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113 results on '"Chow, William"'

1. A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

Author

de Jong, Tristan V, Pan, Yanchao, Rastas, Pasi, Munro, Daniel, Tutaj, Monika, Akil, Huda, Benner, Chris, Chen, Denghui, Chitre, Apurva S, Chow, William, Colonna, Vincenza, Dalgard, Clifton L, Demos, Wendy M, Doris, Peter A, Garrison, Erik, Geurts, Aron M, Gunturkun, Hakan M, Guryev, Victor, Hourlier, Thibaut, Howe, Kerstin, Huang, Jun, Kalbfleisch, Ted, Kim, Panjun, Li, Ling, Mahaffey, Spencer, Martin, Fergal J, Mohammadi, Pejman, Ozel, Ayse Bilge, Polesskaya, Oksana, Pravenec, Michal, Prins, Pjotr, Sebat, Jonathan, Smith, Jennifer R, Woods, Leah C Solberg, Tabakoff, Boris, Tracey, Alan, Uliano-Silva, Marcela, Villani, Flavia, Wang, Hongyang, Sharp, Burt M, Telese, Francesca, Jiang, Zhihua, Saba, Laura, Wang, Xusheng, Murphy, Terence D, Palmer, Abraham A, Kwitek, Anne E, Dwinell, Melinda R, Williams, Robert W, Li, Jun Z, and Chen, Hao

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Good Health and Well Being, Rats, Animals, Genome, Molecular Sequence Annotation, Genomics, Whole Genome Sequencing, Genetic Variation, Rnor_6.0, genetic map, heterogeneous stock, hybrid rat diversity panel, inbred strains, mRatBN7.2, phylogenetic tree, rat, recombinant inbred, reference genome
Abstract

The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.

Published
2024

2. A genomic basis of vocal rhythm in birds

Author

Sebastianelli, Matteo, Lukhele, Sifiso M, Secomandi, Simona, de Souza, Stacey G, Haase, Bettina, Moysi, Michaella, Nikiforou, Christos, Hutfluss, Alexander, Mountcastle, Jacquelyn, Balacco, Jennifer, Pelan, Sarah, Chow, William, Fedrigo, Olivier, Downs, Colleen T, Monadjem, Ara, Dingemanse, Niels J, Jarvis, Erich D, Brelsford, Alan, vonHoldt, Bridgett M, and Kirschel, Alexander NG

Subjects
Biological Sciences, Ecology, Evolutionary Biology, Genetics, Human Genome, Animals, Vocalization, Animal, Male, Genomics, Genome, Female, Songbirds, Birds
Abstract

Vocal rhythm plays a fundamental role in sexual selection and species recognition in birds, but little is known of its genetic basis due to the confounding effect of vocal learning in model systems. Uncovering its genetic basis could facilitate identifying genes potentially important in speciation. Here we investigate the genomic underpinnings of rhythm in vocal non-learning Pogoniulus tinkerbirds using 135 individual whole genomes distributed across a southern African hybrid zone. We find rhythm speed is associated with two genes that are also known to affect human speech, Neurexin-1 and Coenzyme Q8A. Models leveraging ancestry reveal these candidate loci also impact rhythmic stability, a trait linked with motor performance which is an indicator of quality. Character displacement in rhythmic stability suggests possible reinforcement against hybridization, supported by evidence of asymmetric assortative mating in the species producing faster, more stable rhythms. Because rhythm is omnipresent in animal communication, candidate genes identified here may shape vocal rhythm across birds and other vertebrates.

Published
2024

3. A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes.

Author

Toh, Huishi, Yang, Chentao, Formenti, Giulio, Raja, Kalpana, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie, Zhang, Guojie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Jain, Aashish, Kihara, Daisuke, Rhie, Arang, Phillippy, Adam, Swanson, Scott, Jiang, Peng, Jarvis, Erich, Thomson, James, Stewart, Ron, Chaisson, Mark, Bukhman, Yury, and Clegg, Dennis

Subjects
Arvicanthis niloticus, Diabetes, Diurnal, Genome, Germline mutation rate, Heterozygosity, Long-read genome assembly, Orthology, Positive selection, Retrogenes, Segmental duplications, Humans, Animals, Haplotypes, Diabetes Mellitus, Type 2, Murinae, Genome, Genomics
Abstract

BACKGROUND: The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic. RESULTS: We report a 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated with the Vertebrate Genomes Project (VGP). The assembly is highly contiguous, with contig N50 of 11.1 Mb, scaffold N50 of 83 Mb, and 95.2% of the sequence assigned to chromosomes. We used a novel workflow to identify 3613 segmental duplications and quantify duplicated genes. Comparative analyses revealed unique genomic features of the Nile rat, including some that affect genes associated with type 2 diabetes and metabolic dysfunctions. We discuss 14 genes that are heterozygous in the Nile rat or highly diverged from the house mouse. CONCLUSIONS: Our findings reflect the exceptional level of genomic resolution present in this assembly, which will greatly expand the potential of the Nile rat as a model organism.

