICATION, Biology, Engineering sciences. Technology
Abstract

Siamese fighting (betta) fish are among the most popular and morphologically diverse pet fish, but the genetic bases of their domestication and phenotypic diversification are largely unknown. We assembled de novo the genome of a wildBetta splendensand whole-genome sequenced 98 individuals across five closely related species. We find evidence of bidirectional hybridization between domesticated ornamental betta and other wildBettaspecies. We discoverdmrt1as the main sex determination gene in ornamental betta and that it has lower penetrance in wildB. splendens. Furthermore, we find genes with signatures of recent, strong selection that have large effects on color in specific parts of the body or on the shape of individual fins and that most are unlinked. Our results demonstrate how simple genetic architectures paired with anatomical modularity can lead to vast phenotypic diversity generated during animal domestication and launch betta as a powerful new system for evolutionary genetics.

Published
2022

46. Genomics of cold adaptations in the Antarctic notothenioid fish radiation

Author

Iliana Bista, Jonathan M. D. Wood, Thomas Desvignes, Shane A. McCarthy, Michael Matschiner, Zemin Ning, Alan Tracey, James Torrance, Ying Sims, William Chow, Michelle Smith, Karen Oliver, Leanne Haggerty, Walter Salzburger, John H. Postlethwait, Kerstin Howe, Melody S. Clark, William H. Detrich, C.-H. Christina Cheng, Eric A. Miska, Richard Durbin, Bista, Iliana [0000-0002-6155-3093], Wood, Jonathan MD [0000-0002-7545-2162], Matschiner, Michael [0000-0003-4741-3884], Tracey, Alan [0000-0002-4805-9058], Salzburger, Walter [0000-0002-9988-1674], Postlethwait, John H [0000-0002-5476-2137], Howe, Kerstin [0000-0003-2237-513X], Clark, Melody S [0000-0002-3442-3824], William Detrich, H [0000-0002-0783-4505], Miska, Eric A [0000-0002-4450-576X], Durbin, Richard [0000-0002-9130-1006], and Apollo - University of Cambridge Repository

Subjects
Hemoglobins, Vertebrates, Fishes, Animals, Antarctic Regions, Genomics, Phylogeny, Perciformes
Abstract

Numerous novel adaptations characterise the radiation of notothenioids, the dominant fish group in the freezing seas of the Southern Ocean. To improve understanding of the evolution of this iconic fish group, here we generate and analyse new genome assemblies for 24 species covering all major subgroups of the radiation, including five long-read assemblies. We present a new estimate for the onset of the radiation at 10.7 million years ago, based on a time-calibrated phylogeny derived from genome-wide sequence data. We identify a two-fold variation in genome size, driven by expansion of multiple transposable element families, and use the long-read data to reconstruct two evolutionarily important, highly repetitive gene family loci. First, we present the most complete reconstruction to date of the antifreeze glycoprotein gene family, whose emergence enabled survival in sub-zero temperatures, showing the expansion of the antifreeze gene locus from the ancestral to the derived state. Second, we trace the loss of haemoglobin genes in icefishes, the only vertebrates lacking functional haemoglobins, through complete reconstruction of the two haemoglobin gene clusters across notothenioid families. Both the haemoglobin and antifreeze genomic loci are characterised by multiple transposon expansions that may have driven the evolutionary history of these genes.

