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1. Multi-generational benefits of genetic rescue

Author

Onorato, Dave P., Cunningham, Mark W., Lotz, Mark, Criffield, Marc, Shindle, David, Johnson, Annette, Clemons, Bambi C. F., Shea, Colin P., Roelke-Parker, Melody E., Johnson, Warren E., McClintock, Brett T., Pilgrim, Kristine L., Schwartz, Michael K., and Oli, Madan K.

Published
2024
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2. Standards recommendations for the Earth BioGenome Project

Author

Lawniczak, Mara KN, Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M, Baker, William J, Belov, Katherine, Blaxter, Mark L, Bonet, Tomas Marques, Childers, Anna K, Coddington, Jonathan A, Crandall, Keith A, Crawford, Andrew J, Davey, Robert P, Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J, Howe, Kerstin, Jarvis, Erich D, Johnson, Warren E, Johnson, Rebecca N, Kersey, Paul J, Liu, Xin, Lopez, Jose Victor, Myers, Eugene W, Pettersson, Olga Vinnere, Phillippy, Adam M, Poelchau, Monica F, Pruitt, Kim D, Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A, Soltis, Pamela S, Swarbreck, David, Thibaud-Nissen, Françoise, Wang, Sibo, Wegrzyn, Jill L, Zhang, Guojie, Zhang, He, Lewin, Harris A, and Richards, Stephen

Subjects
Human Genome, Genetics, Animals, Base Sequence, Biodiversity, Eukaryota, Genomics, Humans, Reference Standards, Reference Values, Sequence Analysis, DNA, Earth BioGenome Project, genomics, ethics, genome assembly
Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Published
2022

3. Author Correction: Puma genomes from North and South America provide insights into the genomic consequences of inbreeding.

Author

Saremi, Nedda F, Supple, Megan A, Byrne, Ashley, Cahill, James A, Coutinho, Luiz Lehmann, Dalén, Love, Figueiró, Henrique V, Johnson, Warren E, Milne, Heather J, O'Brien, Stephen J, O'Connell, Brendan, Onorato, David P, Riley, Seth PD, Sikich, Jeff A, Stahler, Daniel R, Villela, Priscilla Marqui Schmidt, Vollmers, Christopher, Wayne, Robert K, Eizirik, Eduardo, Corbett-Detig, Russell B, Green, Richard E, Wilmers, Christopher C, and Shapiro, Beth

Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2019

5. Puma genomes from North and South America provide insights into the genomic consequences of inbreeding.

Author

Saremi, Nedda F, Supple, Megan A, Byrne, Ashley, Cahill, James A, Coutinho, Luiz Lehmann, Dalén, Love, Figueiró, Henrique V, Johnson, Warren E, Milne, Heather J, O'Brien, Stephen J, O'Connell, Brendan, Onorato, David P, Riley, Seth PD, Sikich, Jeff A, Stahler, Daniel R, Villela, Priscilla Marqui Schmidt, Vollmers, Christopher, Wayne, Robert K, Eizirik, Eduardo, Corbett-Detig, Russell B, Green, Richard E, Wilmers, Christopher C, and Shapiro, Beth

Subjects
Animals, Puma, Inbreeding, Genetics, Population, Genomics, Phylogeny, Geography, North America, South America, Gene Flow, Genetic Variation, Genome-Wide Association Study, Genetics, Population
Abstract

Pumas are the most widely distributed felid in the Western Hemisphere. Increasingly, however, human persecution and habitat loss are isolating puma populations. To explore the genomic consequences of this isolation, we assemble a draft puma genome and a geographically broad panel of resequenced individuals. We estimate that the lineage leading to present-day North American pumas diverged from South American lineages 300-100 thousand years ago. We find signatures of close inbreeding in geographically isolated North American populations, but also that tracts of homozygosity are rarely shared among these populations, suggesting that assisted gene flow would restore local genetic diversity. The genome of a Florida panther descended from translocated Central American individuals has long tracts of homozygosity despite recent outbreeding. This suggests that while translocations may introduce diversity, sustaining diversity in small and isolated populations will require either repeated translocations or restoration of landscape connectivity. Our approach provides a framework for genome-wide analyses that can be applied to the management of similarly small and isolated populations.

