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499 results on '"Koepfli, Klaus‐Peter"'

1. Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements.

Author

Wirthlin, Morgan, Schmid, Tobias, Elie, Julie, Zhang, Xiaomeng, Kowalczyk, Amanda, Redlich, Ruby, Shvareva, Varvara, Rakuljic, Ashley, Ji, Maria, Bhat, Ninad, Kaplow, Irene, Schäffer, Daniel, Lawler, Alyssa, Wang, Andrew, Phan, BaDoi, Annaldasula, Siddharth, Brown, Ashley, Lu, Tianyu, Lim, Byung, Azim, Eiman, Clark, Nathan, Meyer, Wynn, Pond, Sergei, Chikina, Maria, Yartsev, Michael, Pfenning, Andreas, Andrews, Gregory, Armstrong, Joel, Bianchi, Matteo, Birren, Bruce, Bredemeyer, Kevin, Breit, Ana, Christmas, Matthew, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole, Forsberg-Nilsson, Karin, Garcia, Carlos, Gatesy, John, Gazal, Steven, Genereux, Diane, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela, Harris, Andrew, Hickey, Glenn, Hiller, Michael, Hindle, Allyson, Hubley, Robert, Hughes, Graham, Johnson, Jeremy, Juan, David, Karlsson, Elinor, Keough, Kathleen, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer, Kozyrev, Sergey, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle, Lewin, Harris, Li, Xue, Lind, Abigail, Lindblad-Toh, Kerstin, Mackay-Smith, Ava, Marinescu, Voichita, Marques-Bonet, Tomas, Mason, Victor, Meadows, Jennifer, Moore, Jill, Moreira, Lucas, Moreno-Santillan, Diana, Morrill, Kathleen, Muntané, Gerard, Murphy, William, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole, Pollard, Katherine, Pratt, Henry, Ray, David, Reilly, Steven, Rosen, Jeb, and Ruf, Irina

Subjects
Animals, Chiroptera, Vocalization, Animal, Motor Cortex, Chromatin, Enhancer Elements, Genetic, Motor Neurons, Larynx, Epigenesis, Genetic, Genome, Gene Expression Regulation, Evolution, Molecular, Proteins, Amino Acid Sequence, Eutheria, Machine Learning
Abstract

Vocal production learning (vocal learning) is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from the Egyptian fruit bat (Rousettus aegyptiacus) with analyses of the genomes of 215 placental mammals. First, we identified a set of proteins evolving more slowly in vocal learners. Then, we discovered a vocal motor cortical region in the Egyptian fruit bat, an emergent vocal learner, and leveraged that knowledge to identify active cis-regulatory elements in the motor cortex of vocal learners. Machine learning methods applied to motor cortex open chromatin revealed 50 enhancers robustly associated with vocal learning whose activity tended to be lower in vocal learners. Our research implicates convergent losses of motor cortex regulatory elements in mammalian vocal learning evolution.

Published
2024

2. Semen proteome and transcriptome of the endangered black-footed ferret (Mustela nigripes) show association with the environment and fertility outcome.

Author

Ali, Nadya, Amelkina, Olga, Santymire, Rachel, Koepfli, Klaus-Peter, Comizzoli, Pierre, and Vazquez, Juan

Subjects
Humans, Animals, Semen, Ferrets, Proteome, Transcriptome, Fertility
Abstract

The ex situ population of the endangered black-footed ferret (Mustela nigripes) has been experiencing declines in reproductive success over the past 30 years of human-managed care. A potential cause may be environmental-dependent inbreeding depression with diet being one of the contributing factors since ferrets are not fed their natural diet of prairie dogs. Here, we generated and analyzed semen proteome and transcriptome data from both wild and ex situ ferrets maintained on various diets. We identified 1757 proteins across all samples, with 149 proteins unique to the semen of wild ferrets and forming a ribosomal predicted protein-protein interaction cluster. Wild ferrets also differed from ex situ ferrets in their transcriptomic profile, showing enrichment in ribosomal RNA processing and potassium ion transport. Successful fertility outcomes documented for ex situ ferrets showed the strongest association with the semen transcriptome, with enrichment in genes involved in translation initiation and focal adhesion. Fertility also synergized with the effect of diet on differentially expressed transcriptomes, mainly affecting genes enriched in mitochondrial function. Our data and functional networks are important for understanding the causes and mechanisms of declining fertility in the ex situ ferret population and can be used as a resource for future conservation efforts.

