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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. Population genomics of the critically endangered kākāpō

Author

Dussex, Nicolas, van der Valk, Tom, Morales, Hernán E, Wheat, Christopher W, Díez-del-Molino, David, von Seth, Johanna, Foster, Yasmin, Kutschera, Verena E, Guschanski, Katerina, Rhie, Arang, Phillippy, Adam M, Korlach, Jonas, Howe, Kerstin, Chow, William, Pelan, Sarah, Damas, Joanna D Mendes, Lewin, Harris A, Hastie, Alex R, Formenti, Giulio, Fedrigo, Olivier, Guhlin, Joseph, Harrop, Thomas WR, Le Lec, Marissa F, Dearden, Peter K, Haggerty, Leanne, Martin, Fergal J, Kodali, Vamsi, Thibaud-Nissen, Françoise, Iorns, David, Knapp, Michael, Gemmell, Neil J, Robertson, Fiona, Moorhouse, Ron, Digby, Andrew, Eason, Daryl, Vercoe, Deidre, Howard, Jason, Jarvis, Erich D, Robertson, Bruce C, and Dalén, Love

Subjects
Human Genome, Genetics, Life on Land, bottleneck, conservation, inbreeding, kākāpō, mutational load, purging
Abstract

The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for kākāpō, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP). We also sequenced and analyzed 35 modern genomes from the sole surviving island population and 14 genomes from the extinct mainland population. While theory suggests that such a small population is likely to have accumulated deleterious mutations through genetic drift, our analyses on the impact of the long-term small population size in kākāpō indicate that present-day island kākāpō have a reduced number of harmful mutations compared to mainland individuals. We hypothesize that this reduced mutational load is due to the island population having been subjected to a combination of genetic drift and purging of deleterious mutations, through increased inbreeding and purifying selection, since its isolation from the mainland ∼10,000 years ago. Our results provide evidence that small populations can survive even when isolated for hundreds of generations. This work provides key insights into kākāpō breeding and recovery and more generally into the application of genetic tools in conservation efforts for endangered species.

Published
2021

6. 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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7. Reference genome and demographic history of the most endangered marine mammal, the vaquita

Author

Morin, Phillip A, Archer, Frederick I, Avila, Catherine D, Balacco, Jennifer R, Bukhman, Yury V, Chow, William, Fedrigo, Olivier, Formenti, Giulio, Fronczek, Julie A, Fungtammasan, Arkarachai, Gulland, Frances MD, Haase, Bettina, Heide‐Jorgensen, Mads Peter, Houck, Marlys L, Howe, Kerstin, Misuraca, Ann C, Mountcastle, Jacquelyn, Musser, Whitney, Paez, Sadye, Pelan, Sarah, Phillippy, Adam, Rhie, Arang, Robinson, Jacqueline, Rojas‐Bracho, Lorenzo, Rowles, Teri K, Ryder, Oliver A, Smith, Cynthia R, Stevenson, Sacha, Taylor, Barbara L, Teilmann, Jonas, Torrance, James, Wells, Randall S, Westgate, Andrew J, and Jarvis, Erich D

Subjects
Genetics, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Generic health relevance, Life on Land, Animals, Chromosomes, Endangered Species, Female, Genetics, Population, Genome, Phocoena, Conservation genomics, genome diversity, historical demography, Phocoena sinus, porpoise, Vertebrate Genomes Project, Biological Sciences, Evolutionary Biology
Abstract

The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline for more than 20 years resulting from inadvertent deaths due to the increasing use of large-mesh gillnets. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome-length autosome scaffolds and the X-chromosome scaffold, with a scaffold N50 of 115 Mb. Genome-wide heterozygosity is the lowest (0.01%) of any mammalian species analysed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long-term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long-term population stability at less than 5,000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.

Published
2021

8. 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

9. Telomere-to-telomere assembly of a complete human X chromosome

Author

Miga, Karen H, Koren, Sergey, Rhie, Arang, Vollger, Mitchell R, Gershman, Ariel, Bzikadze, Andrey, Brooks, Shelise, Howe, Edmund, Porubsky, David, Logsdon, Glennis A, Schneider, Valerie A, Potapova, Tamara, Wood, Jonathan, Chow, William, Armstrong, Joel, Fredrickson, Jeanne, Pak, Evgenia, Tigyi, Kristof, Kremitzki, Milinn, Markovic, Christopher, Maduro, Valerie, Dutra, Amalia, Bouffard, Gerard G, Chang, Alexander M, Hansen, Nancy F, Wilfert, Amy B, Thibaud-Nissen, Françoise, Schmitt, Anthony D, Belton, Jon-Matthew, Selvaraj, Siddarth, Dennis, Megan Y, Soto, Daniela C, Sahasrabudhe, Ruta, Kaya, Gulhan, Quick, Josh, Loman, Nicholas J, Holmes, Nadine, Loose, Matthew, Surti, Urvashi, Risques, Rosa ana, Graves Lindsay, Tina A, Fulton, Robert, Hall, Ira, Paten, Benedict, Howe, Kerstin, Timp, Winston, Young, Alice, Mullikin, James C, Pevzner, Pavel A, Gerton, Jennifer L, Sullivan, Beth A, Eichler, Evan E, and Phillippy, Adam M

