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141 results on '"Houck, Marlys L"'

1. Evolution of the ancestral mammalian karyotype and syntenic regions

Author

Damas, Joana, Corbo, Marco, Kim, Jaebum, Turner-Maier, Jason, Farré, Marta, Larkin, Denis M, Ryder, Oliver A, Steiner, Cynthia, Houck, Marlys L, Hall, Shaune, Shiue, Lily, Thomas, Stephen, Swale, Thomas, Daly, Mark, Korlach, Jonas, Uliano-Silva, Marcela, Mazzoni, Camila J, Birren, Bruce W, Genereux, Diane P, Johnson, Jeremy, Lindblad-Toh, Kerstin, Karlsson, Elinor K, Nweeia, Martin T, Johnson, Rebecca N, Lewin, Harris A, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, and Ryan, Louise

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Evolutionary Biology, Genetics, Human Genome, Generic health relevance, Animals, Cattle, Chromosomes, Mammalian, Eutheria, Evolution, Molecular, Humans, Karyotype, Mammals, Phylogeny, Sloths, Synteny, chromosome evolution, mammals, synteny conservation, ancestral genome reconstruction, topologically associating domains, Zoonomia Consortium
Abstract

Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes and syntenic relationships at 16 nodes along the mammalian phylogeny. Three different reference genomes (human, sloth, and cattle) representing phylogenetically distinct mammalian superorders were used to assess reference bias in the reconstructed ancestral karyotypes and to expand the number of clades with reconstructed genomes. The mammalian ancestor likely had 19 pairs of autosomes, with nine of the smallest chromosomes shared with the common ancestor of all amniotes (three still conserved in extant mammals), demonstrating a striking conservation of synteny for ∼320 My of vertebrate evolution. The numbers and types of chromosome rearrangements were classified for transitions between the ancestral mammalian karyotype, descendent ancestors, and extant species. For example, 94 inversions, 16 fissions, and 14 fusions that occurred over 53 My differentiated the therian from the descendent eutherian ancestor. The highest breakpoint rate was observed between the mammalian and therian ancestors (3.9 breakpoints/My). Reconstructed mammalian ancestor chromosomes were found to have distinct evolutionary histories reflected in their rates and types of rearrangements. The distributions of genes, repetitive elements, topologically associating domains, and actively transcribed regions in multispecies homologous synteny blocks and evolutionary breakpoint regions indicate that purifying selection acted over millions of years of vertebrate evolution to maintain syntenic relationships of developmentally important genes and regulatory landscapes of gene-dense chromosomes.

Published
2022

2. 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

3. Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity

Author

Houck, Marlys L., Koepfli, Klaus-Peter, Hains, Taylor, Khan, Ruqayya, Charter, Suellen J., Fronczek, Julie A., Misuraca, Ann C., Kliver, Sergei, Perelman, Polina L., Beklemisheva, Violetta, Graphodatsky, Alexander, Luo, Shu-Jin, O’Brien, Stephen J., Lim, Norman T.-L., Chin, Jason S. C., Guerra, Vanessa, Tamazian, Gaik, Omer, Arina, Weisz, David, Kaemmerer, Kenneth, Sturgeon, Ginger, Gaspard, Joseph, Hahn, Alicia, McDonough, Mark, Garcia-Treviño, Isabel, Gentry, Jordan, Coke, Rob L., Janecka, Jan E., Harrigan, Ryan J., Tinsman, Jen, Smith, Thomas B., Aiden, Erez Lieberman, and Dudchenko, Olga

Published
2023
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4. A comparative genomics multitool for scientific discovery and conservation