Published
2022

4. The complete sequence of a human genome

Author

Nurk, Sergey, Koren, Sergey, Rhie, Arang, Rautiainen, Mikko, Bzikadze, Andrey V, Mikheenko, Alla, Vollger, Mitchell R, Altemose, Nicolas, Uralsky, Lev, Gershman, Ariel, Aganezov, Sergey, Hoyt, Savannah J, Diekhans, Mark, Logsdon, Glennis A, Alonge, Michael, Antonarakis, Stylianos E, Borchers, Matthew, Bouffard, Gerard G, Brooks, Shelise Y, Caldas, Gina V, Chen, Nae-Chyun, Cheng, Haoyu, Chin, Chen-Shan, Chow, William, de Lima, Leonardo G, Dishuck, Philip C, Durbin, Richard, Dvorkina, Tatiana, Fiddes, Ian T, Formenti, Giulio, Fulton, Robert S, Fungtammasan, Arkarachai, Garrison, Erik, Grady, Patrick GS, Graves-Lindsay, Tina A, Hall, Ira M, Hansen, Nancy F, Hartley, Gabrielle A, Haukness, Marina, Howe, Kerstin, Hunkapiller, Michael W, Jain, Chirag, Jain, Miten, Jarvis, Erich D, Kerpedjiev, Peter, Kirsche, Melanie, Kolmogorov, Mikhail, Korlach, Jonas, Kremitzki, Milinn, Li, Heng, Maduro, Valerie V, Marschall, Tobias, McCartney, Ann M, McDaniel, Jennifer, Miller, Danny E, Mullikin, James C, Myers, Eugene W, Olson, Nathan D, Paten, Benedict, Peluso, Paul, Pevzner, Pavel A, Porubsky, David, Potapova, Tamara, Rogaev, Evgeny I, Rosenfeld, Jeffrey A, Salzberg, Steven L, Schneider, Valerie A, Sedlazeck, Fritz J, Shafin, Kishwar, Shew, Colin J, Shumate, Alaina, Sims, Ying, Smit, Arian FA, Soto, Daniela C, Sović, Ivan, Storer, Jessica M, Streets, Aaron, Sullivan, Beth A, Thibaud-Nissen, Françoise, Torrance, James, Wagner, Justin, Walenz, Brian P, Wenger, Aaron, Wood, Jonathan MD, Xiao, Chunlin, Yan, Stephanie M, Young, Alice C, Zarate, Samantha, Surti, Urvashi, McCoy, Rajiv C, Dennis, Megan Y, Alexandrov, Ivan A, Gerton, Jennifer L, O’Neill, Rachel J, Timp, Winston, Zook, Justin M, Schatz, Michael C, Eichler, Evan E, Miga, Karen H, and Phillippy, Adam M

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Cell Line, Chromosomes, Artificial, Bacterial, Chromosomes, Human, Genome, Human, Human Genome Project, Humans, Reference Values, Sequence Analysis, DNA, General Science & Technology
Abstract

Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion-base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

Published
2022

5. The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Published
2023
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6. A chromosome-level reference genome and pangenome for barn swallow population genomics

Author

Secomandi, Simona, Gallo, Guido R., Sozzoni, Marcella, Iannucci, Alessio, Galati, Elena, Abueg, Linelle, Balacco, Jennifer, Caprioli, Manuela, Chow, William, Ciofi, Claudio, Collins, Joanna, Fedrigo, Olivier, Ferretti, Luca, Fungtammasan, Arkarachai, Haase, Bettina, Howe, Kerstin, Kwak, Woori, Lombardo, Gianluca, Masterson, Patrick, Messina, Graziella, Møller, Anders P., Mountcastle, Jacquelyn, Mousseau, Timothy A., Ferrer Obiol, Joan, Olivieri, Anna, Rhie, Arang, Rubolini, Diego, Saclier, Marielle, Stanyon, Roscoe, Stucki, David, Thibaud-Nissen, Françoise, Torrance, James, Torroni, Antonio, Weber, Kristina, Ambrosini, Roberto, Bonisoli-Alquati, Andrea, Jarvis, Erich D., Gianfranceschi, Luca, and Formenti, Giulio

Published
2023
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8. A role for vocal rhythm in avian speciation

Author

Kirschel, Alexander, primary, Sebastianelli, Matteo, additional, Lukhele, Sifiso, additional, Secomandi, Simona, additional, de Souza, Stacey, additional, Haase, Bettina, additional, Moysi, Michaella, additional, Nikiforou, Christos, additional, Hutfluss, Alexander, additional, Mountcastle, Jacquelyn, additional, Balacco, Jennifer, additional, Pelan, Sarah, additional, Chow, William, additional, Fedrigo, Olivier, additional, Downs, Colleen, additional, Monadjem, Ara, additional, Dingemanse, Niels, additional, Jarvis, Erich, additional, Brelsford, Alan, additional, and vonHoldt, Bridgett, additional

Published
2023
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9. 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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10. A national seismic risk model for Canada: Methodology and scientific basis

Author

Hobbs, Tiegan E, primary, Journeay, J Murray, additional, Rao, Anirudh S, additional, Kolaj, Michal, additional, Martins, Luis, additional, LeSueur, Philip, additional, Simionato, Michele, additional, Silva, Vitor, additional, Pagani, Marco, additional, Johnson, Kendra, additional, Rotheram, Drew, additional, and Chow, William, additional