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Bioengineering, Nanotechnology, Human Genome, Generic health relevance, Centromere, Chromosomes, Human, X, CpG Islands, DNA Methylation, DNA, Satellite, Female, Genome, Human, Humans, Hydatidiform Mole, Male, Pregnancy, Reproducibility of Results, Telomere, Testis, General Science & Technology
Abstract

After two decades of improvements, the current human reference genome (GRCh38) is the most accurate and complete vertebrate genome ever produced. However, no single chromosome has been finished end to end, and hundreds of unresolved gaps persist1,2. Here we present a human genome assembly that surpasses the continuity of GRCh382, along with a gapless, telomere-to-telomere assembly of a human chromosome. This was enabled by high-coverage, ultra-long-read nanopore sequencing of the complete hydatidiform mole CHM13 genome, combined with complementary technologies for quality improvement and validation. Focusing our efforts on the human X chromosome3, we reconstructed the centromeric satellite DNA array (approximately 3.1 Mb) and closed the 29 remaining gaps in the current reference, including new sequences from the human pseudoautosomal regions and from cancer-testis ampliconic gene families (CT-X and GAGE). These sequences will be integrated into future human reference genome releases. In addition, the complete chromosome X, combined with the ultra-long nanopore data, allowed us to map methylation patterns across complex tandem repeats and satellite arrays. Our results demonstrate that finishing the entire human genome is now within reach, and the data presented here will facilitate ongoing efforts to complete the other human chromosomes.

Published
2020

10. Reference genome and demographic history of the most endangered marine mammal, the vaquita

Author

Morin, Phillip A, Archer, Frederick I, Avila, Catherine D, Balacco, Jennifer R, Bukhman, Yury V, Chow, William, Fedrigo, Olivier, Formenti, Giulio, Fronczek, Julie A, Fungtammasan, Arkarachai, Gulland, Frances MD, Haase, Bettina, Heide-Jorgensen, Mads Peter, Houck, Marlys L, Howe, Kerstin, Misuraca, Ann C, Mountcastle, Jacquelyn, Musser, Whitney, Paez, Sadye, Pelan, Sarah, Phillippy, Adam, Rhie, Arang, Robinson, Jacqueline, Rojas-Bracho, Lorenzo, Rowles, Teri K, Ryder, Oliver A, Smith, Cynthia R, Stevenson, Sacha, Taylor, Barbara L, Teilmann, Jonas, Torrance, James, Wells, Randall S, Westgate, Andrew, and Jarvis, Erich D

Subjects
Human Genome, Genetics, Generic health relevance, Life on Land
Abstract

AbstractThe vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline resulting from inadvertent deaths due to the increasing use of large-mesh gillnets for more than 20 years. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome-length autosome scaffolds and the X-chromosome scaffold, with a scaffold N50 of 115 Mb. Genome-wide heterozygosity is the lowest (0.01%) of any mammalian species analyzed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long-term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long-term population stability at less than 5000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.

Published
2020

11. 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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12. Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci

Author

Lilue, Jingtao, Doran, Anthony G, Fiddes, Ian T, Abrudan, Monica, Armstrong, Joel, Bennett, Ruth, Chow, William, Collins, Joanna, Collins, Stephan, Czechanski, Anne, Danecek, Petr, Diekhans, Mark, Dolle, Dirk-Dominik, Dunn, Matt, Durbin, Richard, Earl, Dent, Ferguson-Smith, Anne, Flicek, Paul, Flint, Jonathan, Frankish, Adam, Fu, Beiyuan, Gerstein, Mark, Gilbert, James, Goodstadt, Leo, Harrow, Jennifer, Howe, Kerstin, Ibarra-Soria, Ximena, Kolmogorov, Mikhail, Lelliott, Chris J, Logan, Darren W, Loveland, Jane, Mathews, Clayton E, Mott, Richard, Muir, Paul, Nachtweide, Stefanie, Navarro, Fabio CP, Odom, Duncan T, Park, Naomi, Pelan, Sarah, Pham, Son K, Quail, Mike, Reinholdt, Laura, Romoth, Lars, Shirley, Lesley, Sisu, Cristina, Sjoberg-Herrera, Marcela, Stanke, Mario, Steward, Charles, Thomas, Mark, Threadgold, Glen, Thybert, David, Torrance, James, Wong, Kim, Wood, Jonathan, Yalcin, Binnaz, Yang, Fengtang, Adams, David J, Paten, Benedict, and Keane, Thomas M