Published
2019

6. Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks

Author

Farré, Marta, Kim, Jaebum, Proskuryakova, Anastasia A, Zhang, Yang, Kulemzina, Anastasia I, Li, Qiye, Zhou, Yang, Xiong, Yingqi, Johnson, Jennifer L, Perelman, Polina L, Johnson, Warren E, Warren, Wesley C, Kukekova, Anna V, Zhang, Guojie, O'Brien, Stephen J, Ryder, Oliver A, Graphodatsky, Alexander S, Ma, Jian, Lewin, Harris A, and Larkin, Denis M

Subjects
Human Genome, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Animals, Chromosome Breakpoints, DNA Transposable Elements, Enhancer Elements, Genetic, Evolution, Molecular, Karyotype, Protein Binding, Ruminants, Selection, Genetic, Synteny, Transcription Factors, Biological Sciences, Medical and Health Sciences, Bioinformatics
Abstract

The role of chromosome rearrangements in driving evolution has been a long-standing question of evolutionary biology. Here we focused on ruminants as a model to assess how rearrangements may have contributed to the evolution of gene regulation. Using reconstructed ancestral karyotypes of Cetartiodactyls, Ruminants, Pecorans, and Bovids, we traced patterns of gross chromosome changes. We found that the lineage leading to the ruminant ancestor after the split from other cetartiodactyls was characterized by mostly intrachromosomal changes, whereas the lineage leading to the pecoran ancestor (including all livestock ruminants) included multiple interchromosomal changes. We observed that the liver cell putative enhancers in the ruminant evolutionary breakpoint regions are highly enriched for DNA sequences under selective constraint acting on lineage-specific transposable elements (TEs) and a set of 25 specific transcription factor (TF) binding motifs associated with recently active TEs. Coupled with gene expression data, we found that genes near ruminant breakpoint regions exhibit more divergent expression profiles among species, particularly in cattle, which is consistent with the phylogenetic origin of these breakpoint regions. This divergence was significantly greater in genes with enhancers that contain at least one of the 25 specific TF binding motifs and located near bovidae-to-cattle lineage breakpoint regions. Taken together, by combining ancestral karyotype reconstructions with analysis of cis regulatory element and gene expression evolution, our work demonstrated that lineage-specific regulatory elements colocalized with gross chromosome rearrangements may have provided valuable functional modifications that helped to shape ruminant evolution.

Published
2019

7. Earth BioGenome Project: Sequencing life for the future of life

Author

Lewin, Harris A, Robinson, Gene E, Kress, W John, Baker, William J, Coddington, Jonathan, Crandall, Keith A, Durbin, Richard, Edwards, Scott V, Forest, Félix, Gilbert, M Thomas P, Goldstein, Melissa M, Grigoriev, Igor V, Hackett, Kevin J, Haussler, David, Jarvis, Erich D, Johnson, Warren E, Patrinos, Aristides, Richards, Stephen, Castilla-Rubio, Juan Carlos, van Sluys, Marie-Anne, Soltis, Pamela S, Xu, Xun, Yang, Huanming, and Zhang, Guojie

Subjects
Information and Computing Sciences, Biological Sciences, Library and Information Studies, Life on Land, Biodiversity, Earth, Planet, Endangered Species, Genome, High-Throughput Nucleotide Sequencing, biodiversity, genome sequencing, access and benefit sharing, genomics, data science
Abstract

Increasing our understanding of Earth's biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evolution, functions, and interactions among millions of the planet's organisms. Herein, we present a perspective on the Earth BioGenome Project (EBP), a moonshot for biology that aims to sequence, catalog, and characterize the genomes of all of Earth's eukaryotic biodiversity over a period of 10 years. The outcomes of the EBP will inform a broad range of major issues facing humanity, such as the impact of climate change on biodiversity, the conservation of endangered species and ecosystems, and the preservation and enhancement of ecosystem services. We describe hurdles that the project faces, including data-sharing policies that ensure a permanent, freely available resource for future scientific discovery while respecting access and benefit sharing guidelines of the Nagoya Protocol. We also describe scientific and organizational challenges in executing such an ambitious project, and the structure proposed to achieve the project's goals. The far-reaching potential benefits of creating an open digital repository of genomic information for life on Earth can be realized only by a coordinated international effort.