Published
2023

47. The era of reference genomes in conservation genomics

Author

Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn, Claudio Ciofi, Angelica Crottini, José A. Godoy, Jacob Höglund, Joanna Malukiewicz, Alice Mouton, Rebekah A. Oomen, Sadye Paez, Per J. Palsbøll, Christophe Pampoulie, María J. Ruiz-López, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Camila J. Mazzoni, Erich D. Jarvis, Miklós Bálint, Fedor Čiampor, Jacob Hoglund, Per Palsbøll, María José Ruiz-López, Goujie Zhang, Erich Jarvis, Sargis A. Aghayan, Tyler S. Alioto, Isabel Almudi, Nadir Alvarez, Paulo C. Alves, Isabel R. Amorim, Agostinho Antunes, Paula Arribas, Petr Baldrian, Paul R. Berg, Giorgio Bertorelle, Astrid Böhne, Andrea Bonisoli-Alquati, Ljudevit L. Boštjančić, Bastien Boussau, Catherine M. Breton, Elena Buzan, Paula F. Campos, Carlos Carreras, L. FIlipe Castro, Luis J. Chueca, Elena Conti, Robert Cook-Deegan, Daniel Croll, Mónica V. Cunha, Frédéric Delsuc, Alice B. Dennis, Dimitar Dimitrov, Rui Faria, Adrien Favre, Olivier D. Fedrigo, Rosa Fernández, Gentile Francesco Ficetola, Jean-François Flot, Toni Gabaldón, Dolores R. Galea Agius, Guido R. Gallo, Alice M. Giani, M. Thomas P. Gilbert, Tine Grebenc, Katerina Guschanski, Romain Guyot, Bernhard Hausdorf, Oliver Hawlitschek, Peter D. Heintzman, Berthold Heinze, Michael Hiller, Martin Husemann, Alessio Iannucci, Iker Irisarri, Kjetill S. Jakobsen, Sissel Jentoft, Peter Klinga, Agnieszka Kloch, Claudius F. Kratochwil, Henrik Kusche, Kara K.S. Layton, Jennifer A. Leonard, Emmanuelle Lerat, Gianni Liti, Tereza Manousaki, Tomas Marques-Bonet, Pável Matos-Maraví, Michael Matschiner, Florian Maumus, Ann M. Mc Cartney, Shai Meiri, José Melo-Ferreira, Ximo Mengual, Michael T. Monaghan, Matteo Montagna, Robert W. Mysłajek, Marco T. Neiber, Violaine Nicolas, Marta Novo, Petar Ozretić, Ferran Palero, Lucian Pârvulescu, Marta Pascual, Octávio S. Paulo, Martina Pavlek, Cinta Pegueroles, Loïc Pellissier, Graziano Pesole, Craig R. Primmer, Ana Riesgo, Lukas Rüber, Diego Rubolini, Daniele Salvi, Ole Seehausen, Matthias Seidel, Simona Secomandi, Bruno Studer, Spyros Theodoridis, Marco Thines, Lara Urban, Anti Vasemägi, Adriana Vella, Noel Vella, Sonja C. Vernes, Cristiano Vernesi, David R. Vieites, Robert M. Waterhouse, Christopher W. Wheat, Gert Wörheide, Yannick Wurm, Gabrielle Zammit, Repositório da Universidade de Lisboa, Formenti, Giulio, Theissinger, Kathrin, Fernandes, Carlo, Bista, Iliana, Bombarely, Aureliano, Bleidorn, Christoph, Ciofi, Claudio, Crottini, Angelica, Godoy, José A., Höglund, Jacob, Malukiewicz, Joanna, Mouton, Alice, Oomen, Rebekah A., Paez, Sadye, Palsbøll, Per J., Pampoulie, Christophe, Ruiz-López, María J., Svardal, Hanne, Theofanopoulou, Constantina, de Vries, Jan, Waldvogel, Ann-Marie, Zhang, Guojie, Mazzoni, Camila J., Jarvis, Erich D., Bálint, Mikló, Čiampor, Fedor, Hoglund, Jacob, Palsbøll, Per, José Ruiz-López, María, Zhang, Goujie, Jarvis, Erich, Aghayan, Sargis A., Alioto, Tyler S., Almudi, Isabel, Alvarez, Nadir, Alves, Paulo C., R Amorim, Isabel, Antunes, Agostinho, Arribas, Paula, Baldrian, Petr, R Berg, Paul, Bertorelle, Giorgio, Böhne, Astrid, Bonisoli-Alquati, Andrea, L Boštjančić, Ljudevit, Boussau, Bastien, M Breton, Catherine, Buzan, Elena, F Campos, Paula, Carreras, Carlo, FIlipe Castro, L., Chueca, Luis J., Conti, Elena, Cook-Deegan, Robert, Croll, Daniel, V Cunha, Mónica, Delsuc, Frédéric, Dennis, Alice B., Dimitrov, Dimitar, Faria, Rui, Favre, Adrien, Fedrigo, Olivier D., Fernández, Rosa, Francesco Ficetola, Gentile, Flot, Jean-Françoi, Gabaldón, Toni, Galea Agius, Dolores R., Gallo, Guido R., Giani, Alice M., Thomas P Gilbert, M., Grebenc, Tine, Guschanski, Katerina, Guyot, Romain, Hausdorf, Bernhard, Hawlitschek, Oliver, D Heintzman, Peter, Heinze, Berthold, Hiller, Michael, Husemann, Martin, Iannucci, Alessio, Irisarri, Iker, S Jakobsen, Kjetill, Jentoft, Sissel, Klinga, Peter, Kloch, Agnieszka, F Kratochwil, Claudiu, Kusche, Henrik, KS Layton, Kara, A Leonard, Jennifer, Lerat, Emmanuelle, Liti, Gianni, Manousaki, Tereza, Marques-Bonet, Toma, Matos-Maraví, Pável, Matschiner, Michael, Maumus, Florian, Mc Cartney, Ann M., Meiri, Shai, Melo-Ferreira, José, Mengual, Ximo, Monaghan, Michael T., Montagna, Matteo, Robertwmysłajek, T Neiber, Marco, Nicolas, Violaine, Novo, Marta, Ozretić, Petar, Palero, Ferran, Pârvulescu, Lucian, Pascual, Marta, Paulo, Octávio S., Pavlek, Martina, Pegueroles, Cinta, Pellissier, Loc, Pesole, Graziano, R Primmer, Craig, Riesgo, Ana, Rüber, Luka, Rubolini, Diego, Salvi, Daniele, Seehausen, Ole, Seidel, Matthia, Secomandi, Simona, Studer, Bruno, Theodoridis, Spyro, Thines, Marco, Urban, Lara, Vasemägi, Anti, Vella, Adriana, Vella, Noel, C Vernes, Sonja, Vernesi, Cristiano, R Vieites, David, M Waterhouse, Robert, W Wheat, Christopher, Wörheide, Gert, Wurm, Yannick, Zammit., and Gabrielle, Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Eléments transposables, évolution, populations, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Barcelona Supercomputing Center, European Reference Genome Atlas (ERGA) Consortium, University of St Andrews. School of Biology, University of St Andrews. St Andrews Bioinformatics Unit, Palsbøll lab, Marine Biology, University of Zurich, and Bálint, Miklós