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Animals, Animals, Laboratory, Chromosome Mapping, Genetic Loci, Genome, Haplotypes, Mice, Mice, Inbred BALB C, Mice, Inbred C3H, Mice, Inbred C57BL, Mice, Inbred CBA, Mice, Inbred DBA, Mice, Inbred NOD, Mice, Inbred Strains, Molecular Sequence Annotation, Phylogeny, Polymorphism, Single Nucleotide, Species Specificity, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

We report full-length draft de novo genome assemblies for 16 widely used inbred mouse strains and find extensive strain-specific haplotype variation. We identify and characterize 2,567 regions on the current mouse reference genome exhibiting the greatest sequence diversity. These regions are enriched for genes involved in pathogen defence and immunity and exhibit enrichment of transposable elements and signatures of recent retrotransposition events. Combinations of alleles and genes unique to an individual strain are commonly observed at these loci, reflecting distinct strain phenotypes. We used these genomes to improve the mouse reference genome, resulting in the completion of 10 new gene structures. Also, 62 new coding loci were added to the reference genome annotation. These genomes identified a large, previously unannotated, gene (Efcab3-like) encoding 5,874 amino acids. Mutant Efcab3-like mice display anomalies in multiple brain regions, suggesting a possible role for this gene in the regulation of brain development.

Published
2018

13. A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

Author

Warren, Wesley C, Hillier, LaDeana W, Tomlinson, Chad, Minx, Patrick, Kremitzki, Milinn, Graves, Tina, Markovic, Chris, Bouk, Nathan, Pruitt, Kim D, Thibaud-Nissen, Francoise, Schneider, Valerie, Mansour, Tamer A, Brown, C Titus, Zimin, Aleksey, Hawken, Rachel, Abrahamsen, Mitch, Pyrkosz, Alexis B, Morisson, Mireille, Fillon, Valerie, Vignal, Alain, Chow, William, Howe, Kerstin, Fulton, Janet E, Miller, Marcia M, Lovell, Peter, Mello, Claudio V, Wirthlin, Morgan, Mason, Andrew S, Kuo, Richard, Burt, David W, Dodgson, Jerry B, and Cheng, Hans H

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Generic health relevance, Animals, Chickens, Chromosomes, Artificial, Bacterial, Computational Biology, Contig Mapping, Genome, Molecular Sequence Annotation, Sequence Analysis, DNA, Gallus gallus, genome assembly, MHC, Biochemistry and cell biology, Statistics
Abstract

The importance of the Gallus gallus (chicken) as a model organism and agricultural animal merits a continuation of sequence assembly improvement efforts. We present a new version of the chicken genome assembly (Gallus_gallus-5.0; GCA_000002315.3), built from combined long single molecule sequencing technology, finished BACs, and improved physical maps. In overall assembled bases, we see a gain of 183 Mb, including 16.4 Mb in placed chromosomes with a corresponding gain in the percentage of intact repeat elements characterized. Of the 1.21 Gb genome, we include three previously missing autosomes, GGA30, 31, and 33, and improve sequence contig length 10-fold over the previous Gallus_gallus-4.0. Despite the significant base representation improvements made, 138 Mb of sequence is not yet located to chromosomes. When annotated for gene content, Gallus_gallus-5.0 shows an increase of 4679 annotated genes (2768 noncoding and 1911 protein-coding) over those in Gallus_gallus-4.0. We also revisited the question of what genes are missing in the avian lineage, as assessed by the highest quality avian genome assembly to date, and found that a large fraction of the original set of missing genes are still absent in sequenced bird species. Finally, our new data support a detailed map of MHC-B, encompassing two segments: one with a highly stable gene copy number and another in which the gene copy number is highly variable. The chicken model has been a critical resource for many other fields of study, and this new reference assembly will substantially further these efforts.