Author

Genereux, Diane P, Serres, Aitor, Armstrong, Joel, Johnson, Jeremy, Marinescu, Voichita D, Muren, Eva, Juan, David, Bejerano, Gill, Casewell, Nicholas R, Chemnick, Leona G, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Fiddes, Ian T, Garber, Manuel, Gladyshev, Vadim N, Goodman, Linda, Haerty, Wilfried, Houck, Marlys L, Hubley, Robert, Kivioja, Teemu, Koepfli, Klaus-Peter, Kuderna, Lukas FK, Lander, Eric S, Meadows, Jennifer RS, Murphy, William J, Nash, Will, Noh, Hyun Ji, Nweeia, Martin, Pfenning, Andreas R, Pollard, Katherine S, Ray, David A, Shapiro, Beth, Smit, Arian FA, Springer, Mark S, Steiner, Cynthia C, Swofford, Ross, Taipale, Jussi, Teeling, Emma C, Turner-Maier, Jason, Alfoldi, Jessica, Birren, Bruce, Ryder, Oliver A, Lewin, Harris A, Paten, Benedict, Marques-Bonet, Tomas, Lindblad-Toh, Kerstin, and Karlsson, Elinor K

Subjects
Human Genome, Genetics, Biotechnology, Life on Land, Animals, Biodiversity, Biomedical Research, Conservation of Natural Resources, Eutheria, Evolution, Molecular, Extinction, Biological, Genetic Speciation, Genetic Variation, Genomics, Humans, Infections, Knowledge Discovery, Loss of Heterozygosity, Neoplasms, Phylogeny, Risk Assessment, Selection, Genetic, Sequence Alignment, Species Specificity, Venoms, Zoonomia Consortium, General Science & Technology
Abstract

The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.

Published
2020

5. 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

7. Genomic signatures of high-altitude adaptation and chromosomal polymorphism in geladas

Author

Chiou, Kenneth L., Janiak, Mareike C., Schneider-Crease, India A., Sen, Sharmi, Ayele, Ferehiwot, Chuma, Idrissa S., Knauf, Sascha, Lemma, Alemayehu, Signore, Anthony V., D’Ippolito, Anthony M., Abebe, Belayneh, Haile, Abebaw Azanaw, Kebede, Fanuel, Fashing, Peter J., Nguyen, Nga, McCann, Colleen, Houck, Marlys L., Wall, Jeffrey D., Burrell, Andrew S., Bergey, Christina M., Rogers, Jeffrey, Phillips-Conroy, Jane E., Jolly, Clifford J., Melin, Amanda D., Storz, Jay F., Lu, Amy, Beehner, Jacinta C., Bergman, Thore J., and Snyder-Mackler, Noah

Published
2022
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8. Endangered Przewalski's horse, Equus pzrewalskii, cloned from historically cryopreserved cells

Author

Novak, Ben Jacob, primary, Ryder, Oliver A, additional, Houck, Marlys L, additional, Putnam, Andrea S, additional, Walker, Kelcey, additional, Russell, Lexie, additional, Russell, Blake, additional, Walker, Shawn, additional, Arenivas, Sanaz Sadeghieh, additional, Aston, Lauren, additional, Veneklasen, Gregg, additional, Ivy, Jamie A, additional, Koepfli, Klaus-Peter, additional, Rusnak, Anna, additional, Simek, Jaroslav, additional, Zhuk, Anna, additional, and Phelan, Ryan, additional

Published
2023
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9. 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

13. 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

17. A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population

Author

Wilder, Aryn P, primary, Dudchenko, Olga, additional, Curry, Caitlin, additional, Korody, Marisa, additional, Turbek, Sheela P, additional, Daly, Mark, additional, Misuraca, Ann, additional, Wang, Gaojianyong, additional, Khan, Ruqayya, additional, Weisz, David, additional, Fronczek, Julie, additional, Aiden, Erez Lieberman, additional, Houck, Marlys L, additional, Shier, Debra M, additional, Ryder, Oliver A, additional, and Steiner, Cynthia C, additional

Published
2022
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18. Genomic signatures of high-altitude adaptation and chromosomal polymorphism in geladas

Author

Chiou, Kenneth L, Janiak, MC, Schneider-Crease, India A, Sen, Sharmi, Ayele, Ferehiwot, Chuma, Idrissa S, Knauf, Sascha, Lemma, Alemayehu, Signore, Anthony V, D'Ippolito, Anthony M, Abebe, Belayneh, Haile, Abebaw Azanaw, Kebede, Fanuel, Fashing, Peter J, Nguyen, Nga, McCann, Colleen, Houck, Marlys L, Wall, Jeffrey D, Burrell, Andrew S, Bergey, Christina M, Rogers, Jeffrey, Phillips-Conroy, Jane E, Jolly, Clifford J, Melin, Amanda D, Storz, Jay F, Lu, Amy, Beehner, Jacinta C, Bergman, Thore J, and Snyder-Mackler, Noah