Published
2024

4. Comprehensive genome assembly reveals genetic diversity and carcass consumption insights in critically endangered Asian king vultures

Author

Buthasane, Wannapol, Shotelersuk, Vorasuk, Chetruengchai, Wanna, Srichomthong, Chalurmpon, Assawapitaksakul, Adjima, Tangphatsornruang, Sithichoke, Pootakham, Wirulda, Sonthirod, Chutima, Tongsima, Sissades, Wangkumhang, Pongsakorn, Wilantho, Alisa, Thongphakdee, Ampika, Sanannu, Saowaphang, Poksawat, Chaianan, Nipanunt, Tarasak, Kasorndorkbua, Chaiyan, Koepfli, Klaus-Peter, Pukazhenthi, Budhan S., Suriyaphol, Prapat, Wongsurawat, Thidathip, Jenjaroenpun, Piroon, and Suriyaphol, Gunnaporn

Published
2024
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6. A genomic timescale for placental mammal evolution

Author

Foley, Nicole M, Mason, Victor C, Harris, Andrew J, Bredemeyer, Kevin R, Damas, Joana, Lewin, Harris A, Eizirik, Eduardo, Gatesy, John, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Springer, Mark S, Murphy, William J, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Fan, Kaili, Fanter, Cornelia, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, 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, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, 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, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, Steiner, Cynthia, Storer, Jessica M, Sullivan, Kevin AM, Sullivan, Patrick F, and Sundström, Elisabeth

Subjects
Genetics, Human Genome, Biotechnology, Animals, Female, Biological Evolution, Eutheria, Evolution, Molecular, Fossils, Genomics, Phylogeny, Genetic Variation, Time Factors, Zoonomia Consortium‡, General Science & Technology
Abstract

The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic time trees reveal an accumulation of cladogenic events before and immediately after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance and the K-Pg extinction in the placental radiation.

Published
2023

7. Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs

Author

Moon, Katherine L, Huson, Heather J, Morrill, Kathleen, Wang, Ming-Shan, Li, Xue, Srikanth, Krishnamoorthy, Lindblad-Toh, Kerstin, Svenson, Gavin J, Karlsson, Elinor K, Shapiro, Beth, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, 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, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, 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, Lewin, Harris A, 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, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, Steiner, Cynthia, Storer, Jessica M, Sullivan, Kevin AM, Sullivan, Patrick F, Sundström, Elisabeth, Supple, Megan A, and Swofford, Ross

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Genetics, Animals, Dogs, Male, Genome, Genomics, Genotype, Phenotype, Wolves, Biodiversity, Genetic Variation, Zoonomia Consortium, General Science & Technology
Abstract

We reconstruct the phenotype of Balto, the heroic sled dog renowned for transporting diphtheria antitoxin to Nome, Alaska, in 1925, using evolutionary constraint estimates from the Zoonomia alignment of 240 mammals and 682 genomes from dogs and wolves of the 21st century. Balto shares just part of his diverse ancestry with the eponymous Siberian husky breed. Balto's genotype predicts a combination of coat features atypical for modern sled dog breeds, and a slightly smaller stature. He had enhanced starch digestion compared with Greenland sled dogs and a compendium of derived homozygous coding variants at constrained positions in genes connected to bone and skin development. We propose that Balto's population of origin, which was less inbred and genetically healthier than that of modern breeds, was adapted to the extreme environment of 1920s Alaska.

Published
2023

8. The contribution of historical processes to contemporary extinction risk in placental mammals

Author

Wilder, Aryn P, Supple, Megan A, Subramanian, Ayshwarya, Mudide, Anish, Swofford, Ross, Serres-Armero, Aitor, Steiner, Cynthia, Koepfli, Klaus-Peter, Genereux, Diane P, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Marques-Bonet, Tomas, Munoz Fuentes, Violeta, Foley, Kathleen, Meyer, Wynn K, Ryder, Oliver A, Shapiro, Beth, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, 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, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Mason, Victor C, Meadows, Jennifer RS, 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, Ryan, Louise, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Smit, Arian FA, Springer, Mark, and Srinivasan, Chaitanya

Subjects
Biological Sciences, Evolutionary Biology, Genetics, Behavioral and Social Science, Human Genome, Basic Behavioral and Social Science, Life on Land, Animals, Female, Pregnancy, Eutheria, Extinction, Biological, Genetic Variation, Genome, Population Density, Risk, Zoonomia Consortium‡, General Science & Technology
Abstract

Species persistence can be influenced by the amount, type, and distribution of diversity across the genome, suggesting a potential relationship between historical demography and resilience. In this study, we surveyed genetic variation across single genomes of 240 mammals that compose the Zoonomia alignment to evaluate how historical effective population size (Ne) affects heterozygosity and deleterious genetic load and how these factors may contribute to extinction risk. We find that species with smaller historical Ne carry a proportionally larger burden of deleterious alleles owing to long-term accumulation and fixation of genetic load and have a higher risk of extinction. This suggests that historical demography can inform contemporary resilience. Models that included genomic data were predictive of species' conservation status, suggesting that, in the absence of adequate census or ecological data, genomic information may provide an initial risk assessment.