Published
2018

8. The evolutionary history of extinct and living lions

Author

de Manuel, Marc, Barnett, Ross, Sandoval-Velasco, Marcela, Yamaguchi, Nobuyuki, Vieira, Filipe Garrett, Mendoza, M. Lisandra Zepeda, Liu, Shiping, Martin, Michael D., Sinding, Mikkel-Holger S., Mak, Sarah S. T., Carøe, Christian, Liu, Shanlin, Guo, Chunxue, Zheng, Jiao, Zazula, Grant, Baryshnikov, Gennady, Eizirik, Eduardo, Koepfli, Klaus-Peter, Johnson, Warren E., Antunes, Agostinho, Sicheritz-Ponten, Thomas, Gopalakrishnan, Shyam, Larson, Greger, Yang, Huanming, O’Brien, Stephen J., Hansen, Anders J., Zhang, Guojie, Marques-Bonet, Tomas, and Gilbert, M. Thomas P.

Published
2020

9. Towards complete and error-free genome assemblies of all vertebrate species

Author

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

Published
2021
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10. History of Diversification and Adaptation from North to South Revealed by Genomic Data: Guanacos from the Desert to Sub-Antarctica.

Author

León, Fabiola, Pizarro, Eduardo J, Noll, Daly, Pertierra, Luis R, Gonzalez, Benito A, Johnson, Warren E, Marín, Juan Carlos, and Vianna, Juliana A

Subjects
ANTHROPOGENIC effects on nature, EXTREME environments, DESERTS, GENETIC variation, SUBSPECIES, UNGULATES, PHYSIOLOGICAL adaptation
Abstract

The increased availability of quality genomic data has greatly improved the scope and resolution of our understanding of the recent evolutionary history of wild species adapted to extreme environments and their susceptibility to anthropogenic impacts. The guanaco (Lama guanicoe), the largest wild ungulate in South America, is a good example. The guanaco is well adapted to a wide range of habitats, including the Sechura Desert, the high Andes Mountains to the north, and the extreme temperatures and conditions of Navarino Island to the south. Guanacos also have a long history of overexploitation by humans. To assess the evolutionary impact of these challenging habitats on the genomic diversity, we analyzed 38 genomes (∼10 to 16×) throughout their extensive latitudinal distribution from the Sechura and Atacama Desert to southward into Tierra del Fuego Island. These included analyses of patterns of unique differentiation in the north and geographic region further south with admixture among L. g. cacsilensis and L. g. guanicoe. Our findings provide new insights on the divergence of the subspecies ∼800,000 yr BP and document two divergent demographic trajectories and to the initial expansion of guanaco into the more southern portions of the Atacama Desert. Patagonian guanacos have experienced contemporary reductions in effective population sizes, likely the consequence of anthropogenic impacts. The lowest levels of genetic diversity corresponded to their northern and western limits of distribution and some varying degrees of genetic differentiation. Adaptive genomic diversity was strongly linked with environmental variables and was linked with colonization toward the south followed by adaptation. [ABSTRACT FROM AUTHOR]

Published
2024
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11. Genome-wide Evidence Reveals that African and Eurasian Golden Jackals Are Distinct Species

Author

Koepfli, Klaus-Peter, Pollinger, John, Godinho, Raquel, Robinson, Jacqueline, Lea, Amanda, Hendricks, Sarah, Schweizer, Rena M, Thalmann, Olaf, Silva, Pedro, Fan, Zhenxin, Yurchenko, Andrey A, Dobrynin, Pavel, Makunin, Alexey, Cahill, James A, Shapiro, Beth, Álvares, Francisco, Brito, José C, Geffen, Eli, Leonard, Jennifer A, Helgen, Kristofer M, Johnson, Warren E, O’Brien, Stephen J, Van Valkenburgh, Blaire, and Wayne, Robert K

Subjects
Genetics, Biotechnology, Africa, Animals, Biological Evolution, Female, Genome, Jackals, Male, Molecular Sequence Data, Phylogeny, Sequence Analysis, DNA, Wolves, Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences, Developmental Biology
Abstract