Published
2023
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11. The evolution of two transmissible cancers in Tasmanian devils

Author

Stammnitz, Maximilian R., primary, Gori, Kevin, additional, Kwon, Young Mi, additional, Harry, Edward, additional, Martin, Fergal J., additional, Billis, Konstantinos, additional, Cheng, Yuanyuan, additional, Baez-Ortega, Adrian, additional, Chow, William, additional, Comte, Sebastien, additional, Eggertsson, Hannes, additional, Fox, Samantha, additional, Hamede, Rodrigo, additional, Jones, Menna, additional, Lazenby, Billie, additional, Peck, Sarah, additional, Pye, Ruth, additional, Quail, Michael A., additional, Swift, Kate, additional, Wang, Jinhong, additional, Wood, Jonathan, additional, Howe, Kerstin, additional, Stratton, Michael R., additional, Ning, Zemin, additional, and Murchison, Elizabeth P., additional

Published
2023
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12. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Author

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

Abstract

Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of noncollinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared with other reptiles, and harbor a higher genetic load compared with green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage.

Published
2023
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13. Genomics of cold adaptations in the Antarctic notothenioid fish radiation

Author

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

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

14. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Author

University of Massachusetts, National Marine Fisheries Service (US), National Science Foundation (US), National Research Council of Canada, Rockefeller University, Howard Hughes Medical Institute, Wellcome Sanger Institute, Max Planck Society, Agencia Nacional de Investigación y Desarrollo (Chile), Fundação de Amparo à Pesquisa do Estado de São Paulo, Federal Ministry of Education and Research (Germany), National Library of Medicine (US), Generalitat de Catalunya, Fundación la Caixa, Vienna Science and Technology Fund, Welsh Government, European Commission, Sea Turtle Conservancy (US), Kuhlwilm, Martin [0000-0002-0115-1797], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Bentley, Blair P., Carrasco-Valenzuela, Tomás, Ramos, Elisa K. S., Pawar, Harvinder, Souza Arantes, Larissa, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, Todd, Erica V., Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Françoise, Nery, Mariana F., Marqués-Bonet, Tomàs, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., Komoroske, Lisa M., University of Massachusetts, National Marine Fisheries Service (US), National Science Foundation (US), National Research Council of Canada, Rockefeller University, Howard Hughes Medical Institute, Wellcome Sanger Institute, Max Planck Society, Agencia Nacional de Investigación y Desarrollo (Chile), Fundação de Amparo à Pesquisa do Estado de São Paulo, Federal Ministry of Education and Research (Germany), National Library of Medicine (US), Generalitat de Catalunya, Fundación la Caixa, Vienna Science and Technology Fund, Welsh Government, European Commission, Sea Turtle Conservancy (US), Kuhlwilm, Martin [0000-0002-0115-1797], Marqués-Bonet, Tomàs [0000-0002-5597-3075], Bentley, Blair P., Carrasco-Valenzuela, Tomás, Ramos, Elisa K. S., Pawar, Harvinder, Souza Arantes, Larissa, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, Todd, Erica V., Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Françoise, Nery, Mariana F., Marqués-Bonet, Tomàs, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., and Komoroske, Lisa M.

Abstract

[Significance] Sea turtle populations have undergone recent global declines. We analyzed de novo assembled genomes for both extant sea turtle families through the Vertebrate Genomes Project to inform their conservation and evolutionary biology. These highly conserved genomes were differentiated by localized gene-rich regions of divergence, particularly within microchromosomes, suggesting that these genomic elements play key functional roles in the evolution of sea turtles and possibly other vertebrates. We further demonstrate that dissimilar evolutionary histories impact standing genomic diversity and genetic load, and are critical to consider when using these metrics to assess adaptive potential and extinction risk. Our results also demonstrate how reference genome quality impacts inferences of comparative and conservation genomics analyses that need to be considered in their application., [Abstract] Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of noncollinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared with other reptiles, and harbor a higher genetic load compared with green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage.

Published
2023

15. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Author

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

Published
2023
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16. Sex-specific changes in autosomal methylation rate in ageing common terns

Author

Meyer, Britta S., primary, Moiron, Maria, additional, Caswara, Calvinna, additional, Chow, William, additional, Fedrigo, Olivier, additional, Formenti, Giulio, additional, Haase, Bettina, additional, Howe, Kerstin, additional, Mountcastle, Jacquelyn, additional, Uliano-Silva, Marcela, additional, Wood, Jonathan, additional, Jarvis, Erich D., additional, Liedvogel, Miriam, additional, and Bouwhuis, Sandra, additional

Published
2023
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17. Additional file 13 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 13: Supplementary Table S11. Differentially expressed cytokine or cytokine related genes in infected avian endothelial cells.

Published
2023
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18. Additional file 4 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 4: Supplementary Table S2. BUSCO analysis of the final genomes.