Published
2023

9. The functional and evolutionary impacts of human-specific deletions in conserved elements

Author

Xue, James R, Mackay-Smith, Ava, Mouri, Kousuke, Garcia, Meilin Fernandez, Dong, Michael X, Akers, Jared F, Noble, Mark, Li, Xue, Lindblad-Toh, Kerstin, Karlsson, Elinor K, Noonan, James P, Capellini, Terence D, Brennand, Kristen J, Tewhey, Ryan, Sabeti, Pardis C, Reilly, Steven K, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, 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, Lewin, Harris A, Lind, Abigail, 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, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Schäffer, Daniel E, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, and Steiner, Cynthia

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Neurosciences, Human Genome, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Neurological, Humans, Conserved Sequence, Evolution, Molecular, Genome, Genomics, RNA-Binding Proteins, Sequence Deletion, Brain, Gene Expression Regulation, Developmental, Zoonomia Consortium†, General Science & Technology
Abstract

Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) deletions are enriched for human brain functions across genetic, epigenomic, and transcriptomic datasets. Using massively parallel reporter assays in six cell types, we discovered 800 hCONDELs conferring significant differences in regulatory activity, half of which enhance rather than disrupt regulatory function. We highlight several hCONDELs with putative human-specific effects on brain development, including HDAC5, CPEB4, and PPP2CA. Reverting an hCONDEL to the ancestral sequence alters the expression of LOXL2 and developmental genes involved in myelination and synaptic function. Our data provide a rich resource to investigate the evolutionary mechanisms driving new traits in humans and other species.

Published
2023

10. Integrating gene annotation with orthology inference at scale

Author

Kirilenko, Bogdan M, Munegowda, Chetan, Osipova, Ekaterina, Jebb, David, Sharma, Virag, Blumer, Moritz, Morales, Ariadna E, Ahmed, Alexis-Walid, Kontopoulos, Dimitrios-Georgios, Hilgers, Leon, Lindblad-Toh, Kerstin, Karlsson, Elinor K, Hiller, Michael, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, 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, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, 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, Lewin, Harris A, 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, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, Steiner, Cynthia, Storer, Jessica M, Sullivan, Kevin AM, and Sullivan, Patrick F

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Generic health relevance, Animals, Female, Mice, Eutheria, Genome, Genomics, Molecular Sequence Annotation, Birds, Zoonomia Consortium‡, General Science & Technology
Abstract

Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method that integrates structural gene annotation and orthology inference. TOGA implements a different paradigm to infer orthologous loci, improves ortholog detection and annotation of conserved genes compared with state-of-the-art methods, and handles even highly fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 501 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. TOGA is a powerful and scalable method to annotate and compare genes in the genomic era.

Published
2023

11. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning

Author

Kaplow, Irene M, Lawler, Alyssa J, Schäffer, Daniel E, Srinivasan, Chaitanya, Sestili, Heather H, Wirthlin, Morgan E, Phan, BaDoi N, Prasad, Kavya, Brown, Ashley R, Zhang, Xiaomeng, Foley, Kathleen, Genereux, Diane P, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Meyer, Wynn K, Pfenning, Andreas R, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, 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, Johnson, Jeremy, Juan, David, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, 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, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, and Steiner, Cynthia

Subjects
Biological Sciences, Genetics, Pediatric, Human Genome, Rare Diseases, Congenital Structural Anomalies, Underpinning research, 1.1 Normal biological development and functioning, Neurological, Mental health, Animals, Enhancer Elements, Genetic, Genetic Variation, Machine Learning, Mammals, Phenotype, Zoonomia Consortium**, General Science & Technology
Abstract

Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.

Published
2023

12. Three-dimensional genome rewiring in loci with human accelerated regions

Author

Keough, Kathleen C, Whalen, Sean, Inoue, Fumitaka, Przytycki, Pawel F, Fair, Tyler, Deng, Chengyu, Steyert, Marilyn, Ryu, Hane, Lindblad-Toh, Kerstin, Karlsson, Elinor, Nowakowski, Tomasz, Ahituv, Nadav, Pollen, Alex, Pollard, Katherine S, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, 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, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Karlsson, Elinor K, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, 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, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, Steiner, Cynthia, Storer, Jessica M, and Sullivan, Kevin AM

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Stem Cell Research, Human Genome, Biotechnology, Underpinning research, 1.1 Normal biological development and functioning, Animals, Humans, Chromatin, Genome, Human, Genomics, Pan troglodytes, Genetic Loci, Neurogenesis, Deep Learning, Zoonomia Consortium§, General Science & Technology
Abstract

Human accelerated regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with an automated pipeline and an alignment of 241 mammalian genomes. Combining deep learning with chromatin capture experiments in human and chimpanzee neural progenitor cells, we discovered a significant enrichment of HARs in topologically associating domains containing human-specific genomic variants that change three-dimensional (3D) genome organization. Differential gene expression between humans and chimpanzees at these loci suggests rewiring of regulatory interactions between HARs and neurodevelopmental genes. Thus, comparative genomics together with models of 3D genome folding revealed enhancer hijacking as an explanation for the rapid evolution of HARs.