Subjects
Oxygen, Theropithecus, Ecology, Altitude, Animals, Genomics, Hypoxia, Ecology, Evolution, Behavior and Systematics, Chromosomes
Abstract

Primates have adapted to numerous environments and lifestyles but very few species are native to high elevations. Here we investigated high-altitude adaptations in the gelada (Theropithecus gelada), a monkey endemic to the Ethiopian Plateau. We examined genome-wide variation in conjunction with measurements of haematological and morphological traits. Our new gelada reference genome is highly intact and assembled at chromosome-length levels. Unexpectedly, we identified a chromosomal polymorphism in geladas that could potentially contribute to reproductive barriers between populations. Compared with baboons at low altitude, we found that high-altitude geladas exhibit significantly expanded chest circumferences, potentially allowing for greater lung surface area for increased oxygen diffusion. We identified gelada-specific amino acid substitutions in the alpha-chain subunit of adult haemoglobin but found that gelada haemoglobin does not exhibit markedly altered oxygenation properties compared with lowland primates. We also found that geladas at high altitude do not exhibit elevated blood haemoglobin concentrations, in contrast to the normal acclimatization response to hypoxia in lowland primates. The absence of altitude-related polycythaemia suggests that geladas are able to sustain adequate tissue-oxygen delivery despite environmental hypoxia. Finally, we identified numerous genes and genomic regions exhibiting accelerated rates of evolution, as well as gene families exhibiting expansions in the gelada lineage, potentially reflecting altitude-related selection. Our findings lend insight into putative mechanisms of high-altitude adaptation while suggesting promising avenues for functional hypoxia research. [Abstract copyright: © 2022. The Author(s), under exclusive licence to Springer Nature Limited.]

Published
2021

21. High-altitude adaptation and incipient speciation in geladas

Author

Chiou, Kenneth L., primary, Janiak, Mareike C., additional, Schneider-Crease, India, additional, Sen, Sharmi, additional, Ayele, Ferehiwot, additional, Chuma, Idrissa S., additional, Knauf, Sascha, additional, Lemma, Alemayehu, additional, Signore, Anthony V., additional, D’Ippolito, Anthony M., additional, Abebe, Belayneh, additional, Haile, Abebaw Azanaw, additional, Kebede, Fanuel, additional, Fashing, Peter J., additional, Nguyen, Nga, additional, McCann, Colleen, additional, Houck, Marlys L., additional, Wall, Jeffrey D., additional, Burrell, Andrew S., additional, Bergey, Christina M., additional, Rogers, Jeffrey, additional, Phillips-Conroy, Jane E., additional, Jolly, Clifford J., additional, Melin, Amanda D., additional, Storz, Jay F., additional, Lu, Amy, additional, Beehner, Jacinta C., additional, Bergman, Thore J., additional, and Snyder-Mackler, Noah, additional

Published
2021
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23. 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

25. Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population.

Author

Wilder, Aryn P, Dudchenko, Olga, Curry, Caitlin, Korody, Marisa, Turbek, Sheela P, Daly, Mark, Misuraca, Ann, Wang, Gaojianyong, Khan, Ruqayya, Weisz, David, Fronczek, Julie, Aiden, Erez Lieberman, Houck, Marlys L, Shier, Debra M, Ryder, Oliver A, and Steiner, Cynthia C

Subjects
GENETIC load, MITOCHONDRIAL DNA, INBREEDING, GENOMES, GENETIC variation, BIODIVERSITY conservation
Abstract