Published
2017

14. Evolutionary and biomedical insights from a marmoset diploid genome assembly

Author

Yang, Chentao, Zhou, Yang, Marcus, Stephanie, Formenti, Giulio, Bergeron, Lucie A., Song, Zhenzhen, Bi, Xupeng, Bergman, Juraj, Rousselle, Marjolaine Marie C., Zhou, Chengran, Zhou, Long, Deng, Yuan, Fang, Miaoquan, Xie, Duo, Zhu, Yuanzhen, Tan, Shangjin, Mountcastle, Jacquelyn, Haase, Bettina, Balacco, Jennifer, Wood, Jonathan, Chow, William, Rhie, Arang, Pippel, Martin, Fabiszak, Margaret M., Koren, Sergey, Fedrigo, Olivier, Freiwald, Winrich A., Howe, Kerstin, Yang, Huanming, Phillippy, Adam M., Schierup, Mikkel Heide, Jarvis, Erich D., and Zhang, Guojie

Published
2021
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17. 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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18. 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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19. 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

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

Author

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

Abstract

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

Published
2023

22. 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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23. 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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24. 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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25. 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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26. 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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27. 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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28. 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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29. 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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30. 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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31. 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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32. 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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33. 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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34. 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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35. A Chromosome-Level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus)

Author

Sætre, Camilla Lo Cascio, primary, Eroukhmanoff, Fabrice, additional, Rönkä, Katja, additional, Kluen, Edward, additional, Thorogood, Rose, additional, Torrance, James, additional, Tracey, Alan, additional, Chow, William, additional, Pelan, Sarah, additional, Howe, Kerstin, additional, Jakobsen, Kjetill S, additional, and Tørresen, Ole K, additional

Published
2021
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36. The genome sequence of the European turtle dove, Streptopelia turtur Linnaeus 1758

Author

Dunn, Jenny C., primary, Hamer, Keith C., additional, Morris, Antony J., additional, Grice, Philip V., additional, Smith, Michelle, additional, Corton, Craig, additional, Oliver, Karen, additional, Skelton, Jason, additional, Betteridge, Emma, additional, Dolucan, Jale, additional, Quail, Michael A., additional, McCarthy, Shane A., additional, Uliano-Silva, Marcela, additional, Howe, Kerstin, additional, Torrance, James, additional, Chow, William, additional, Pelan, Sarah, additional, Sims, Ying, additional, Challis, Richard, additional, Threlfall, Jonathan, additional, Mead, Daniel, additional, and Blaxter, Mark, additional

Published
2021
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37. 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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38. A 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, Olsen, Björn, Jarvis, Erich D., Smith, Jacqueline, Eory, Lel, Kraus, Robert H. S., 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, Olsen, Björn, Jarvis, Erich D., Smith, Jacqueline, Eory, Lel, and Kraus, Robert H. S.

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.

Published
2021
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39. Towards complete and error-free genome assemblies of all vertebrate species