Published
2023
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19. sj-pdf-1-eqs-10.1177_87552930231173446 – Supplemental material for A national seismic risk model for Canada: Methodology and scientific basis

Author

Hobbs, Tiegan E, Journeay, J Murray, Rao, Anirudh S, Kolaj, Michal, Martins, Luis, LeSueur, Philip, Simionato, Michele, Silva, Vitor, Pagani, Marco, Johnson, Kendra, Rotheram, Drew, and Chow, William

Subjects
FOS: Other engineering and technologies, 99999 Engineering not elsewhere classified
Abstract

Supplemental material, sj-pdf-1-eqs-10.1177_87552930231173446 for A national seismic risk model for Canada: Methodology and scientific basis by Tiegan E Hobbs, J Murray Journeay, Anirudh S Rao, Michal Kolaj, Luis Martins, Philip LeSueur, Michele Simionato, Vitor Silva, Marco Pagani, Kendra Johnson, Drew Rotheram and William Chow in Earthquake Spectra

Published
2023
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20. Additional file 5 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 5: Supplementary Table S3. CEGMA analysis of the final genomes.

Published
2023
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21. Additional file 7 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 7: Supplementary Table S5. List of genes known to affect plumage colour in birds.

Published
2023
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22. Additional file 2 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 2: Supplementary Table S1. Heterozygosity, QV and completeness values for swan genomes.

Published
2023
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23. Additional file 6 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 6: Supplementary Table S4. GO biological process annotation of inverted genes in the Mallard duck (relative to the black swan).

Published
2023
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24. Additional file 3 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 3: Online Methods.

Published
2023
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25. Additional file 8 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 8: Supplementary Table S6. Immune gene families are contractive in black swans compared to mute swans. The number of genes in each immune gene sub-family identified is given in each column for the corresponding species.

Published
2023
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26. A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Author

Toh, Huishi, primary, Yang, Chentao, additional, Formenti, Giulio, additional, Raja, Kalpana, additional, Yan, Lily, additional, Tracey, Alan, additional, Chow, William, additional, Howe, Kerstin, additional, Bergeron, Lucie A., additional, Zhang, Guojie, additional, Haase, Bettina, additional, Mountcastle, Jacquelyn, additional, Fedrigo, Olivier, additional, Fogg, John, additional, Kirilenko, Bogdan, additional, Munegowda, Chetan, additional, Hiller, Michael, additional, Jain, Aashish, additional, Kihara, Daisuke, additional, Rhie, Arang, additional, Phillippy, Adam M., additional, Swanson, Scott A., additional, Jiang, Peng, additional, Clegg, Dennis O., additional, Jarvis, Erich D., additional, Thomson, James A., additional, Stewart, Ron, additional, Chaisson, Mark J. P., additional, and Bukhman, Yury V., additional

Published
2022
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27. Segmental duplications

Author

Chaisson, Mark, Toh, Huishi, Stewart, Ron, Bukhman, Yury, Formenti, Giulio, Raja, Kalpana, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie, Zhang, Guojie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Jain, Aashish, Kihara, Daisuke, Rhie, Arang, Phillippy, Adam, Swanson, Scott, Jiang, Peng, Clegg, Dennis, Jarvis, Erich, and Thomson, James

Published
2022
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28. Heterozygosity spectrum

Author

Yang, Chentao, Zhang, Guojie, Formenti, Giulio, Raja, Kalpana, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Jain, Aashish, Kihara, Daisuke, Rhie, Arang, Phillippy, Adam, Swanson, Scott, Jiang, Peng, Clegg, Dennis, Jarvis, Erich, and Thomson, James

Abstract

Chentao Yang's heterozygosity spectrum analysis

Published
2022
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29. Comparison of house mouse gene complement to Nile rat using TOGA

Author

Bukhman, Yury, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Toh, Huishi, Chaisson, Mark, Stewart, Ron, Yang, Chentao, Formenti, Giulio, Raja, Kalpana, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie, Zhang, Guojie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Jain, Aashish, Kihara, Daisuke, Rhie, Arang, Phillippy, Adam, Swanson, Scott, Jiang, Peng, Clegg, Dennis, Jarvis, Erich, and Thomson, James

Published
2022
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30. Gene lists

Author

Bukhman, Yury, Toh, Huishi, Chaisson, Mark, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Raja, Kalpana, Yang, Chentao, Zhang, Guojie, Stewart, Ron, Formenti, Giulio, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Jain, Aashish, Kihara, Daisuke, Rhie, Arang, Phillippy, Adam, Swanson, Scott, Jiang, Peng, Clegg, Dennis, Jarvis, Erich, and Thomson, James

Published
2022
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31. Assembly quality

Author

Bukhman, Yury, Formenti, Giulio, Chaisson, Mark, Toh, Huishi, Yang, Chentao, Raja, Kalpana, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie, Zhang, Guojie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Jain, Aashish, Kihara, Daisuke, Rhie, Arang, Phillippy, Adam, Swanson, Scott, Jiang, Peng, Clegg, Dennis, Jarvis, Erich, Thomson, James, and Stewart, Ron

Abstract

Nile rat assembly quality metrics compared to other representative genomes of the Murinae

Published
2022
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32. Diversification selection