High-quality reference genomes are fundamental tools for understanding population history, and can provide estimates of genetic and demographic parameters relevant to the conservation of biodiversity. The federally endangered Pacific pocket mouse (PPM), which persists in three small, isolated populations in southern California, is a promising model for studying how demographic history shapes genetic diversity, and how diversity in turn may influence extinction risk. To facilitate these studies in PPM, we combined PacBio HiFi long reads with Omni-C and Hi-C data to generate a de novo genome assembly, and annotated the genome using RNAseq. The assembly comprised 28 chromosome-length scaffolds (N50 = 72.6 MB) and the complete mitochondrial genome, and included a long heterochromatic region on chromosome 18 not represented in the previously available short-read assembly. Heterozygosity was highly variable across the genome of the reference individual, with 18% of windows falling in runs of homozygosity (ROH) >1 MB, and nearly 9% in tracts spanning >5 MB. Yet outside of ROH, heterozygosity was relatively high (0.0027), and historical Ne estimates were large. These patterns of genetic variation suggest recent inbreeding in a formerly large population. Currently the most contiguous assembly for a heteromyid rodent, this reference genome provides insight into the past and recent demographic history of the population, and will be a critical tool for management and future studies of outbreeding depression, inbreeding depression, and genetic load. [ABSTRACT FROM AUTHOR]

Published
2022
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27. A comparative genomics multitool for scientific discovery and conservation

Author

Genereux, Diane P., Serres, Aitor, Armstrong, Joel, Johnson, Jeremy, Marinescu, Voichita, Murén, Eva, Juan, David, Bejerano, Gill, Casewell, Nicholas R., Chemnick, Leona G., Damas, Joana, Di Palma, Federica, Diekhans, Mark, Fiddes, Ian T., Garber, Manuel, Gladyshev, Vadim N., Goodman, Linda, Haerty, Wilfried, Houck, Marlys L., Hubley, Robert, Kivioja, Teemu, Koepfli, Klaus-Peter, Kuderna, Lukas F. K., Lander, Eric S., Meadows, Jennifer, Murphy, William J., Nash, Will, Noh, Hyun Ji, Nweeia, Martin, Pfenning, Andreas R., Pollard, Katherine S., Ray, David A., Shapiro, Beth, Smit, Arian F. A., Springer, Mark S., Steiner, Cynthia C., Swofford, Ross, Taipale, Jussi, Teeling, Emma C., Turner-Maier, Jason, Alfoldi, Jessica, Birren, Bruce, Ryder, Oliver A., Lewin, Harris A., Paten, Benedict, Marques-Bonet, Tomas, Lindblad-Toh, Kerstin, Karlsson, Elinor K., Genereux, Diane P., Serres, Aitor, Armstrong, Joel, Johnson, Jeremy, Marinescu, Voichita, Murén, Eva, Juan, David, Bejerano, Gill, Casewell, Nicholas R., Chemnick, Leona G., Damas, Joana, Di Palma, Federica, Diekhans, Mark, Fiddes, Ian T., Garber, Manuel, Gladyshev, Vadim N., Goodman, Linda, Haerty, Wilfried, Houck, Marlys L., Hubley, Robert, Kivioja, Teemu, Koepfli, Klaus-Peter, Kuderna, Lukas F. K., Lander, Eric S., Meadows, Jennifer, Murphy, William J., Nash, Will, Noh, Hyun Ji, Nweeia, Martin, Pfenning, Andreas R., Pollard, Katherine S., Ray, David A., Shapiro, Beth, Smit, Arian F. A., Springer, Mark S., Steiner, Cynthia C., Swofford, Ross, Taipale, Jussi, Teeling, Emma C., Turner-Maier, Jason, Alfoldi, Jessica, Birren, Bruce, Ryder, Oliver A., Lewin, Harris A., Paten, Benedict, Marques-Bonet, Tomas, Lindblad-Toh, Kerstin, and Karlsson, Elinor K.