Author

National Institutes of Health (US), National Human Genome Research Institute (US), Ministry of Health and Welfare (South Korea), Wellcome Trust, European Molecular Biology Laboratory, Howard Hughes Medical Institute, Rockefeller University, Robert and Rosabel Osborne Endowment, European Commission, National Library of Medicine (US), Korea Institute of Marine Science & Technology, Ministry of Oceans and Fisheries (South Korea), Alfred P. Sloan Foundation, Max Planck Society, Maine Department of Inland Fisheries & Wildlife, National Science Foundation (US), University of Queensland, Science Exchange, Northeastern University (US), Federal Ministry of Education and Research (Germany), EMBO, National Key Research and Development Program (China), Qatar Society of Al-Gannas (Algannas), Katara Cultural Village, Government of Qatar, Monash University Malaysia, Hessen State Ministry of Higher Education, Research and the Arts, Ministry of Science, Research and Art Baden-Württemberg, Agency for Science, Technology and Research A*STAR (Singapore), European Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Fundación la Caixa, Generalitat de Catalunya, Irish Research Council, Danish National Research Foundation, Australian Research Council, Rhie, Arang, McCarthy, Shane A., Fedrigo, Olivier, Damas, Joana, Formenti, Giulio, Koren, Sergey, Uliano-Silva, Marcela, Chow, William, Fungtammasan, Arkarachai, Kim, Juwan, Lee, Chul, Haase, Bettina, Mountcastle, Jacquelyn, Winkler, Sylke, Paez, Sadye, Howard, Jason, Vernes, Sonja C, Lama, Tanya M, Grützner, Frank, Warren, Wesley C., Balakrishnan, Christopher N., Pippel, Martin, Burt, Dave, George, Julia M., Biegler, Matthew T., Iorns, David, Digby, Andrew, Eason, Daryl, Robertson, Bruce, Edwards, Taylor, Wilkinson, Mark, Turner, George, Malinsky, Milan, Meyer, Axel, Kautt, Andreas F., Franchini, Paolo, Detrich III, H. William, Svardal, Hannes, Wagner, Maximilian, Naylor, Gavin J. P., Mooney, Mark, Simbirsky, Maria, Hannigan, Brett T., Pesout, Trevor, Houck, Marlys L., Misuraca, Ann, Kingan, Sarah B., Hall, Richard, Wood, Jonathan, Kronenberg, Zev, Sović, Ivan, Dunn, Christopher, Ning, Zemin, Hastie, Alex, Lee, Joyce, Selvaraj, Siddarth, Green, Richard E., Putnam, Nicholas H., Gut, Ivo, Dagnew, Robel E., Ghurye, Jay, Garrison, Erik, Sims, Ying, Collins, Joanna, Pelan, Sarah, Torrance, James, Tracey, Alan, Guan, Dengfeng, London, Sarah E., Clayton, David F., Mello, Claudio V., Friedrich, Samantha R., Lovell, Peter V., Osipova, Ekaterina, Al-Ajli, Farooq O., Diekhans, Mark, Secomandi, Simona, Kim, Heebal, Theofanopoulou, Constantina, Hiller, Michael, Zhou, Yang, Harris, Robert S., Makova, Kateryna D., Medvedev, Paul, Hoffman, Jinna, Masterson, Patrick, Nassar, Luis, Clark, Karen, Martin, Fergal, Howe, Kevin, Flicek, Paul, Walenz, Brian P., Kwak, Woori, Clawson, Hiram, Paten, Benedict, Kraus, Robert H. S., Crawford, Andrew J., Gilbert, M. Thomas P., Zhang, Guojie, Venkatesh, Byrappa, Murphy, Robert W., Koepfli, Klaus-Peter, Ko, Byung June, Shapiro, Beth, Johnson, Warren E., Di Palma, Federica, Marqués-Bonet, Tomàs, Teeling, Emma C., Warnow, Tandy, Marshall Graves, Jennifer, Ryder, Oliver A., Haussler, David, O’Brien, Stephen J., Chaisson, Mark, Korlach, Jonas, Lewin, Harris A., Howe, Kerstin, Myers, Eugene W., Durbin, Richard, Phillippy, Adam M., Jarvis, Erich D., Gedman, Gregory L., Cantin, Lindsey J., Thibaud-Nissen, Francoise, Haggerty, Leanne, Bista, Iliana, Smith, Michelle, National Institutes of Health (US), National Human Genome Research Institute (US), Ministry of Health and Welfare (South Korea), Wellcome Trust, European Molecular Biology Laboratory, Howard Hughes Medical Institute, Rockefeller University, Robert and Rosabel Osborne Endowment, European Commission, National Library of Medicine (US), Korea Institute of Marine Science & Technology, Ministry of Oceans and Fisheries (South Korea), Alfred P. Sloan Foundation, Max Planck Society, Maine Department of Inland Fisheries & Wildlife, National Science Foundation (US), University of Queensland, Science Exchange, Northeastern University (US), Federal Ministry of Education and Research (Germany), EMBO, National Key Research and Development Program (China), Qatar Society of Al-Gannas (Algannas), Katara Cultural Village, Government of Qatar, Monash University Malaysia, Hessen State Ministry of Higher Education, Research and the Arts, Ministry of Science, Research and Art Baden-Württemberg, Agency for Science, Technology and Research A*STAR (Singapore), European Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Fundación la Caixa, Generalitat de Catalunya, Irish Research Council, Danish National Research Foundation, Australian Research Council, Rhie, Arang, McCarthy, Shane A., Fedrigo, Olivier, Damas, Joana, Formenti, Giulio, Koren, Sergey, Uliano-Silva, Marcela, Chow, William, Fungtammasan, Arkarachai, Kim, Juwan, Lee, Chul, Haase, Bettina, Mountcastle, Jacquelyn, Winkler, Sylke, Paez, Sadye, Howard, Jason, Vernes, Sonja C, Lama, Tanya M, Grützner, Frank, Warren, Wesley C., Balakrishnan, Christopher N., Pippel, Martin, Burt, Dave, George, Julia M., Biegler, Matthew T., Iorns, David, Digby, Andrew, Eason, Daryl, Robertson, Bruce, Edwards, Taylor, Wilkinson, Mark, Turner, George, Malinsky, Milan, Meyer, Axel, Kautt, Andreas F., Franchini, Paolo, Detrich III, H. William, Svardal, Hannes, Wagner, Maximilian, Naylor, Gavin J. P., Mooney, Mark, Simbirsky, Maria, Hannigan, Brett T., Pesout, Trevor, Houck, Marlys L., Misuraca, Ann, Kingan, Sarah B., Hall, Richard, Wood, Jonathan, Kronenberg, Zev, Sović, Ivan, Dunn, Christopher, Ning, Zemin, Hastie, Alex, Lee, Joyce, Selvaraj, Siddarth, Green, Richard E., Putnam, Nicholas H., Gut, Ivo, Dagnew, Robel E., Ghurye, Jay, Garrison, Erik, Sims, Ying, Collins, Joanna, Pelan, Sarah, Torrance, James, Tracey, Alan, Guan, Dengfeng, London, Sarah E., Clayton, David F., Mello, Claudio V., Friedrich, Samantha R., Lovell, Peter V., Osipova, Ekaterina, Al-Ajli, Farooq O., Diekhans, Mark, Secomandi, Simona, Kim, Heebal, Theofanopoulou, Constantina, Hiller, Michael, Zhou, Yang, Harris, Robert S., Makova, Kateryna D., Medvedev, Paul, Hoffman, Jinna, Masterson, Patrick, Nassar, Luis, Clark, Karen, Martin, Fergal, Howe, Kevin, Flicek, Paul, Walenz, Brian P., Kwak, Woori, Clawson, Hiram, Paten, Benedict, Kraus, Robert H. S., Crawford, Andrew J., Gilbert, M. Thomas P., Zhang, Guojie, Venkatesh, Byrappa, Murphy, Robert W., Koepfli, Klaus-Peter, Ko, Byung June, Shapiro, Beth, Johnson, Warren E., Di Palma, Federica, Marqués-Bonet, Tomàs, Teeling, Emma C., Warnow, Tandy, Marshall Graves, Jennifer, Ryder, Oliver A., Haussler, David, O’Brien, Stephen J., Chaisson, Mark, Korlach, Jonas, Lewin, Harris A., Howe, Kerstin, Myers, Eugene W., Durbin, Richard, Phillippy, Adam M., Jarvis, Erich D., Gedman, Gregory L., Cantin, Lindsey J., Thibaud-Nissen, Francoise, Haggerty, Leanne, Bista, Iliana, and Smith, Michelle