Author

Yang, Chentao, Formenti, Giulio, Raja, Kalpana, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie, Zhang, Guojie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Jain, Aashish, Kihara, Daisuke, Rhie, Arang, Phillippy, Adam, Swanson, Scott, Jiang, Peng, Clegg, Dennis, Jarvis, Erich, and Thomson, James

Abstract

Chentao Yang's dN/dS analysis of Nile rat vs. house mouse, Norway rat, and human

Published
2022
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33. GO term predictions

Author

Jain, Aashish, Kihara, Daisuke, Yang, Chentao, Formenti, Giulio, Raja, Kalpana, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie, Zhang, Guojie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Rhie, Arang, Phillippy, Adam, Swanson, Scott, Jiang, Peng, Clegg, Dennis, Jarvis, Erich, Thomson, James, and Chaisson, Mark

Published
2022
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34. Interesting genes

Author

Toh, Huishi, Yang, Chentao, Raja, Kalpana, Formenti, Giulio, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie, Zhang, Guojie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Jain, Aashish, Kihara, Daisuke, Rhie, Arang, Phillippy, Adam, Swanson, Scott, Jiang, Peng, Clegg, Dennis, Jarvis, Erich, Thomson, James, Stewart, Ron, Chaisson, Mark, and Bukhman, Yury

Published
2022
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35. Nile rat genome paper supplementary materials

Author

Toh, Huishi, Yang, Chentao, Formenti, Giulio, Raja, Kalpana, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie, Zhang, Guojie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Jain, Aashish, Kihara, Daisuke, Rhie, Arang, Phillippy, Adam, Swanson, Scott, Jiang, Peng, Clegg, Dennis, Jarvis, Erich, Thomson, James, Stewart, Ron, Chaisson, Mark, and Bukhman, Yury

Subjects
viruses, virus diseases, nervous system diseases
Abstract

Nile rat genome paper supplementary materials

Published
2022
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36. 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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37. The evolution of two transmissible cancers in Tasmanian devils

Author

Stammnitz, Maximilian R., primary, Gori, Kevin, additional, Kwon, Young Mi, additional, Harry, Ed, additional, Martin, Fergal J., additional, Billis, Konstantinos, additional, Cheng, Yuanyuan, additional, Baez-Ortega, Adrian, additional, Chow, William, additional, Comte, Sebastien, additional, Eggertsson, Hannes, additional, Fox, Samantha, additional, Hamede, Rodrigo, additional, Jones, Menna E., additional, Lazenby, Billie, additional, Peck, Sarah, additional, Pye, Ruth, additional, Quail, Michael A., additional, Swift, Kate, additional, Wang, Jinhong, additional, Wood, Jonathan, additional, Howe, Kerstin, additional, Stratton, Michael R., additional, Ning, Zemin, additional, and Murchison, Elizabeth P., additional

Published
2022
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39. The swan genome and transcriptome: its not all black and white

Author

Karawita, Anjana C., primary, Cheng, Yuanyuan, additional, Chew, Keng Yih, additional, Challgula, Arjun, additional, Kraus, Robert, additional, Mueller, Ralf C., additional, Tong, Marcus Z. W., additional, Hulme, Katina D., additional, Beielefeldt-Ohmann, Helle, additional, Steele, Lauren E., additional, Wu, Melanie, additional, Sng, Julian, additional, Noye, Ellesandra, additional, Bruxner, Timothy J., additional, Au, Gough G., additional, Lowther, Suzanne, additional, Blommaert, Julie, additional, Suh, Alexander, additional, McCauley, Alexander J., additional, Kaur, Parwinder, additional, Dudchenko, Olga, additional, Aiden, Erez, additional, Fedrigo, Olivier, additional, Formenti, Giulio, additional, Mountcastle, Jacquelyn, additional, Chow, William, additional, Martin, Fergal J., additional, Ogeh, Denye N., additional, Thiaud-Nissen, Françoise, additional, Howe, Kerstin, additional, Collins, Joanna, additional, Tracey, Alan, additional, Smith, Jacqueline, additional, Kuo, Richard I., additional, Renfree, Marilyn B., additional, Kimura, Takashi, additional, Sakoda, Yoshihiro, additional, McDougall, Mathew, additional, Spencer, Hamish G., additional, Pyne, Michael, additional, Tolf, Conny, additional, Waldenström, Jonas, additional, Jarvis, Erich D., additional, Baker, Michelle L., additional, Burt, David W., additional, and Short, Kirsty R., additional

Published
2022
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40. Pangenomics provides insights into the role of synanthropy in barn swallow evolution