Abstract

A whole-genome alignment of 240 phylogenetically diverse species of eutherian mammal-including 131 previously uncharacterized species-from the Zoonomia Project provides data that support biological discovery, medical research and conservation. The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity., Group Authors: Zoonomia Consortium

Published
2020
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28. A comparative genomics multitool for scientific discovery and conservation

Author

National Institutes of Health (US), Swedish Research Council, Knut and Alice Wallenberg Foundation, Uppsala University, European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Howard Hughes Medical Institute, European Research Council, Fundación la Caixa, Wellcome Trust, Royal Society (UK), Ministerio de Economía y Competitividad (España), Fondation Prince Albert II de Monaco, Smithsonian Institution, Irish Research Council, Medical Research Council (UK), National Science Foundation (US), Academy of Finland, Genereux, Diane P., Serres-Armero, Aitor, Armstrong, Joel, Johnson, Jeremy, Marinescu, Voichita D., Murén, Eva, Juan, David, Bejerano, Gill, Casewell, Nicholas R., Chemnick, Leona G., Damas, Joana, Di Palma, Federica, Diekhans, Mark, Fiddes, Ian T., Garber, Manuel, Gladyshev, Vadim N., Goodman, Linda, Haerty, Wilfried, Houck, Marlys L., Hubley, Robert, Kivioja, Teemu, Koepfli, Klaus-Peter, Kuderna, Lukas F. K., Lander, Eric S., Meadows, Jennifer R.S., Murphy, William J., Nash, Will, Noh, Hyun Ji, Nweeia, Martin, Pfenning, Andreas R., Pollard, Katherine S., Ray, David A., Shapiro, Beth, Smit, Arian F. A., Springer, Mark S., Steiner, Cynthia C., Swofford, Ross, Taipale, Jussi, Teeling, Emma C., Turner-Maier, Jason, Alfoldi, Jessica, Birren, Bruce, Ryder, Oliver A., Lewin, Harris A., Paten, Benedict, Marqués-Bonet, Tomàs, Lindblad-Toh, Kerstin, Karlsson, Elinor K., National Institutes of Health (US), Swedish Research Council, Knut and Alice Wallenberg Foundation, Uppsala University, European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Howard Hughes Medical Institute, European Research Council, Fundación la Caixa, Wellcome Trust, Royal Society (UK), Ministerio de Economía y Competitividad (España), Fondation Prince Albert II de Monaco, Smithsonian Institution, Irish Research Council, Medical Research Council (UK), National Science Foundation (US), Academy of Finland, Genereux, Diane P., Serres-Armero, Aitor, Armstrong, Joel, Johnson, Jeremy, Marinescu, Voichita D., Murén, Eva, Juan, David, Bejerano, Gill, Casewell, Nicholas R., Chemnick, Leona G., Damas, Joana, Di Palma, Federica, Diekhans, Mark, Fiddes, Ian T., Garber, Manuel, Gladyshev, Vadim N., Goodman, Linda, Haerty, Wilfried, Houck, Marlys L., Hubley, Robert, Kivioja, Teemu, Koepfli, Klaus-Peter, Kuderna, Lukas F. K., Lander, Eric S., Meadows, Jennifer R.S., Murphy, William J., Nash, Will, Noh, Hyun Ji, Nweeia, Martin, Pfenning, Andreas R., Pollard, Katherine S., Ray, David A., Shapiro, Beth, Smit, Arian F. A., Springer, Mark S., Steiner, Cynthia C., Swofford, Ross, Taipale, Jussi, Teeling, Emma C., Turner-Maier, Jason, Alfoldi, Jessica, Birren, Bruce, Ryder, Oliver A., Lewin, Harris A., Paten, Benedict, Marqués-Bonet, Tomàs, Lindblad-Toh, Kerstin, and Karlsson, Elinor K.

Abstract

The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.

Published
2020

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

Author

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

Published
2020
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36. Tissue sampling methods 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, and Murphy Robert W

Subjects
Genome 10K, Sequencing, Vertebrates, Genomics, Tissue sampling, Tissue storage, Cell line, Tissue culture, RNA, DNA, Computer applications to medicine. Medical informatics, R858-859.7
Abstract

Abstract The 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
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38. A comparative genomics multitool for scientific discovery and conservation.

Author

Zoonomia Consortium, Genereux, Diane P., Serres, Aitor, Armstrong, Joel, Johnson, Jeremy, Marinescu, Voichita D., Murén, Eva, Juan, David, Bejerano, Gill, Casewell, Nicholas R., Chemnick, Leona G., Damas, Joana, Di Palma, Federica, Diekhans, Mark, Fiddes, Ian T., Garber, Manuel, Gladyshev, Vadim N., Goodman, Linda, Haerty, Wilfried, and Houck, Marlys L.