Published
2023

13. Evolutionary constraint and innovation across hundreds of placental mammals

Author

Christmas, Matthew J, Kaplow, Irene M, Genereux, Diane P, Dong, Michael X, Hughes, Graham M, Li, Xue, Sullivan, Patrick F, Hindle, Allyson G, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Breit, Ana M, Diekhans, Mark, Fanter, Cornelia, Foley, Nicole M, Goodman, Daniel B, Goodman, Linda, Keough, Kathleen C, Kirilenko, Bogdan, Kowalczyk, Amanda, Lawless, Colleen, Lind, Abigail L, Meadows, Jennifer RS, Moreira, Lucas R, Redlich, Ruby W, Ryan, Louise, Swofford, Ross, Valenzuela, Alejandro, Wagner, Franziska, Wallerman, Ola, Brown, Ashley R, Damas, Joana, Fan, Kaili, Gatesy, John, Grimshaw, Jenna, Johnson, Jeremy, Kozyrev, Sergey V, Lawler, Alyssa J, Marinescu, Voichita D, Morrill, Kathleen M, Osmanski, Austin, Paulat, Nicole S, Phan, BaDoi N, Reilly, Steven K, Schäffer, Daniel E, Steiner, Cynthia, Supple, Megan A, Wilder, Aryn P, Wirthlin, Morgan E, Xue, James R, Birren, Bruce W, Gazal, Steven, Hubley, Robert M, Koepfli, Klaus-Peter, Marques-Bonet, Tomas, Meyer, Wynn K, Nweeia, Martin, Sabeti, Pardis C, Shapiro, Beth, Smit, Arian FA, Springer, Mark S, Teeling, Emma C, Weng, Zhiping, Hiller, Michael, Levesque, Danielle L, Lewin, Harris A, Murphy, William J, Navarro, Arcadi, Paten, Benedict, Pollard, Katherine S, Ray, David A, Ruf, Irina, Ryder, Oliver A, Pfenning, Andreas R, Lindblad-Toh, Kerstin, Karlsson, Elinor K, Bredemeyer, Kevin R, Clawson, Hiram, Di Palma, Federica, Eizirik, Eduardo, Forsberg-Nilsson, Karin, Garcia, Carlos J, and Halsey, Michaela K

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Animals, Female, Humans, Conserved Sequence, Eutheria, Evolution, Molecular, Genome, Human, Zoonomia Consortium§, General Science & Technology
Abstract

Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.

Published
2023

14. Leveraging base-pair mammalian constraint to understand genetic variation and human disease

Author

Sullivan, Patrick F, Meadows, Jennifer RS, Gazal, Steven, Phan, BaDoi N, Li, Xue, Genereux, Diane P, Dong, Michael X, Bianchi, Matteo, Andrews, Gregory, Sakthikumar, Sharadha, Nordin, Jessika, Roy, Ananya, Christmas, Matthew J, Marinescu, Voichita D, Wang, Chao, Wallerman, Ola, Xue, James, Yao, Shuyang, Sun, Quan, Szatkiewicz, Jin, Wen, Jia, Huckins, Laura M, Lawler, Alyssa, Keough, Kathleen C, Zheng, Zhili, Zeng, Jian, Wray, Naomi R, Li, Yun, Johnson, Jessica, Chen, Jiawen, Paten, Benedict, Reilly, Steven K, Hughes, Graham M, Weng, Zhiping, Pollard, Katherine S, Pfenning, Andreas R, Forsberg-Nilsson, Karin, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Armstrong, Joel C, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Garcia, Carlos J, Gatesy, John, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Lind, Abigail, Mackay-Smith, Ava, Marques-Bonet, Tomas, Mason, Victor C, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, and Navarro, Arcadi

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Clinical Research, Human Genome, Brain Disorders, Generic health relevance, Animals, Humans, Biological Evolution, Genetic Variation, Genome, Human, Genome-Wide Association Study, Genomics, Molecular Sequence Annotation, Polymorphism, Single Nucleotide, Disease, Zoonomia Consortium§, General Science & Technology
Abstract

Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.

Published
2023

15. 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

16. Robust haplotype-resolved assembly of diploid individuals without parental data

Author

Cheng, Haoyu, Jarvis, Erich D., Fedrigo, Olivier, Koepfli, Klaus-Peter, Urban, Lara, Gemmell, Neil J., and Li, Heng

Subjects
Quantitative Biology - Genomics
Abstract

Routine single-sample haplotype-resolved assembly remains an unresolved problem. Here we describe a new algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction data to produce a haplotype-resolved assembly without the sequencing of parents. Applied to human and other vertebrate samples, our algorithm consistently outperforms existing single-sample assembly pipelines and generates assemblies of comparable quality to the best pedigree-based assemblies.