Author

Secomandi, Simona, primary, Gallo, Guido Roberto, additional, Sozzoni, Marcella, additional, Iannucci, Alessio, additional, Galati, Elena, additional, Abueg, Linelle, additional, Balacco, Jennifer, additional, Caprioli, Manuela, additional, Chow, William, additional, Ciofi, Claudio, additional, Collins, Joanna, additional, Fedrigo, Olivier, additional, Ferretti, Luca, additional, Fungtammasan, Arkarachai, additional, Haase, Bettina, additional, Howe, Kerstin, additional, Kwak, Woori, additional, Lombardo, Gianluca, additional, Masterson, Patrick, additional, Messina, Graziella, additional, Møller, Anders Pape, additional, Mountcastle, Jacquelyn, additional, Mousseau, Timothy A., additional, Ferrer-Obiol, Joan, additional, Olivieri, Anna, additional, Rhie, Arang, additional, Rubolini, Diego, additional, Saclier, Marielle, additional, Stanyon, Roscoe, additional, Stucki, David, additional, Thibaud-Nissen, Françoise, additional, Torrance, James, additional, Torroni, Antonio, additional, Weber, Kristina, additional, Ambrosini, Roberto, additional, Bonisoli-Alquati, Andrea, additional, Jarvis, Erich D., additional, Gianfranceschi, Luca, additional, and Formenti, Giulio, additional

Published
2022
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41. 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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42. Sex-specific changes in autosomal methylation rate in ageing common terns

Author

Meyer, Britta, primary, Moiron, Maria, additional, Caswara, Calvinna, additional, Chow, William, additional, Fedrigo, Olivier, additional, Formenti, Giulio, additional, Haase, Bettina, additional, Howe, Kerstin, additional, Mountcastle, Jacquelyn, additional, Uliano-Silva, Marcela, additional, Wood, Jonathan, additional, Jarvis, Erich, additional, Liedvogel, Miriam, additional, and Bouwhuis, Sandra, additional

Published
2022
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43. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Author

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

Published
2022
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44. The genome sequence of the European golden eagle, Aquila chrysaetos chrysaetos Linnaeus 1758

Author

Mead, Dan, Ogden, Rob, Meredith, Anna, Peniche, Gabriela, Smith, Michelle, Corton, Craig, Oliver, Karen, Skelton, Jason, Betteridge, Emma, Doulcan, Jale, Holmes, Nadine, Wright, Victoria, Loose, Matt, Quail, Michael A, McCarthy, Shane A, Howe, Kerstin, Chow, William, Torrance, James, Collins, Joanna, Challis, Richard, Durbin, Richard, Blaxter, Mark, Mead, Dan [0000-0001-7717-4330], Ogden, Rob [0000-0002-2831-0428], Doulcan, Jale [0000-0002-3551-1770], Wright, Victoria [0000-0002-9288-4338], Loose, Matt [0000-0002-5264-0929], McCarthy, Shane A [0000-0002-2715-4187], Howe, Kerstin [0000-0003-2237-513X], Torrance, James [0000-0002-6117-8190], Challis, Richard [0000-0002-3502-1122], Durbin, Richard [0000-0002-9130-1006], and Apollo - University of Cambridge Repository

Subjects
Aquila chrysaetos, genome sequence, European golden eagle, chromosomal
Abstract

We present a genome assembly from an individual female Aquila chrysaetos chrysaetos (the European golden eagle; Chordata; Aves; Accipitridae). The genome sequence is 1.23 gigabases in span. The majority of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the W and Z sex chromosomes.

Published
2021
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45. Recombination suppression and selection affect local ancestries in genomes of a migratory songbird

Author

Ishigohoka, Jun, primary, Bascón-Cardozo, Karen, additional, Bours, Andrea, additional, Fuß, Janina, additional, Rhie, Arang, additional, Mountcastle, Jacquelyn, additional, Haase, Bettina, additional, Chow, William, additional, Collins, Joanna, additional, Howe, Kerstin, additional, Uliano-Silva, Marcela, additional, Fedrigo, Olivier, additional, Jarvis, Erich D., additional, Pérez-Tris, Javier, additional, Illera, Juan Carlos, additional, and Liedvogel, Miriam, additional

Published
2021
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46. A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)

Author

Mueller, Ralf C, primary, Ellström, Patrik, additional, Howe, Kerstin, additional, Uliano-Silva, Marcela, additional, Kuo, Richard I, additional, Miedzinska, Katarzyna, additional, Warr, Amanda, additional, Fedrigo, Olivier, additional, Haase, Bettina, additional, Mountcastle, Jacquelyn, additional, Chow, William, additional, Torrance, James, additional, Wood, Jonathan M D, additional, Järhult, Josef D, additional, Naguib, Mahmoud M, additional, Olsen, Björn, additional, Jarvis, Erich D, additional, Smith, Jacqueline, additional, Eöry, Lél, additional, and Kraus, Robert H S, additional

Published
2021
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47. high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck).