Abstract

The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity. A whole-genome alignment of 240 phylogenetically diverse species of eutherian mammal—including 131 previously uncharacterized species—from the Zoonomia Project provides data that support biological discovery, medical research and conservation. [ABSTRACT FROM AUTHOR]

Published
2020
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40. Comparative analysis of gene-expression patterns in human and African great ape cultured fibroblasts

Author

Karaman, Mazen W., Houck, Marlys L., Chemnick, Leona G., Nagpal, Shailender, Chawannakul, Daniel, Sudano, Dominick, Pike, Brian L., Ho, Vincent V., Ryder, Oliver A., and Hacia, Joseph G.

Subjects
Variation (Biology) -- Genetic aspects, Genetic regulation -- Analysis, Phenotype -- Genetic aspects, Genetic transcription -- Physiological aspects, Man -- Genetic aspects, Human beings -- Genetic aspects, Apes -- Genetic aspects, Fibroblasts -- Genetic aspects, Gene expression -- Physiological aspects, Genetic research -- Comparative analysis, Genomes -- Research, Health
Abstract

Research has been conducted on genetic variation in human and African great ape genomes. The authors have investigated gene-expression profiles in cell populations from humans, bonobos and gorillas in the effort to define transcriptional regulatory network which contribute to the complex phenotypes unique to human and African great apes.

Published
2003

42. Whole genome sequence of the behaviorally polymorphic white-throated sparrow. 1: Mapping genes for sociogenomics

Author

Tuttle, Elaina M, Korody, Marisa L, Lear, T L, Gonser, Rusty A., Houck, Marlys L, Ryder, Oliver A., Romanov, Michael N, Balakrishnan, Christopher, Bergland, A, Warren, Wesley, Tuttle, Elaina M, Korody, Marisa L, Lear, T L, Gonser, Rusty A., Houck, Marlys L, Ryder, Oliver A., Romanov, Michael N, Balakrishnan, Christopher, Bergland, A, and Warren, Wesley

Abstract

Chromosomal inversions are thought to lead to adaptation and speciation as they reduce recombination thereby protecting favorable genetic linkages. If this is the case, it is predicted that beneficial combinations of genes associated with fitness be located within chromosomal inversions. Here, we use whole genome sequencing and mapping with bacterial artificial chromosomes (BAC) to understand how gene arrangement leads to the morphological, behavioral, and physiological differences exhibited by two morphs of the white-throated sparrow (Zonotrichia albicollis). In this species, both sexes occur as white or tan morphs that have adopted alternative life-history strategies. Morph is determined by the presence or absence of a large rearrangement, which limits recombination of the second autosome. We have amassed 25 years of detailed data on this species making it possible to identify the genetic, epigenetic, and environmental bases of behavior. To begin these analyses we generated a high-quality 1Gb reference genome with N50 contig length of 104kb and scaffold length of 4.9Mb. We then used high-resolution BAC mapping to anchor the genome, and in doing so we were able to identify the breakpoint in this chromosome as well as several other smaller rearrangements of gene order. Despite considerable synteny in avian genomes, evolutionary analyses indicate minimums of 11 rearrangements between white and tan morphs, 35 rearrangements between chicken and sparrow, and 26 rearrangements between zebra finch and sparrow. Morphs of the white-throated sparrow provide a unique opportunity to study intraspecific genomic differences, which have resulted from two separate, yet linked evolutionary trajectories - such results can transform our understanding of the evolution of genomes as well as highlight the importance of inversions as drivers of evolution.