Abstract

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1,2,3,4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

Published
2021

40. Analyses of pig genomes provide insight into porcine demography and evolution

Author

Groenen, Martien A. M., Archibald, Alan L., Uenishi, Hirohide, Tuggle, Christopher K., Takeuchi, Yasuhiro, Rothschild, Max F., Rogel-Gaillard, Claire, Park, Chankyu, Milan, Denis, Megens, Hendrik-Jan, Li, Shengting, Larkin, Denis M., Kim, Heebal, Frantz, Laurent A. F., Caccamo, Mario, Ahn, Hyeonju, Aken, Bronwen L., Anselmo, Anna, Anthon, Christian, Auvil, Loretta, Badaoui, Bouabid, Beattie, Craig W., Bendixen, Christian, Berman, Daniel, Blecha, Frank, Blomberg, Jonas, Bolund, Lars, Bosse, Mirte, Botti, Sara, Bujie, Zhan, Bystrom, Megan, Capitanu, Boris, Carvalho-Silva, Denise, Chardon, Patrick, Chen, Celine, Cheng, Ryan, Choi, Sang-Haeng, Chow, William, Clark, Richard C., Clee, Christopher, Crooijmans, Richard P. M. A., Dawson, Harry D., Dehais, Patrice, De Sapio, Fioravante, Dibbits, Bert, Drou, Nizar, Du, Zhi-Qiang, Eversole, Kellye, Fadista, João, Fairley, Susan, Faraut, Thomas, Faulkner, Geoffrey J., Fowler, Katie E., Fredholm, Merete, Fritz, Eric, Gilbert, James G. R., Giuffra, Elisabetta, Gorodkin, Jan, Griffin, Darren K., Harrow, Jennifer L., Hayward, Alexander, Howe, Kerstin, Hu, Zhi-Liang, Humphray, Sean J., Hunt, Toby, Hornshøj, Henrik, Jeon, Jin-Tae, Jern, Patric, Jones, Matthew, Jurka, Jerzy, Kanamori, Hiroyuki, Kapetanovic, Ronan, Kim, Jaebum, Kim, Jae-Hwan, Kim, Kyu-Won, Kim, Tae-Hun, Larson, Greger, Lee, Kyooyeol, Lee, Kyung-Tai, Leggett, Richard, Lewin, Harris A., Li, Yingrui, Liu, Wansheng, Loveland, Jane E., Lu, Yao, Lunney, Joan K., Ma, Jian, Madsen, Ole, Mann, Katherine, Matthews, Lucy, McLaren, Stuart, Morozumi, Takeya, Murtaugh, Michael P., Narayan, Jitendra, Truong Nguyen, Dinh, Ni, Peixiang, Oh, Song-Jung, Onteru, Suneel, Panitz, Frank, Park, Eung-Woo, Park, Hong-Seog, Pascal, Geraldine, Paudel, Yogesh, Perez-Enciso, Miguel, Ramirez-Gonzalez, Ricardo, Reecy, James M., Rodriguez-Zas, Sandra, Rohrer, Gary A., Rund, Lauretta, Sang, Yongming, Schachtschneider, Kyle, Schraiber, Joshua G., Schwartz, John, Scobie, Linda, Scott, Carol, Searle, Stephen, Servin, Bertrand, Southey, Bruce R., Sperber, Goran, Stadler, Peter, Sweedler, Jonathan V., Tafer, Hakim, Thomsen, Bo, Wali, Rashmi, Wang, Jian, Wang, Jun, White, Simon, Xu, Xun, Yerle, Martine, Zhang, Guojie, Zhang, Jianguo, Zhang, Jie, Zhao, Shuhong, Rogers, Jane, Churcher, Carol, and Schook, Lawrence B.