Author

Mueller, Ralf C, Ellström, Patrik, Howe, Kerstin, Uliano-Silva, Marcela, Kuo, Richard I, Miedzinska, Katarzyna, Warr, Amanda, Fedrigo, Olivier, Haase, Bettina, Mountcastle, Jacquelyn, Chow, William, Torrance, James, Wood, Jonathan M D, Järhult, Josef D, Naguib, Mahmoud M, Olsen, Björn, Jarvis, Erich D, Smith, Jacqueline, Eöry, Lél, and Kraus, Robert H S

Subjects
PLANT chromosomes, AVIAN influenza A virus, AVIAN influenza, SEX chromosomes, GENOMES, DUCK plague, COMPLEMENTARY DNA
Abstract

Background The tufted duck is a non-model organism that experiences high mortality in highly pathogenic avian influenza outbreaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian influenza viruses. Studies in non-model bird species are crucial to disentangle the role of the host response in avian influenza virus infection in the natural reservoir. Such endeavour requires a high-quality genome assembly and transcriptome. Findings This study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project pipeline. We sequenced RNA (complementary DNA) from brain, ileum, lung, ovary, spleen, and testis using Illumina short-read and Pacific Biosciences long-read sequencing platforms, which were used for annotation. We found 34 autosomes plus Z and W sex chromosomes in the curated genome assembly, with 99.6% of the sequence assigned to chromosomes. Functional annotation revealed 14,099 protein-coding genes that generate 111,934 transcripts, which implies a mean of 7.9 isoforms per gene. We also identified 246 small RNA families. Conclusions This annotated genome contributes to continuing research into the host response in avian influenza virus infections in a natural reservoir. Our findings from a comparison between short-read and long-read reference transcriptomics contribute to a deeper understanding of these competing options. In this study, both technologies complemented each other. We expect this annotation to be a foundation for further comparative and evolutionary genomic studies, including many waterfowl relatives with differing susceptibilities to avian influenza viruses. [ABSTRACT FROM AUTHOR]

Published
2021
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48. Genomic consequences of domestication of the Siamese fighting fish.

Author

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

Subjects
*DOMESTICATION of animals, *LOCUS (Genetics), *SEX determination, *MOSAICISM, *BIOLOGICAL evolution, *LIFE sciences
Abstract

The article presents a study which explores genomic consequences of domestication of the Siamese fighting fish. It 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
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49. The complete sequence of a human genome