Published
2014

43. Emerging trends for biobanking amphibian genetic resources: The hope, reality and challenges for the next decade

Author

Kouba, Andrew J, Lloyd, Rhiannon E, Houck, Marlys L, Silla, Aimee J, Calatayud, Natalie, Trudeau, Vance L, Clulow, John, Molinia, Frank, Langhorne, Cecilia, Vance, Carrie, Arregui, Lucia, Germano, J, Lermen, Dominik, Della Togna, Gina, Kouba, Andrew J, Lloyd, Rhiannon E, Houck, Marlys L, Silla, Aimee J, Calatayud, Natalie, Trudeau, Vance L, Clulow, John, Molinia, Frank, Langhorne, Cecilia, Vance, Carrie, Arregui, Lucia, Germano, J, Lermen, Dominik, and Della Togna, Gina

Abstract

How to conserve our planet's rapidly disappearing biodiversity is one of the greatest challenges of our generation. Among terrestrial vertebrate taxa, amphibians are most at risk with 41% of all known species experiencing population declines and one-third threatened with extinction. Although many institutions have responded by establishing captive assurance colonies for several critically endangered amphibians, the resources provided by these conservation organizations will not be enough to save all species 'at risk' without a multi-pronged approach. Around the world, zoos, aquariums, governments, and conservation NGOs are beginning to establish amphibian gene banks to conserve, in perpetuity, the remaining extant genetic diversity for many of these critically endangered species. A suite of biomaterials has been targeted for cryoconservation including blood, cell cultures, tissues, spermatozoa, eggs, and embryos. Several international workshops on amphibian gene banking and assisted reproductive technologies have been held between 2010 and 2012, bringing together leading experts in the fields of amphibian ecology, physiology, and cryobiology to synthesize emerging trends for biobanking amphibian genetic resources, provide opportunities for collaboration, and discuss future research directions. The following review paper and summary will provide a synopsis of these international workshops, in particular the hopes, realities, and current challenges inherent to this applied research field.

Published
2013

44. Behavioral genomics in the white-throated sparrow

Author

Tuttle, Elaina M, Gonser, Rusty A, Romanov, Michael N, Korody, Marisa L, Houck, Marlys L, Modi, William S, Ryder, Oliver A, Lear, T L, Tuttle, Elaina M, Gonser, Rusty A, Romanov, Michael N, Korody, Marisa L, Houck, Marlys L, Modi, William S, Ryder, Oliver A, and Lear, T L

Abstract

Most behavioral traits are complex and are the product of interactions between multiple genes and/or environments. Therefore, ideal models in which to examine the relative roles of genetic effects should have, 1) variation in behavioral phenotypes, 2) the potential to identify the genetic bases of these behavioral traits, 3) an obvious association between phenotype and genotype, 4) the potential to identify relevant environmental conditions contributing to the establishment of behavioral phenotypes so that partitioning of gene-by-environment effects is possible, and 5) a strong understanding of the evolutionary forces influencing the system. Given these desires, an unexpected new animal model emerges for the study of behavioral genomics – morphs of the white-throated sparrow (Zonotrichia albicollis) exhibit alternative strategies of monogamy/high parental effort vs. promiscuity/low parental effort. These behaviors are absolutely correlated with the presence or absence of a large chromosomal rearrangement. We have amassed 22+ years of detailed behavioral, physiological, ecological, and evolutionary data on this species making it possible to identify the genetic, epigenetic, and environmental bases of behavior. Here we further outline the utility of the species, as well as present current cytogenetic and molecular data showing that rearrangements and linkage in multiple chromosomes are key to the evolution of alternative phenotypes. In addition, comparative analyses among the Zonotrichia suggest an interesting and slightly counterintuitive evolutionary pathway in this group. Genomic studies in the white-throated sparrow will identify the gene(s) associated with complex behaviors, as well as provide us with information on how environment interacts with genetic architecture to affect aggressive, social, sexual, and parental phenotypes. Morphs of the sparrow provide us with a unique opportunity to study intraspecific genomic differences, which have resulted from two sepa