Published
2021

17. Comparative genomics and genome-wide SNPs of endangered Eld’s deer provide breeder selection for inbreeding avoidance

Author

Pumpitakkul, Vichayanee, Chetruengchai, Wanna, Srichomthong, Chalurmpon, Phokaew, Chureerat, Pootakham, Wirulda, Sonthirod, Chutima, Nawae, Wanapinun, Tongsima, Sissades, Wangkumhang, Pongsakorn, Wilantho, Alisa, Utara, Yongchai, Thongpakdee, Ampika, Sanannu, Saowaphang, Maikaew, Umaporn, Khuntawee, Suphattharaphonnaphan, Changpetch, Wirongrong, Phromwat, Phairot, Raschasin, Kacharin, Sarnkhaeveerakul, Phunyaphat, Supapannachart, Pannawat, Buthasane, Wannapol, Pukazhenthi, Budhan S., Koepfli, Klaus-Peter, Suriyaphol, Prapat, Tangphatsornruang, Sithichoke, Suriyaphol, Gunnaporn, and Shotelersuk, Vorasuk

Published
2023
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18. Genome Sequencing of a Gray Wolf from Peninsular India Provides New Insights into the Evolution and Hybridization of Gray Wolves

Author

Wang, Ming-Shan, Thakur, Mukesh, Jhala, Yadvendradev, Wang, Sheng, Srinivas, Yellapu, Dai, Shan-Shan, Liu, Zheng-Xi, Chen, Hong-Man, Green, Richard E, Koepfli, Klaus-Peter, and Shapiro, Beth

Subjects
Biotechnology, Human Genome, Genetics, Life on Land, Animals, Gene Flow, Hybridization, Genetic, India, Phylogeny, Wolves, gray wolf, Canis lupus pallipes, hybridization, gene flow, evolutionary history, Pleistocene refugium, Canis lupus pallipes, Biochemistry and Cell Biology, Evolutionary Biology, Developmental Biology
Abstract

The gray wolf (Canis lupus) is among the few large carnivores that survived the Late Pleistocene megafaunal extinctions. Thanks to their complex history of admixture and extensive geographic range, the number of gray wolf subspecies and their phylogenetic relationships remain poorly understood. Here, we perform whole-genome sequencing of a gray wolf collected from peninsular India that was phenotypically distinct from gray wolves outside India. Genomic analyses reveal that the Indian gray wolf is an evolutionarily distinct lineage that diverged from other extant gray wolf lineages ∼110 thousand years ago. Demographic analyses suggest that the Indian wolf population declined continuously decline since separating from other gray wolves and, today, has exceptionally low genetic diversity. We also find evidence for pervasive and mosaic gene flow between the Indian wolf and African canids including African wolf, Ethiopian wolf, and African wild dog despite their current geographical separation. Our results support the hypothesis that the Indian subcontinent was a Pleistocene refugium and center of diversification and further highlight the complex history of gene flow that characterized the evolution of gray wolves.

Published
2022

19. Darwinian genomics and diversity in the tree of life

Author

Stephan, Taylorlyn, Burgess, Shawn M, Cheng, Hans, Danko, Charles G, Gill, Clare A, Jarvis, Erich D, Koepfli, Klaus-Peter, Koltes, James E, Lyons, Eric, Ronald, Pamela, Ryder, Oliver A, Schriml, Lynn M, Soltis, Pamela, VandeWoude, Sue, Zhou, Huaijun, Ostrander, Elaine A, and Karlsson, Elinor K

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, History, Heritage and Archaeology, Historical Studies, Biotechnology, Human Genome, Generic health relevance, Animals, Biodiversity, Biological Evolution, Evolution, Molecular, Genetic Variation, Genome, Genomics, Humans, Phylogeny, comparative genomics, evolution, biodiversity, natural models, genomics
Abstract

Genomics encompasses the entire tree of life, both extinct and extant, and the evolutionary processes that shape this diversity. To date, genomic research has focused on humans, a small number of agricultural species, and established laboratory models. Fewer than 18,000 of ∼2,000,000 eukaryotic species (

Published
2022

21. 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

22. 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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23. Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates

Author

Damas, Joana, Hughes, Graham M, Keough, Kathleen C, Painter, Corrie A, Persky, Nicole S, Corbo, Marco, Hiller, Michael, Koepfli, Klaus-Peter, Pfenning, Andreas R, Zhao, Huabin, Genereux, Diane P, Swofford, Ross, Pollard, Katherine S, Ryder, Oliver A, Nweeia, Martin T, Lindblad-Toh, Kerstin, Teeling, Emma C, Karlsson, Elinor K, and Lewin, Harris A

Subjects
Emerging Infectious Diseases, Lung, Prevention, Vaccine Related, Biodefense, Infectious Diseases, Pneumonia, Amino Acids, Animals, Betacoronavirus, Binding Sites, COVID-19, Coronavirus Infections, Evolution, Molecular, Genetic Variation, Host Specificity, Humans, Pandemics, Peptidyl-Dipeptidase A, Pneumonia, Viral, Protein Binding, Receptors, Virus, SARS-CoV-2, Selection, Genetic, Spike Glycoprotein, Coronavirus, Vertebrates, ACE2, comparative genomics, species conservation
Abstract