The golden jackal of Africa (Canis aureus) has long been considered a conspecific of jackals distributed throughout Eurasia, with the nearest source populations in the Middle East. However, two recent reports found that mitochondrial haplotypes of some African golden jackals aligned more closely to gray wolves (Canis lupus), which is surprising given the absence of gray wolves in Africa and the phenotypic divergence between the two species. Moreover, these results imply the existence of a previously unrecognized phylogenetically distinct species despite a long history of taxonomic work on African canids. To test the distinct-species hypothesis and understand the evolutionary history that would account for this puzzling result, we analyzed extensive genomic data including mitochondrial genome sequences, sequences from 20 autosomal loci (17 introns and 3 exon segments), microsatellite loci, X- and Y-linked zinc-finger protein gene (ZFX and ZFY) sequences, and whole-genome nuclear sequences in African and Eurasian golden jackals and gray wolves. Our results provide consistent and robust evidence that populations of golden jackals from Africa and Eurasia represent distinct monophyletic lineages separated for more than one million years, sufficient to merit formal recognition as different species: C. anthus (African golden wolf) and C. aureus (Eurasian golden jackal). Using morphologic data, we demonstrate a striking morphologic similarity between East African and Eurasian golden jackals, suggesting parallelism, which may have misled taxonomists and likely reflects uniquely intense interspecific competition in the East African carnivore guild. Our study shows how ecology can confound taxonomy if interspecific competition constrains size diversification.

Published
2015

12. Comparative genomics reveals insights into avian genome evolution and adaptation

Author

Zhang, Guojie, Li, Cai, Li, Qiye, Li, Bo, Larkin, Denis M, Lee, Chul, Storz, Jay F, Antunes, Agostinho, Greenwold, Matthew J, Meredith, Robert W, Ödeen, Anders, Cui, Jie, Zhou, Qi, Xu, Luohao, Pan, Hailin, Wang, Zongji, Jin, Lijun, Zhang, Pei, Hu, Haofu, Yang, Wei, Hu, Jiang, Xiao, Jin, Yang, Zhikai, Liu, Yang, Xie, Qiaolin, Yu, Hao, Lian, Jinmin, Wen, Ping, Zhang, Fang, Li, Hui, Zeng, Yongli, Xiong, Zijun, Liu, Shiping, Zhou, Long, Huang, Zhiyong, An, Na, Wang, Jie, Zheng, Qiumei, Xiong, Yingqi, Wang, Guangbiao, Wang, Bo, Wang, Jingjing, Fan, Yu, da Fonseca, Rute R, Alfaro-Núñez, Alonzo, Schubert, Mikkel, Orlando, Ludovic, Mourier, Tobias, Howard, Jason T, Ganapathy, Ganeshkumar, Pfenning, Andreas, Whitney, Osceola, Rivas, Miriam V, Hara, Erina, Smith, Julia, Farré, Marta, Narayan, Jitendra, Slavov, Gancho, Romanov, Michael N, Borges, Rui, Machado, João Paulo, Khan, Imran, Springer, Mark S, Gatesy, John, Hoffmann, Federico G, Opazo, Juan C, Håstad, Olle, Sawyer, Roger H, Kim, Heebal, Kim, Kyu-Won, Kim, Hyeon Jeong, Cho, Seoae, Li, Ning, Huang, Yinhua, Bruford, Michael W, Zhan, Xiangjiang, Dixon, Andrew, Bertelsen, Mads F, Derryberry, Elizabeth, Warren, Wesley, Wilson, Richard K, Li, Shengbin, Ray, David A, Green, Richard E, O’Brien, Stephen J, Griffin, Darren, Johnson, Warren E, Haussler, David, Ryder, Oliver A, Willerslev, Eske, Graves, Gary R, Alström, Per, Fjeldså, Jon, Mindell, David P, Edwards, Scott V, Braun, Edward L, Rahbek, Carsten, Burt, David W, Houde, Peter, and Zhang, Yong

Subjects
Human Genome, Biotechnology, Genetics, Adaptation, Physiological, Animals, Biodiversity, Biological Evolution, Birds, Conserved Sequence, Diet, Evolution, Molecular, Female, Flight, Animal, Genes, Genetic Variation, Genome, Genomics, Male, Molecular Sequence Annotation, Phylogeny, Reproduction, Selection, Genetic, Sequence Analysis, DNA, Synteny, Vision, Ocular, Vocalization, Animal, Avian Genome Consortium, General Science & Technology
Abstract

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

Published
2014

13. Tissue sampling and standards for vertebrate genomics

Author

Wong, Pamela BY, Wiley, Edward O, Johnson, Warren E, Ryder, Oliver A, O’Brien, Stephen J, Haussler, David, Koepfli, Klaus-Peter, Houck, Marlys L, Perelman, Polina, Mastromonaco, Gabriela, Bentley, Andrew C, Venkatesh, Byrappa, Zhang, Ya-ping, Murphy, Robert W, and rochelle@soe.ucsc.edu