Author

Sergey Nurk, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V. Bzikadze, Alla Mikheenko, Mitchell R. Vollger, Nicolas Altemose, Lev Uralsky, Ariel Gershman, Sergey Aganezov, Savannah J. Hoyt, Mark Diekhans, Glennis A. Logsdon, Michael Alonge, Stylianos E. Antonarakis, Matthew Borchers, Gerard G. Bouffard, Shelise Y. Brooks, Gina V. Caldas, Nae-Chyun Chen, Haoyu Cheng, Chen-Shan Chin, William Chow, Leonardo G. de Lima, Philip C. Dishuck, Richard Durbin, Tatiana Dvorkina, Ian T. Fiddes, Giulio Formenti, Robert S. Fulton, Arkarachai Fungtammasan, Erik Garrison, Patrick G. S. Grady, Tina A. Graves-Lindsay, Ira M. Hall, Nancy F. Hansen, Gabrielle A. Hartley, Marina Haukness, Kerstin Howe, Michael W. Hunkapiller, Chirag Jain, Miten Jain, Erich D. Jarvis, Peter Kerpedjiev, Melanie Kirsche, Mikhail Kolmogorov, Jonas Korlach, Milinn Kremitzki, Heng Li, Valerie V. Maduro, Tobias Marschall, Ann M. McCartney, Jennifer McDaniel, Danny E. Miller, James C. Mullikin, Eugene W. Myers, Nathan D. Olson, Benedict Paten, Paul Peluso, Pavel A. Pevzner, David Porubsky, Tamara Potapova, Evgeny I. Rogaev, Jeffrey A. Rosenfeld, Steven L. Salzberg, Valerie A. Schneider, Fritz J. Sedlazeck, Kishwar Shafin, Colin J. Shew, Alaina Shumate, Ying Sims, Arian F. A. Smit, Daniela C. Soto, Ivan Sović, Jessica M. Storer, Aaron Streets, Beth A. Sullivan, Françoise Thibaud-Nissen, James Torrance, Justin Wagner, Brian P. Walenz, Aaron Wenger, Jonathan M. D. Wood, Chunlin Xiao, Stephanie M. Yan, Alice C. Young, Samantha Zarate, Urvashi Surti, Rajiv C. McCoy, Megan Y. Dennis, Ivan A. Alexandrov, Jennifer L. Gerton, Rachel J. O’Neill, Winston Timp, Justin M. Zook, Michael C. Schatz, Evan E. Eichler, Karen H. Miga, Adam M. Phillippy, Nurk, Sergey [0000-0003-1301-5749], Koren, Sergey [0000-0002-1472-8962], Rhie, Arang [0000-0002-9809-8127], Rautiainen, Mikko [0000-0003-2971-267X], Bzikadze, Andrey V [0000-0002-7928-7950], Vollger, Mitchell R [0000-0002-8651-1615], Altemose, Nicolas [0000-0002-7231-6026], Uralsky, Lev [0000-0002-5565-7961], Gershman, Ariel [0000-0001-8899-8781], Aganezov, Sergey [0000-0003-2458-8323], Hoyt, Savannah J [0000-0001-7804-3236], Diekhans, Mark [0000-0002-0430-0989], Logsdon, Glennis A [0000-0003-2396-0656], Alonge, Michael [0000-0002-3692-1819], Antonarakis, Stylianos E [0000-0001-8907-5823], Borchers, Matthew [0000-0001-5903-3489], Bouffard, Gerard G [0000-0001-8744-6440], Chen, Nae-Chyun [0000-0002-4140-4568], Cheng, Haoyu [0000-0002-9209-5793], Chin, Chen-Shan [0000-0003-4394-2455], Chow, William [0000-0002-9056-201X], de Lima, Leonardo G [0000-0001-6340-6065], Dishuck, Philip C [0000-0003-2223-9787], Durbin, Richard [0000-0002-9130-1006], Fiddes, Ian T [0000-0002-1580-7443], Formenti, Giulio [0000-0002-7554-5991], Fungtammasan, Arkarachai [0000-0003-2398-0358], Garrison, Erik [0000-0003-3821-631X], Grady, Patrick GS [0000-0003-0180-7810], Graves-Lindsay, Tina A [0000-0002-0409-891X], Hall, Ira M [0000-0003-4442-6655], Hansen, Nancy F [0000-0002-0950-0699], Haukness, Marina [0000-0001-9991-8089], Howe, Kerstin [0000-0003-2237-513X], Jain, Miten [0000-0002-4571-3982], Jarvis, Erich D [0000-0001-8931-5049], Kirsche, Melanie [0000-0002-6631-4761], Kolmogorov, Mikhail [0000-0002-5489-9045], Korlach, Jonas [0000-0003-3047-4250], Kremitzki, Milinn [0000-0001-7980-3153], Li, Heng [0000-0003-4874-2874], Maduro, Valerie V [0000-0001-8250-9844], Marschall, Tobias [0000-0002-9376-1030], McDaniel, Jennifer [0000-0003-1987-0914], Miller, Danny E [0000-0001-6096-8601], Mullikin, James C [0000-0003-0825-3750], Myers, Eugene W [0000-0002-6580-7839], Olson, Nathan D [0000-0003-2585-3037], Paten, Benedict [0000-0001-8863-3539], Pevzner, Pavel A [0000-0002-0418-165X], Porubsky, David [0000-0001-8414-8966], Potapova, Tamara [0000-0003-2761-1795], Rosenfeld, Jeffrey A [0000-0002-8750-2841], Salzberg, Steven L [0000-0002-8859-7432], Sedlazeck, Fritz J [0000-0001-6040-2691], Shafin, Kishwar [0000-0001-5252-3434], Shumate, Alaina [0000-0002-4450-1857], Smit, Arian FA [0000-0003-2088-3165], Soto, Daniela C [0000-0002-6292-655X], Sović, Ivan [0000-0002-5900-4319], Storer, Jessica M [0000-0002-9619-5265], Streets, Aaron [0000-0002-3909-8389], Sullivan, Beth A [0000-0001-5216-4603], Thibaud-Nissen, Françoise [0000-0003-4957-7807], Torrance, James [0000-0002-6117-8190], Walenz, Brian P [0000-0001-8431-1428], Wenger, Aaron [0000-0003-1183-0432], Wood, Jonathan MD [0000-0002-7545-2162], Xiao, Chunlin [0000-0001-8702-4889], Yan, Stephanie M [0000-0002-6880-465X], Young, Alice C [0000-0003-0549-9261], Zarate, Samantha [0000-0001-5570-2059], McCoy, Rajiv C [0000-0003-0615-146X], Dennis, Megan Y [0000-0002-8502-5420], Alexandrov, Ivan A [0000-0003-4342-2003], Gerton, Jennifer L [0000-0003-0743-3637], O'Neill, Rachel J [0000-0002-1525-6821], Timp, Winston [0000-0003-2083-6027], Zook, Justin M [0000-0003-2309-8402], Schatz, Michael C [0000-0002-4118-4446], Eichler, Evan E [0000-0002-8246-4014], Miga, Karen H [0000-0001-9709-4565], Phillippy, Adam M [0000-0003-2983-8934], and Apollo - University of Cambridge Repository

Subjects
Chromosomes, Artificial, Bacterial, Genome, Multidisciplinary, General Science & Technology, Genome, Human, 1.1 Normal biological development and functioning, Human Genome, Bacterial, DNA, Sequence Analysis, DNA, Chromosomes, Cell Line, Underpinning research, Reference Values, Artificial, Human Genome Project, Genetics, Chromosomes, Human, Humans, Generic health relevance, Sequence Analysis, Human
Abstract

Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion–base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

Published
2022
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50. Laser interstitial thermal therapy for treatment of a recurrent skull base chordoma: illustrative case.

Author

Chow WD, Lehman VT, and Gompel JJV

Abstract

Background: The authors applied laser interstitial thermal therapy (LITT) to a recurrent skull base chordoma, which has not been previously described., Observations: A 63-year-old man was initially diagnosed with an 8-cm destructive clival chordoma, which was aggressively resected endoscopically but recurred despite multiple operations, proton radiation therapy, and chemotherapy. The patient underwent uncomplicated LITT for a subtemporal mass, which palliated the tumor for 10 months. However, it did not ultimately prevent the need for resection, although it may have delayed the surgery., Lessons: This case study demonstrates the feasibility and safety of LITT in treating these typically surgically challenging tumors. https://thejns.org/doi/10.3171/CASE24534.

Published
2024
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