Subjects
QH301 Biology, 580 Plants (Botany), Genetics -- Research, Evolutionsbiologi, biodiversity conservation, conservation genetics, ERGA, European Reference Genome Atlas, Conservation genetics, Biodiversity conservation, Animal genome mapping, udc:630*1, Genome, GE, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDE.BE.BIOD]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.biod, Biodiversity [MeSH], Genomics [MeSH], Ecology, Evolution, Behavior and Systematics, Genome [MeSH], 3rd-DAS, Genomics, Biodiversity, referenčni genomi, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDE.BE.BEC]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.bec, Chemistry, 10121 Department of Systematic and Evolutionary Botany, genomika, GE Environmental Sciences, Informàtica::Aplicacions de la informàtica::Bioinformàtica [Àrees temàtiques de la UPC], biodiverziteta, Settore BIO/18 - GENETICA, education, QH426 Genetics, QH301, VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470, [SDE.BE.EVO]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.evo, Genetics, genomi, 10211 Zurich-Basel Plant Science Center, Genomes, Genetik, Biology, QH426, Evolutionary Biology, Ambientale, Ecología, Genética, 1105 Ecology, Evolution, Behavior and Systematics, Wildlife conservation, 570 Life sciences, biology, Human medicine, Animal genetics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Genètica
Abstract

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics., Trends in Ecology & Evolution, 37 (3), ISSN:0169-5347, ISSN:1872-8383