The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19. The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of ACE2 sequences from 410 vertebrate species, including 252 mammals, to study the conservation of ACE2 and its potential to be used as a receptor by SARS-CoV-2. We designed a five-category binding score based on the conservation properties of 25 amino acids important for the binding between ACE2 and the SARS-CoV-2 spike protein. Only mammals fell into the medium to very high categories and only catarrhine primates into the very high category, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 spike protein binding and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (frequency

Published
2020

27. Population Genomic Analysis of North American Eastern Wolves (Canis lycaon) Supports Their Conservation Priority Status

Author

Heppenheimer, Elizabeth, Harrigan, Ryan J, Rutledge, Linda Y, Koepfli, Klaus-Peter, DeCandia, Alexandra L, Brzeski, Kristin E, Benson, John F, Wheeldon, Tyler, Patterson, Brent R, Kays, Roland, Hohenlohe, Paul A, and von Holdt, Bridgett M

Subjects
Biological Sciences, Ecology, Genetics, Human Genome, Life on Land, canine, geographic isolation, spatial structure, restriction-site associated DNA, conservation genomics
Abstract

The threatened eastern wolf is found predominantly in protected areas of central Ontario and has an evolutionary history obscured by interbreeding with coyotes and gray wolves, which challenges its conservation status and subsequent management. Here, we used a population genomics approach to uncover spatial patterns of variation in 281 canids in central Ontario and the Great Lakes region. This represents the first genome-wide single nucleotide polymorphism (SNP) dataset with substantial sample sizes of representative populations. Although they comprise their own genetic cluster, we found evidence of eastern wolf dispersal outside of the boundaries of protected areas, in that the frequency of eastern wolf genetic variation decreases with increasing distance from provincial parks. We detected eastern wolf alleles in admixed coyotes along the northeastern regions of Lake Huron and Lake Ontario. Our analyses confirm the unique genomic composition of eastern wolves, which are mostly restricted to small fragmented patches of protected habitat in central Ontario. We hope this work will encourage an innovative discussion regarding a plan for managed introgression, which could conserve eastern wolf genetic material in any genome regardless of their potential mosaic ancestry composition and the habitats that promote them.

Published
2018

28. Parameterizing Pantherinae: de novo mutation rate estimates from Panthera and Neofelis pedigrees

Author

Armstrong, Ellie E, primary, Carey, Sarah B., additional, Harkess, Alex, additional, Zenato Lazzari, Gabriele, additional, Solari, Katherine A, additional, Maldonado, Jesus E., additional, Fleischer, Robert C., additional, Aziz, Neel, additional, Walsh, Pattie, additional, Koepfli, Klaus-Peter, additional, Eizirik, Eduardo, additional, Petrov, Dmitri A., additional, and Campana, Michael, additional

Published
2024
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30. The gut microbiomes of Channel Island foxes and island spotted skunks exhibit fine‐scale differentiation across host species and island populations

Author

Pasciullo Boychuck, Samantha, primary, Brenner, Lara J., additional, Gagorik, Calypso N., additional, Schamel, Juliann T., additional, Baker, Stacy, additional, Tran, Elton, additional, vonHoldt, Bridgett M., additional, Koepfli, Klaus‐Peter, additional, Maldonado, Jesús E., additional, and DeCandia, Alexandra L., additional

Published
2024
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32. 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

34. 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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35. Gut bacterial composition shows sex-specific shifts during breeding season in ex situ managed black-footed ferrets.

Author

DeCandia, Alexandra L, Adeduro, Laura, Thacher, Piper, Crosier, Adrienne, Marinari, Paul, Bortner, Robyn, Garelle, Della, Livieri, Travis, Santymire, Rachel, Comizzoli, Pierre, Maslanka, Michael, Maldonado, Jesús E, Koepfli, Klaus-Peter, Muletz-Wolz, Carly, and Bornbusch, Sally L

Subjects
FERRET, SEX (Biology), ANIMAL populations, GUT microbiome, BACTERIAL communities, CONSERVATION biology, MICROBIAL communities, SEASONS
Abstract