Published
2012
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41. The genome sequence of the Norway rat, Rattus norvegicus Berkenhout 1769

Author

Howe, Kerstin, primary, Dwinell, Melinda, additional, Shimoyama, Mary, additional, Corton, Craig, additional, Betteridge, Emma, additional, Dove, Alexander, additional, Quail, Michael A., additional, Smith, Michelle, additional, Saba, Laura, additional, Williams, Robert W., additional, Chen, Hao, additional, Kwitek, Anne E., additional, McCarthy, Shane A., additional, Uliano-Silva, Marcela, additional, Chow, William, additional, Tracey, Alan, additional, Torrance, James, additional, Sims, Ying, additional, Challis, Richard, additional, Threlfall, Jonathan, additional, and Blaxter, Mark, additional

Published
2021
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42. The genome sequence of the European golden eagle, Aquila chrysaetos chrysaetos Linnaeus 1758

Author

Mead, Dan, primary, Ogden, Rob, additional, Meredith, Anna, additional, Peniche, Gabriela, additional, Smith, Michelle, additional, Corton, Craig, additional, Oliver, Karen, additional, Skelton, Jason, additional, Betteridge, Emma, additional, Doulcan, Jale, additional, Holmes, Nadine, additional, Wright, Victoria, additional, Loose, Matt, additional, Quail, Michael A., additional, McCarthy, Shane A., additional, Howe, Kerstin, additional, Chow, William, additional, Torrance, James, additional, Collins, Joanna, additional, Challis, Richard, additional, Durbin, Richard, additional, and Blaxter, Mark, additional

Published
2021
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43. The genome sequence of the brown trout, Salmo trutta Linnaeus 1758

Author

Hansen, Tom, primary, Fjelldal, Per Gunnar, additional, Lien, Sigbjørn, additional, Smith, Michelle, additional, Corton, Craig, additional, Oliver, Karen, additional, Skelton, Jason, additional, Betteridge, Emma, additional, Doulcan, Jale, additional, Fedrigo, Olivier, additional, Mountcastle, Jacquelyn, additional, Jarvis, Erich, additional, McCarthy, Shane A., additional, Chow, William, additional, Howe, Kerstin, additional, Torrance, James, additional, Wood, Jonathan, additional, Sims, Ying, additional, Haggerty, Leanne, additional, Challis, Richard, additional, Threlfall, Jonathan, additional, Mead, Daniel, additional, Durbin, Richard, additional, and Blaxter, Mark, additional

Published
2021
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46. The zebrafish reference genome sequence and its relationship to the human genome