Published
2022

48. Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity

Author

Kerry Walsh, Iliana Bista, Gary R. Carvalho, Mathew Seymour, Delphine Lallias, Simon Creer, Martin Christmas, Mehrdad Hajibabaei, Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Horizon House, Environm Agcy, Department of Integrative Biology & Biodiversity Institute of Ontario, University of Guelph, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris-Saclay, Bista, Iliana, and Creer, Simon

Subjects
0106 biological sciences, 0301 basic medicine, chironompupal exuviae, Science, [SDV]Life Sciences [q-bio], Biodiversity, General Physics and Astronomy, amplification, arthropods, 010603 evolutionary biology, 01 natural sciences, environmental dna, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, DNA Barcoding, Taxonomic, primers, Ecosystem, Environmental DNA, 14. Life underwater, Ecosystem diversity, capture, Relative species abundance, abundance, Multidisciplinary, Bacteria, Ecology, fungi, Lake ecosystem, conservation, food and beverages, Biota, tool, DNA, General Chemistry, 15. Life on land, identification, Lakes, 030104 developmental biology, Geography, Species richness
Abstract

The use of environmental DNA (eDNA) in biodiversity assessments offers a step-change in sensitivity, throughput and simultaneous measures of ecosystem diversity and function. There remains, however, a need to examine eDNA persistence in the wild through simultaneous temporal measures of eDNA and biota. Here, we use metabarcoding of two markers of different lengths, derived from an annual time series of aqueous lake eDNA to examine temporal shifts in ecosystem biodiversity and in an ecologically important group of macroinvertebrates (Diptera: Chironomidae). The analyses allow different levels of detection and validation of taxon richness and community composition (β-diversity) through time, with shorter eDNA fragments dominating the eDNA community. Comparisons between eDNA, community DNA, taxonomy and UK species abundance data further show significant relationships between diversity estimates derived across the disparate methodologies. Our results reveal the temporal dynamics of eDNA and validate the utility of eDNA metabarcoding for tracking seasonal diversity at the ecosystem scale., DNA from macrobial taxa can be extracted from environmental samples, including water, and be used to assess biodiversity in the region. Here, Bista and colleagues show that temporal shifts in the biodiversity of a lake invertebrate community can be detected by analysis of environmental DNA (eDNA).

Published
2017

49. Complete vertebrate mitogenomes reveal widespread repeats and gene duplications.

Author

Formenti G, Rhie A, Balacco J, Haase B, Mountcastle J, Fedrigo O, Brown S, Capodiferro MR, Al-Ajli FO, Ambrosini R, Houde P, Koren S, Oliver K, Smith M, Skelton J, Betteridge E, Dolucan J, Corton C, Bista I, Torrance J, Tracey A, Wood J, Uliano-Silva M, Howe K, McCarthy S, Winkler S, Kwak W, Korlach J, Fungtammasan A, Fordham D, Costa V, Mayes S, Chiara M, Horner DS, Myers E, Durbin R, Achilli A, Braun EL, Phillippy AM, and Jarvis ED

Subjects
Animals, Computational Biology methods, Computational Biology standards, Evolution, Molecular, High-Throughput Nucleotide Sequencing, Gene Duplication, Genome, Mitochondrial, Genomics methods, Repetitive Sequences, Nucleic Acid, Vertebrates genetics
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
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50. The genome sequence of the channel bull blenny, Cottoperca gobio (Günther, 1861).

Author

Bista I, McCarthy SA, Wood J, Ning Z, Detrich Iii HW, Desvignes T, Postlethwait J, Chow W, Howe K, Torrance J, Smith M, Oliver K, Miska EA, and Durbin R

Abstract

We present a genome assembly for Cottoperca gobio (channel bull blenny, (Günther, 1861)); Chordata; Actinopterygii (ray-finned fishes), a temperate water outgroup for Antarctic Notothenioids. The size of the genome assembly is 609 megabases, with the majority of the assembly scaffolded into 24 chromosomal pseudomolecules. Gene annotation on Ensembl of this assembly has identified 21,662 coding genes., Competing Interests: No competing interests were disclosed., (Copyright: © 2020 Bista I et al.)

Published
2020
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