The gut microbiome of mammals engages in a dynamic relationship with the body and contributes to numerous physiological processes integral to overall health. Understanding the factors shaping animal-associated bacterial communities is therefore paramount to the maintenance and management in ex situ wildlife populations. Here, we characterized the gut microbiome of 48 endangered black-footed ferrets (Mustela nigripes) housed at Smithsonian's National Zoo and Conservation Biology Institute (Front Royal, Virginia, USA). We collected longitudinal fecal samples from males and females across two distinct reproductive seasons to consider the role of host sex and reproductive physiology in shaping bacterial communities, as measured using 16S rRNA amplicon sequencing. Within each sex, gut microbial composition differed between breeding and non-breeding seasons, with five bacterial taxa emerging as differentially abundant. Between sexes, female and male microbiomes were similar during non-breeding season but significantly different during breeding season, which may result from sex-specific physiological changes associated with breeding. Finally, we found low overall diversity consistent with other mammalian carnivores alongside high relative abundances of potentially pathogenic microbes such as Clostridium, Escherichia, Paeniclostridium , and (to a lesser degree) Enterococcus —all of which have been associated with gastrointestinal or reproductive distress in mammalian hosts, including black-footed ferrets. We recommend further study of these microbes and possible therapeutic interventions to promote more balanced microbial communities. These results have important implications for ex situ management practices that can improve the gut microbial health and long-term viability of black-footed ferrets. [ABSTRACT FROM AUTHOR]

Published
2024
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36. Evolution: Genomes reveal the reticulated history of giraffes.

Author

Koepfli, Klaus-Peter

Subjects
*GIRAFFES, *GENOMES, *GENE flow
Abstract

The diversification and taxonomy of modern giraffe lineages have been a riddle for more than 200 years. A new genomic study shows that divergence with gene flow has played a significant role in the history of this zoological icon. [ABSTRACT FROM AUTHOR]

Published
2024
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37. Genome-wide data support recognition of an additional species of Neotropical river otter (Mammalia, Mustelidae, Lutrinae).

Author

Ferran, Vera de, Figueiró, Henrique Vieira, Trinca, Cristine Silveira, Hernández-Romero, Pablo César, Lorenzana, Gustavo P, Gutiérrez-Rodríguez, Carla, Koepfli, Klaus-Peter, and Eizirik, Eduardo

Subjects
MUSTELIDAE, MAMMALS, SPECIES, OTTERS, PRINCIPAL components analysis, MITOCHONDRIAL DNA
Abstract

Cryptic biodiversity continues to be revealed worldwide, even in apparently well-known groups such as carnivorans. The Neotropical Otter (Lontra longicaudis) presents shape variation in its nose pad, a character that has been used to differentiate species in this group. Based on this, 3 subspecies are recognized: L. l. annectens (Mexico, Central America, and South America west of the Andes), L. l. enudris (Amazon and Orinoco basins), and L. l. longicaudis (Paraná basin and remaining distribution). Previous studies partially supported their distinctness based on mitochondrial DNA markers, morphometrics, and ecological niche modeling. We analyzed genome-wide nuclear markers (ultraconserved elements) of 29 L. longicaudis individuals across the species' range to assess its population structure. Phylogenomic analysis recovered L. longicaudis as paraphyletic with robust support, with 1 clade comprising samples from Mexico and Colombia (trans-Andean populations) and another encompassing the remaining samples (cis-Andean populations), which grouped with 2 other South American species, L. felina and L. provocax. Principal component and admixture analyses strongly differentiated the 2 main L. longicaudis groups, and distinguished the Amazonian individuals from the remaining cis-Andean samples. Our results support the recognition of trans-Andean populations of L. longicaudis as a distinct otter species, which should be recognized as Lontra annectens. [ABSTRACT FROM AUTHOR]

Published
2024
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39. 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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41. 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

42. The Genome 10K Project: A Way Forward

Author

Koepfli, Klaus-Peter, Paten, Benedict, Community of Scientists, the Genome 10K, and O’Brien, Stephen J

Subjects
Biological Sciences, Genetics, Human Genome, Animals, Computational Biology, Forecasting, Genome, Genomics, Humans, Species Specificity, Vertebrates, mammal, amphibian, reptile, bird, fish, genome, Genome 10K Community of Scientists, Animal Production, Veterinary Sciences, Animal production, Veterinary sciences
Abstract

The Genome 10K Project was established in 2009 by a consortium of biologists and genome scientists determined to facilitate the sequencing and analysis of the complete genomes of 10,000 vertebrate species. Since then the number of selected and initiated species has risen from ∼26 to 277 sequenced or ongoing with funding, an approximately tenfold increase in five years. Here we summarize the advances and commitments that have occurred by mid-2014 and outline the achievements and present challenges of reaching the 10,000-species goal. We summarize the status of known vertebrate genome projects, recommend standards for pronouncing a genome as sequenced or completed, and provide our present and future vision of the landscape of Genome 10K. The endeavor is ambitious, bold, expensive, and uncertain, but together the Genome 10K Consortium of Scientists and the worldwide genomics community are moving toward their goal of delivering to the coming generation the gift of genome empowerment for many vertebrate species.