Abstract

AbstractThe recent rise in speed and efficiency of new sequencing technologies have facilitated high-throughput sequencing, assembly and analyses of genomes, advancing ongoing efforts to analyze genetic sequences across major vertebrate groups. Standardized procedures in acquiring high quality DNA and RNA and establishing cell lines from target species will facilitate these initiatives. We provide a legal and methodological guide according to four standards of acquiring and storing tissue for the Genome 10K Project and similar initiatives as follows: four-star (banked tissue/cell cultures, RNA from multiple types of tissue for transcriptomes, and sufficient flash-frozen tissue for 1 mg of DNA, all from a single individual); three-star (RNA as above and frozen tissue for 1 mg of DNA); two-star (frozen tissue for at least 700 μg of DNA); and one-star (ethanol-preserved tissue for 700 μg of DNA or less of mixed quality). At a minimum, all tissues collected for the Genome 10K and other genomic projects should consider each species’ natural history and follow institutional and legal requirements. Associated documentation should detail as much information as possible about provenance to ensure representative sampling and subsequent sequencing. Hopefully, the procedures outlined here will not only encourage success in the Genome 10K Project but also inspire the adaptation of standards by other genomic projects, including those involving other biota.

Published
2012

20. Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes)

Author

Kliver, Sergei, Houck, Marlys L., Perelman, Polina L., Totikov, Azamat, Tomarovsky, Andrei, Dudchenko, Olga, Omer, Arina D., Colaric, Zane, Weisz, David, Aiden, Erez Lieberman, Chan, Saki, Hastie, Alex, Komissarov, Aleksey, Ryder, Oliver A., Graphodatsky, Alexander, Johnson, Warren E., Maldonado, Jesús E., Pukazhenthi, Budhan S., Marinari, Paul E., Wildt, David E., Koepfli, Klaus-Peter, Kliver, Sergei, Houck, Marlys L., Perelman, Polina L., Totikov, Azamat, Tomarovsky, Andrei, Dudchenko, Olga, Omer, Arina D., Colaric, Zane, Weisz, David, Aiden, Erez Lieberman, Chan, Saki, Hastie, Alex, Komissarov, Aleksey, Ryder, Oliver A., Graphodatsky, Alexander, Johnson, Warren E., Maldonado, Jesús E., Pukazhenthi, Budhan S., Marinari, Paul E., Wildt, David E., and Koepfli, Klaus-Peter

Abstract

The black-footed ferret (Mustela nigripes) narrowly avoided extinction to become an oft-cited example of the benefits of intensive management, research, and collaboration to save a species through ex-situ conservation breeding and reintroduction into its former range. However, the species remains at risk due to possible inbreeding, disease susceptibility, and multiple fertility challenges. Here, we report the de novo genome assembly of a male black-footed ferret generated through a combination of linked read sequencing, optical mapping, and Hi-C proximity ligation. In addition, we report the karyotype for this species, which was used to anchor and assign chromosome numbers to the chromosome-length scaffolds. The draft assembly was ~2.5 Gb in length, with 95.6% of it anchored to 19 chromosome-length scaffolds, corresponding to the 2n = 38 chromosomes revealed by the karyotype. The assembly has contig and scaffold N50 values of 148.8 Kbp and 145.4 Mbp, respectively, and is up to 96% complete based on BUSCO analyses. Annotation of the assembly, including evidence from RNA-seq data, identified 21,406 protein-coding genes and a repeat content of 37.35%. Phylogenomic analyses indicated that the black-footed ferret diverged from the European polecat/domestic ferret lineage 1.6 million years ago. This assembly will enable research on the conservation genomics of black-footed ferrets and thereby aid in the further restoration of this endangered species.