Published
2010

45. The value of avian genomics to the conservation of wildlife

Author

Romanov, Michael N, Tuttle, Elaina M., Houck, Marlys L., Modi, William S., Chemnick, Leona G., Korody, Marisa L., Stremel Mork, Emily M., Otten, Christie A., Renner, Tanya, Jones, Kenneth C., Dandekar, Sugandha, Papp, Jeanette C., Da, Yang, Green, Eric D., Magrini, Vincent, Hickenbotham, Matthew T., Glasscock, Jarret, McGrath, Sean, Mardis, Elaine R., Ryder, Oliver A., Romanov, Michael N, Tuttle, Elaina M., Houck, Marlys L., Modi, William S., Chemnick, Leona G., Korody, Marisa L., Stremel Mork, Emily M., Otten, Christie A., Renner, Tanya, Jones, Kenneth C., Dandekar, Sugandha, Papp, Jeanette C., Da, Yang, Green, Eric D., Magrini, Vincent, Hickenbotham, Matthew T., Glasscock, Jarret, McGrath, Sean, Mardis, Elaine R., and Ryder, Oliver A.

Abstract

Background: Genomic studies in non-domestic avian models, such as the California condor and white-throated sparrow, can lead to more comprehensive conservation plans and provide clues for understanding mechanisms affecting genetic variation, adaptation and evolution. Developing genomic tools and resources including genomic libraries and a genetic map of the California condor is a prerequisite for identification of candidate loci for a heritable embryonic lethal condition. The white-throated sparrow exhibits a stable genetic polymorphism (i.e. chromosomal rearrangements) associated with variation in morphology, physiology, and behavior (e.g., aggression, social behavior, sexual behavior, parental care). In this paper we outline the utility of these species as well as report on recent advances in the study of their genomes. Results: Genotyping of the condor resource population at 17 microsatellite loci provided a better assessment of the current population's genetic variation. Specific New World vulture repeats were found in the condor genome. Using condor BAC library and clones, chicken-condor comparative maps were generated. A condor fibroblast cell line transcriptome was characterized using the 454 sequencing technology. Our karyotypic analyses of the sparrow in combination with other studies indicate that the rearrangements in both chromosomes 2(m) and 3(a) are complex and likely involve multiple inversions, interchromosomal linkage, and pleiotropy. At least a portion of the rearrangement in chromosome 2(m) existed in the common ancestor of the four North American species of Zonotrichia, but not in the one South American species, and that the 2(m) form, originally thought to be the derived condition, might actually be the ancestral one. Conclusion: Mining and characterization of candidate loci in the California condor using molecular genetic and genomic techniques as well as linkage and comparative genomic mapping will eventually enable the identification of carri

Published
2009

46. Emerging trends for biobanking amphibian genetic resources: The hope, reality and challenges for the next decade

Author

Kouba, Andrew J., primary, Lloyd, Rhiannon E., additional, Houck, Marlys L., additional, Silla, Aimee J., additional, Calatayud, Natalie, additional, Trudeau, Vance L., additional, Clulow, John, additional, Molinia, Frank, additional, Langhorne, Cecilia, additional, Vance, Carrie, additional, Arregui, Lucia, additional, Germano, Jennifer, additional, Lermen, Dominik, additional, and Della Togna, Gina, additional

Published
2013
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48. Induced pluripotent stem cells from highly endangered species

Author

Friedrich Ben-Nun, Inbar, primary, Montague, Susanne C, additional, Houck, Marlys L, additional, Tran, Ha T, additional, Garitaonandia, Ibon, additional, Leonardo, Trevor R, additional, Wang, Yu-Chieh, additional, Charter, Suellen J, additional, Laurent, Louise C, additional, Ryder, Oliver A, additional, and Loring, Jeanne F, additional

Published
2011
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50. The value of avian genomics to the conservation of wildlife

Author

Romanov, Michael N, primary, Tuttle, Elaina M, additional, Houck, Marlys L, additional, Modi, William S, additional, Chemnick, Leona G, additional, Korody, Marisa L, additional, Mork, Emily, additional, Otten, Christie A, additional, Renner, Tanya, additional, Jones, Kenneth C, additional, Dandekar, Sugandha, additional, Papp, Jeanette C, additional, Da, Yang, additional, Green, Eric D, additional, Magrini, Vincent, additional, Hickenbotham, Matthew T, additional, Glasscock, Jarret, additional, McGrath, Sean, additional, Mardis, Elaine R, additional, and Ryder, Oliver A, additional

Published
2009
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