Published
2015

43. Whole-genome analyses resolve early branches in the tree of life of modern birds

Author

Jarvis, Erich D, Mirarab, Siavash, Aberer, Andre J, Li, Bo, Houde, Peter, Li, Cai, Ho, Simon YW, Faircloth, Brant C, Nabholz, Benoit, Howard, Jason T, Suh, Alexander, Weber, Claudia C, da Fonseca, Rute R, Li, Jianwen, Zhang, Fang, Li, Hui, Zhou, Long, Narula, Nitish, Liu, Liang, Ganapathy, Ganesh, Boussau, Bastien, Bayzid, Md Shamsuzzoha, Zavidovych, Volodymyr, Subramanian, Sankar, Gabaldón, Toni, Capella-Gutiérrez, Salvador, Huerta-Cepas, Jaime, Rekepalli, Bhanu, Munch, Kasper, Schierup, Mikkel, Lindow, Bent, Warren, Wesley C, Ray, David, Green, Richard E, Bruford, Michael W, Zhan, Xiangjiang, Dixon, Andrew, Li, Shengbin, Li, Ning, Huang, Yinhua, Derryberry, Elizabeth P, Bertelsen, Mads Frost, Sheldon, Frederick H, Brumfield, Robb T, Mello, Claudio V, Lovell, Peter V, Wirthlin, Morgan, Schneider, Maria Paula Cruz, Prosdocimi, Francisco, Samaniego, José Alfredo, Vargas Velazquez, Amhed Missael, Alfaro-Núñez, Alonzo, Campos, Paula F, Petersen, Bent, Sicheritz-Ponten, Thomas, Pas, An, Bailey, Tom, Scofield, Paul, Bunce, Michael, Lambert, David M, Zhou, Qi, Perelman, Polina, Driskell, Amy C, Shapiro, Beth, Xiong, Zijun, Zeng, Yongli, Liu, Shiping, Li, Zhenyu, Liu, Binghang, Wu, Kui, Xiao, Jin, Yinqi, Xiong, Zheng, Qiuemei, Zhang, Yong, Yang, Huanming, Wang, Jian, Smeds, Linnea, Rheindt, Frank E, Braun, Michael, Fjeldsa, Jon, Orlando, Ludovic, Barker, F Keith, Jønsson, Knud Andreas, Johnson, Warren, Koepfli, Klaus-Peter, O'Brien, Stephen, Haussler, David, Ryder, Oliver A, Rahbek, Carsten, Willerslev, Eske, Graves, Gary R, Glenn, Travis C, McCormack, John, Burt, Dave, Ellegren, Hans, Alström, Per, Edwards, Scott V, Stamatakis, Alexandros, Mindell, David P, and Cracraft, Joel

Subjects
Human Genome, Genetics, Animals, Avian Proteins, Base Sequence, Biological Evolution, Birds, DNA Transposable Elements, Genes, Genetic Speciation, Genome, INDEL Mutation, Introns, Phylogeny, Sequence Analysis, DNA, General Science & Technology
Abstract

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

Published
2014

44. The complete mitochondrial genome of Meller's mongoose (Rhynchogale melleri).

Author

Sosale, Medhini S., Roelke-Parker, Melody, Machange, Gradson A., Edwards, Cody W., Figueiró, Henrique V., and Koepfli, Klaus-Peter

Subjects
MITOCHONDRIAL DNA, MONGOOSES, MAMMALS, GENOMES, CARNIVORA, SAVANNAS
Abstract

Meller's mongoose (Rhynchogale melleri) is a member of the family Herpestidae (Mammalia: Carnivora) and the sole species in the genus Rhynchogale. It is primarily found in savannas and open woodlands of eastern sub-Saharan Africa. Here, we report the first complete mitochondrial genome for a female Meller's mongoose collected in Tanzania, generated using a genome-skimming approach. The mitogenome had a final length of 16,644 bp and a total of 37 annotated genes. Phylogenetic analysis validated the placement of this species in the herpestid subfamily Herpestinae. Ultimately, the outcomes of this research offer a genetic foundation for future studies of Meller's mongoose. [ABSTRACT FROM AUTHOR]

Published
2024
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45. Gut bacterial composition shows sex-specific shifts during breeding season in ex situ managed black-footed ferrets

Author

DeCandia, Alexandra L, primary, Adeduro, Laura, additional, Thacher, Piper, additional, Crosier, Adrienne, additional, Marinari, Paul, additional, Bortner, Robyn, additional, Garelle, Della, additional, Livieri, Travis, additional, Santymire, Rachel, additional, Comizzoli, Pierre, additional, Maslanka, Michael, additional, Maldonado, Jesús E, additional, Koepfli, Klaus-Peter, additional, Muletz-Wolz, Carly, additional, and Bornbusch, Sally L, additional

Published
2023
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47. The gut microbiomes of Channel Island foxes and island spotted skunks exhibit fine-scale differentiation across host species and island populations

Author

Boychuck, Samantha Pasciullo, primary, Brenner, Lara, additional, Gagorik, Calypso, additional, Schamel, Juliann, additional, Baker, Stacy, additional, Tran, Elton, additional, vonHoldt, Bridgett, additional, Koepfli, Klaus-Peter, additional, Maldonado, Jesús, additional, and DeCandia, Alexandra, additional

Published
2023
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48. 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

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