Published
2023

21. Comparative genomics uncovers the evolutionary history, demography, and molecular adaptations of South American canids

Author

Chavez, Daniel E., primary, Gronau, Ilan, additional, Hains, Taylor, additional, Dikow, Rebecca B., additional, Frandsen, Paul B., additional, Figueiró, Henrique V., additional, Garcez, Fabrício S., additional, Tchaicka, Ligia, additional, de Paula, Rogério C., additional, Rodrigues, Flávio H. G., additional, Jorge, Rodrigo S. P., additional, Lima, Edson S., additional, Songsasen, Nucharin, additional, Johnson, Warren E., additional, Eizirik, Eduardo, additional, Koepfli, Klaus-Peter, additional, and Wayne, Robert K., additional

Published
2022
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22. Complex Evolutionary History of the South American Fox Genus Lycalopex (Mammalia, Carnivora, Canidae) Inferred from Multiple Mitochondrial and Nuclear Markers

Author

Favarini, Marina O., primary, Simão, Taiz L. L., additional, Macedo, Gabriel S., additional, Garcez, Fabrício S., additional, Oliveira, Larissa R., additional, Cárdenas-Alayza, Susana, additional, Cardeña Mormontoy, Marco, additional, Angulo, Fernando, additional, Kasper, Carlos Benhur, additional, Johnson, Warren E., additional, and Eizirik, Eduardo, additional

Published
2022
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23. Genomic signatures of divergent ecological strategies in a recent radiation of Neotropical wild cats

Author

Ramirez, Jorge L., primary, Lescroart, Jonas, additional, Figueiró, Henrique V., additional, Torres-Florez, Juan Pablo, additional, Villela, Priscilla M. S., additional, Coutinho, Luiz L., additional, Freitas, Patricia D., additional, Johnson, Warren E., additional, Antunes, Agostinho, additional, Galetti, Pedro M., additional, and Eizirik, Eduardo, additional

Published
2022
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24. Incomplete lineage sorting and phenotypic evolution in marsupials

Author

Feng, Shaohong, primary, Bai, Ming, additional, Rivas-González, Iker, additional, Li, Cai, additional, Liu, Shiping, additional, Tong, Yijie, additional, Yang, Haidong, additional, Chen, Guangji, additional, Xie, Duo, additional, Sears, Karen E., additional, Franco, Lida M., additional, Gaitan-Espitia, Juan Diego, additional, Nespolo, Roberto F., additional, Johnson, Warren E., additional, Yang, Huanming, additional, Brandies, Parice A., additional, Hogg, Carolyn J., additional, Belov, Katherine, additional, Renfree, Marilyn B., additional, Helgen, Kristofer M., additional, Boomsma, Jacobus J., additional, Schierup, Mikkel Heide, additional, and Zhang, Guojie, additional

Published
2022
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25. The Earth BioGenome Project 2020: Starting the clock

Author

Lewin, Harris A., Richards, Stephen, Aiden, Erez, Allende, Miguel L., Archibald, John M., Bálint, Miklós M., Barker, Katharine M., Baumgartnerk, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark, Cai, Jing, Caperello, Nicolette, Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu-Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., Di Palma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott, Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Marshall Graves, Jennifer A., Greely, Henry, Grigoriev, Igor, Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J.M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin-Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K.N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sofhie, Mazet, Jonna, Mazzoni, Camila J., Myers, Eugene W., O'Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene, Roquet, Cristina, Ryder, Oliver, Sabir, Jamal S.M., Shaffer, Howard Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela, Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne, Zhang, Guojie, Lewin, Harris A., Richards, Stephen, Aiden, Erez, Allende, Miguel L., Archibald, John M., Bálint, Miklós M., Barker, Katharine M., Baumgartnerk, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark, Cai, Jing, Caperello, Nicolette, Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu-Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., Di Palma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott, Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Marshall Graves, Jennifer A., Greely, Henry, Grigoriev, Igor, Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J.M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin-Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K.N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sofhie, Mazet, Jonna, Mazzoni, Camila J., Myers, Eugene W., O'Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene, Roquet, Cristina, Ryder, Oliver, Sabir, Jamal S.M., Shaffer, Howard Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela, Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne, and Zhang, Guojie

Published
2022

26. Standards recommendations for the Earth BioGenome Project

Author

Lawniczak, Mara K.N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J, Belov, Katherine, Blaxter, Mark, Marques-Bonet, Tomas, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina, Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca, Kersey, Paul J., Liu, Xin, Lopez, Jose V., Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica, Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela, Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill, Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, Lawniczak, Mara K.N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J, Belov, Katherine, Blaxter, Mark, Marques-Bonet, Tomas, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina, Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca, Kersey, Paul J., Liu, Xin, Lopez, Jose V., Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica, Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela, Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill, Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen

Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Published
2022

27. Standards recommendations for the Earth BioGenome Project

Author

Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark L., Bonet, Tomas Marques, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, Lopez, Jose Victor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark L., Bonet, Tomas Marques, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, Lopez, Jose Victor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen

Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Published
2022
Full Text
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28. Standards recommendations for the Earth BioGenome Project

Author

National Library of Medicine (US), National Institutes of Health (US), Swedish Research Council, National Museum of Natural History Smithsonian Institution, Howard Hughes Medical Institute, Wellcome, European Molecular Biology Laboratory, National Science Foundation (US), Department of Agriculture (US), Agricultural Research Service (US), Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, National Library of Medicine (US), National Institutes of Health (US), Swedish Research Council, National Museum of Natural History Smithsonian Institution, Howard Hughes Medical Institute, Wellcome, European Molecular Biology Laboratory, National Science Foundation (US), Department of Agriculture (US), Agricultural Research Service (US), Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen

Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Published
2022

29. Incomplete lineage sorting and phenotypic evolution in marsupials

Author

Feng, Shaohong, Bai, Ming, Rivas-González, Iker, Li, Cai, Liu, Shiping, Tong, Yijie, Yang, Haidong, Chen, Guangji, Xie, Duo, Sears, Karen E., Franco, Lida M., Gaitan-Espitia, Juan Diego, Nespolo, Roberto F., Johnson, Warren E., Yang, Huanming, Brandies, Parice A., Hogg, Carolyn J., Belov, Katherine, Renfree, Marilyn B., Helgen, Kristofer M., Boomsma, Jacobus J., Schierup, Mikkel Heide, Zhang, Guojie, Feng, Shaohong, Bai, Ming, Rivas-González, Iker, Li, Cai, Liu, Shiping, Tong, Yijie, Yang, Haidong, Chen, Guangji, Xie, Duo, Sears, Karen E., Franco, Lida M., Gaitan-Espitia, Juan Diego, Nespolo, Roberto F., Johnson, Warren E., Yang, Huanming, Brandies, Parice A., Hogg, Carolyn J., Belov, Katherine, Renfree, Marilyn B., Helgen, Kristofer M., Boomsma, Jacobus J., Schierup, Mikkel Heide, and Zhang, Guojie

Abstract

Incomplete lineage sorting (ILS) makes ancestral genetic polymorphisms persist during rapid speciation events, inducing incongruences between gene trees and species trees. ILS has complicated phylogenetic inference in many lineages, including hominids. However, we lack empirical evidence that ILS leads to incongruent phenotypic variation. Here, we performed phylogenomic analyses to show that the South American monito del monte is the sister lineage of all Australian marsupials, although over 31% of its genome is closer to the Diprotodontia than to other Australian groups due to ILS during ancient radiation. Pervasive conflicting phylogenetic signals across the whole genome are consistent with some of the morphological variation among extant marsupials. We detected hundreds of genes that experienced stochastic fixation during ILS, encoding the same amino acids in non-sister species. Using functional experiments, we confirm how ILS may have directly contributed to hemiplasy in morphological traits that were established during rapid marsupial speciation ca. 60 mya.

Published
2022

30. The Earth BioGenome Project 2020:Starting the clock

Author

Lewin, Harris A., Richards, Stephen, Aiden, Erez Lieberman, Allende, Miguel L., Archibald, John M., Bálint, Miklós, Barker, Katharine B., Baumgartner, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark L., Cai, Jing, Caperello, Nicolette D., Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., DiPalma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott V., Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Graves, Jennifer Marshall, Greely, Henry T., Grigoriev, Igor V., Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J. M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K. N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sophie, Mazet, Jonna A. K., Mazzoni, Camila J., Myers, Eugene W., O’Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene E., Roquet, Cristina, Ryder, Oliver A., Sabir, Jamal S. M., Shaffer, H. Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela S., Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne D., Zhang, Guojie, Lewin, Harris A., Richards, Stephen, Aiden, Erez Lieberman, Allende, Miguel L., Archibald, John M., Bálint, Miklós, Barker, Katharine B., Baumgartner, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark L., Cai, Jing, Caperello, Nicolette D., Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., DiPalma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott V., Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Graves, Jennifer Marshall, Greely, Henry T., Grigoriev, Igor V., Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J. M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K. N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sophie, Mazet, Jonna A. K., Mazzoni, Camila J., Myers, Eugene W., O’Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene E., Roquet, Cristina, Ryder, Oliver A., Sabir, Jamal S. M., Shaffer, H. Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela S., Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne D., and Zhang, Guojie