Author

Howe, Kerstin, Clark, Matthew D., Torroja, Carlos F., Torrance, James, Berthelot, Camille, Muffato, Matthieu, Collins, John E., Humphray, Sean, McLaren, Karen, Matthews, Lucy, McLaren, Stuart, Sealy, Ian, Caccamo, Mario, Churcher, Carol, Scott, Carol, Barrett, Jeffrey C., Koch, Romke, Rauch, Gerd-Jörg, White, Simon, Chow, William, Kilian, Britt, Quintais, Leonor T., Guerra-Assunção, José A., Zhou, Yi, Gu, Yong, Yen, Jennifer, Vogel, Jan-Hinnerk, Eyre, Tina, Redmond, Seth, Banerjee, Ruby, Chi, Jianxiang, Fu, Beiyuan, Langley, Elizabeth, Maguire, Sean F., Laird, Gavin K., Lloyd, David, Kenyon, Emma, Donaldson, Sarah, Sehra, Harminder, Almeida-King, Jeff, Loveland, Jane, Trevanion, Stephen, Jones, Matt, Quail, Mike, Willey, Dave, Hunt, Adrienne, Burton, John, Sims, Sarah, McLay, Kirsten, Plumb, Bob, Davis, Joy, Clee, Chris, Oliver, Karen, Clark, Richard, Riddle, Clare, Eliott, David, Threadgold, Glen, Harden, Glenn, Ware, Darren, Mortimer, Beverly, Kerry, Giselle, Heath, Paul, Phillimore, Benjamin, Tracey, Alan, Corby, Nicole, Dunn, Matthew, Johnson, Christopher, Wood, Jonathan, Clark, Susan, Pelan, Sarah, Griffiths, Guy, Smith, Michelle, Glithero, Rebecca, Howden, Philip, Barker, Nicholas, Stevens, Christopher, Harley, Joanna, Holt, Karen, Panagiotidis, Georgios, Lovell, Jamieson, Beasley, Helen, Henderson, Carl, Gordon, Daria, Auger, Katherine, Wright, Deborah, Collins, Joanna, Raisen, Claire, Dyer, Lauren, Leung, Kenric, Robertson, Lauren, Ambridge, Kirsty, Leongamornlert, Daniel, McGuire, Sarah, Gilderthorp, Ruth, Griffiths, Coline, Manthravadi, Deepa, Nichol, Sarah, Barker, Gary, Whitehead, Siobhan, Kay, Michael, Brown, Jacqueline, Murnane, Clare, Gray, Emma, Humphries, Matthew, Sycamore, Neil, Barker, Darren, Saunders, David, Wallis, Justene, Babbage, Anne, Hammond, Sian, Mashreghi-Mohammadi, Maryam, Barr, Lucy, Martin, Sancha, Wray, Paul, Ellington, Andrew, Matthews, Nicholas, Ellwood, Matthew, Woodmansey, Rebecca, Clark, Graham, Cooper, James, Tromans, Anthony, Grafham, Darren, Skuce, Carl, Pandian, Richard, Andrews, Robert, Harrison, Elliot, Kimberley, Andrew, Garnett, Jane, Fosker, Nigel, Hall, Rebekah, Garner, Patrick, Kelly, Daniel, Bird, Christine, Palmer, Sophie, Gehring, Ines, Berger, Andrea, Dooley, Christopher M., Ersan-Ürün, Zübeyde, Eser, Cigdem, Geiger, Horst, Geisler, Maria, Karotki, Lena, Kirn, Anette, Konantz, Judith, Konantz, Martina, Oberländer, Martina, Rudolph-Geiger, Silke, Teucke, Mathias, Osoegawa, Kazutoyo, Zhu, Baoli, Rapp, Amanda, Widaa, Sara, Langford, Cordelia, Yang, Fengtang, Carter, Nigel P., Harrow, Jennifer, Ning, Zemin, Herrero, Javier, Searle, Steve M. J., Enright, Anton, Geisler, Robert, Plasterk, Ronald H. A., Lee, Charles, Westerfield, Monte, de Jong, Pieter J., Zon, Leonard I., Postlethwait, John H., Nüsslein-Volhard, Christiane, Hubbard, Tim J. P., Crollius, Hugues Roest, Rogers, Jane, and Stemple, Derek L.

Published
2013
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47. An improved pig reference genome sequence to enable pig genetics and genomics research

Author

Warr, Amanda, primary, Affara, Nabeel, primary, Aken, Bronwen, primary, Beiki, Hamid, primary, Bickhart, Derek M, primary, Billis, Konstantinos, primary, Chow, William, primary, Eory, Lel, primary, Finlayson, Heather A, primary, Flicek, Paul, primary, Girón, Carlos G, primary, Griffin, Darren K, primary, Hall, Richard, primary, Hannum, Greg, primary, Hourlier, Thibaut, primary, Howe, Kerstin, primary, Hume, David A, primary, Izuogu, Osagie, primary, Kim, Kristi, primary, Koren, Sergey, primary, Liu, Haibou, primary, Manchanda, Nancy, primary, Martin, Fergal J, primary, Nonneman, Dan J, primary, O'Connor, Rebecca E, primary, Phillippy, Adam M, primary, Rohrer, Gary A, primary, Rosen, Benjamin D, primary, Rund, Laurie A, primary, Sargent, Carole A, primary, Schook, Lawrence B, primary, Schroeder, Steven G, primary, Schwartz, Ariel S, primary, Skinner, Ben M, primary, Talbot, Richard, primary, Tseng, Elizabeth, primary, Tuggle, Christopher K, primary, Watson, Mick, primary, Smith, Timothy P L, primary, and Archibald, Alan L, primary

Published
2020
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50. 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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