Published
2022

35. Genetic Restoration of the Florida Panther

Author

Johnson, Warren E., Onorato, David P., Roelke, Melody E., Land, E. Darrell, Cunningham, Mark, Belden, Robert C., McBride, Roy, Jansen, Deborah, Lotz, Mark, Shindle, David, Howard, JoGayle, Wildt, David E., Penfold, Linda M., Hostetler, Jeffrey A., Oli, Madan K., and O'Brien, Stephen J.

Published
2010

36. The near Eastern Origin of Cat Domestication

Author

Driscoll, Carlos A., Menotti-Raymond, Marilyn, Roca, Alfred L., Hupe, Karsten, Johnson, Warren E., Geffen, Eli, Harley, Eric H., Delibes, Miguel, Pontier, Dominique, Kitchener, Andrew C., Yamaguchi, Nobuyuki, O'Brien, Stephen J., and Macdonald, David W.

Published
2007
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37. The Earth BioGenome Project 2020: Starting the clock

Author

Lewin, Harris A., primary, Richards, Stephen, additional, Lieberman Aiden, Erez, additional, Allende, Miguel L., additional, Archibald, John M., additional, Bálint, Miklós, additional, Barker, Katharine B., additional, Baumgartner, Bridget, additional, Belov, Katherine, additional, Bertorelle, Giorgio, additional, Blaxter, Mark L., additional, Cai, Jing, additional, Caperello, Nicolette D., additional, Carlson, Keith, additional, Castilla-Rubio, Juan Carlos, additional, Chaw, Shu-Miaw, additional, Chen, Lei, additional, Childers, Anna K., additional, Coddington, Jonathan A., additional, Conde, Dalia A., additional, Corominas, Montserrat, additional, Crandall, Keith A., additional, Crawford, Andrew J., additional, DiPalma, Federica, additional, Durbin, Richard, additional, Ebenezer, ThankGod E., additional, Edwards, Scott V., additional, Fedrigo, Olivier, additional, Flicek, Paul, additional, Formenti, Giulio, additional, Gibbs, Richard A., additional, Gilbert, M. Thomas P., additional, Goldstein, Melissa M., additional, Graves, Jennifer Marshall, additional, Greely, Henry T., additional, Grigoriev, Igor V., additional, Hackett, Kevin J., additional, Hall, Neil, additional, Haussler, David, additional, Helgen, Kristofer M., additional, Hogg, Carolyn J., additional, Isobe, Sachiko, additional, Jakobsen, Kjetill Sigurd, additional, Janke, Axel, additional, Jarvis, Erich D., additional, Johnson, Warren E., additional, Jones, Steven J. M., additional, Karlsson, Elinor K., additional, Kersey, Paul J., additional, Kim, Jin-Hyoung, additional, Kress, W. John, additional, Kuraku, Shigehiro, additional, Lawniczak, Mara K. N., additional, Leebens-Mack, James H., additional, Li, Xueyan, additional, Lindblad-Toh, Kerstin, additional, Liu, Xin, additional, Lopez, Jose V., additional, Marques-Bonet, Tomas, additional, Mazard, Sophie, additional, Mazet, Jonna A. K., additional, Mazzoni, Camila J., additional, Myers, Eugene W., additional, O’Neill, Rachel J., additional, Paez, Sadye, additional, Park, Hyun, additional, Robinson, Gene E., additional, Roquet, Cristina, additional, Ryder, Oliver A., additional, Sabir, Jamal S. M., additional, Shaffer, H. Bradley, additional, Shank, Timothy M., additional, Sherkow, Jacob S., additional, Soltis, Pamela S., additional, Tang, Boping, additional, Tedersoo, Leho, additional, Uliano-Silva, Marcela, additional, Wang, Kun, additional, Wei, Xiaofeng, additional, Wetzer, Regina, additional, Wilson, Julia L., additional, Xu, Xun, additional, Yang, Huanming, additional, Yoder, Anne D., additional, and Zhang, Guojie, additional

Published
2022
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48. Supplementary Tables and Legends Standards Recommendations for the Earth BioGenome Project

Author

Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen

Published
2021

49. 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

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