51
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Suzuki IK. Molecular drivers of human cerebral cortical evolution. Neurosci Res 2019; 151:1-14. [PMID: 31175883 DOI: 10.1016/j.neures.2019.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 01/10/2023]
Abstract
One of the most important questions in human evolutionary biology is how our ancestor has acquired an expanded volume of the cerebral cortex, which may have significantly impacted on improving our cognitive abilities. Recent comparative approaches have identified developmental features unique to the human or hominid cerebral cortex, not shared with other animals including conventional experimental models. In addition, genomic, transcriptomic, and epigenomic signatures associated with human- or hominid-specific processes of the cortical development are becoming identified by virtue of technical progress in the deep nucleotide sequencing. This review discusses ontogenic and phylogenetic processes of the human cerebral cortex, followed by the introduction of recent comprehensive approaches identifying molecular mechanisms potentially driving the evolutionary changes in the cortical development.
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Affiliation(s)
- Ikuo K Suzuki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan; VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences, Leuven Brain Institute, KULeuven, 3000 Leuven, Belgium; Université Libre de Bruxelles (U.L.B.), Institut de Recherches en Biologie Humaine et Moléculaire (IRIBHM), ULB Neuroscience Institute (UNI), 1070 Brussels, Belgium.
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52
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Abstract
Human brain organoids, generated from pluripotent stem cells, have emerged as a promising technique for modeling early stages of human neurodevelopment in controlled laboratory conditions. Although the applications for disease modeling in a dish have become routine, the use of these brain organoids as evolutionary tools is only now getting momentum. Here, we will review the current state of the art on the use of brain organoids from different species and the molecular and cellular insights generated from these studies. Besides, we will discuss how this model might be beneficial for human health and the limitations and future perspectives of this technology.
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Affiliation(s)
- Alysson R. Muotri
- Department of Pediatrics/Rady Children's Hospital San Diego, University of California San Diego, School of Medicine, La Jolla, CA, USA
- Department of Cellular & Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
- UCSD Stem Cell Programme, University of California San Diego, School of Medicine, La Jolla, CA, USA
- Center for Academic Research and Training in Anthropogeny (CARTA), La Jolla, CA, USA
- Kavli Institute for Brain and Mind, University of California San Diego, School of Medicine, La Jolla, CA, USA
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53
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Rubenstein DR, Ågren JA, Carbone L, Elde NC, Hoekstra HE, Kapheim KM, Keller L, Moreau CS, Toth AL, Yeaman S, Hofmann HA. Coevolution of Genome Architecture and Social Behavior. Trends Ecol Evol 2019; 34:844-855. [PMID: 31130318 DOI: 10.1016/j.tree.2019.04.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/03/2019] [Accepted: 04/17/2019] [Indexed: 01/02/2023]
Abstract
Although social behavior can have a strong genetic component, it can also result in selection on genome structure and function, thereby influencing the evolution of the genome itself. Here we explore the bidirectional links between social behavior and genome architecture by considering variation in social and/or mating behavior among populations (social polymorphisms) and across closely related species. We propose that social behavior can influence genome architecture via associated demographic changes due to social living. We establish guidelines to exploit emerging whole-genome sequences using analytical approaches that examine genome structure and function at different levels (regulatory vs structural variation) from the perspective of both molecular biology and population genetics in an ecological context.
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Affiliation(s)
- Dustin R Rubenstein
- Columbia University, Department of Ecology, Evolution, and Environmental Biology and Center for Integrative Animal Behavior, New York, NY 10027, USA.
| | - J Arvid Ågren
- Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, MA 02138, USA
| | - Lucia Carbone
- Oregon Health & Science University, Department of Medicine, KCVI, Portland, OR 97239, USA; Oregon National Primate Research Center, Division of Genetics, Beaverton, OR 97006, USA
| | - Nels C Elde
- University of Utah School of Medicine, Department of Human Genetics, Salt Lake City, UT 84112, USA
| | - Hopi E Hoekstra
- Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, MA 02138, USA; Harvard University, Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Cambridge, MA 02138, USA
| | - Karen M Kapheim
- Utah State University, Department of Biology, Logan, UT 84322, USA
| | - Laurent Keller
- University of Lausanne, Department of Ecology and Evolution, Biophore, UNIL, 1015 Lausanne, Switzerland
| | - Corrie S Moreau
- Cornell University, Departments of Entomology and Ecology and Evolutionary Biology, Ithaca, NY 14850, USA
| | - Amy L Toth
- Iowa State University, Department of Ecology, Evolution, and Organismal Biology and Department of Entomology, Ames, IA 50011, USA
| | - Sam Yeaman
- University of Calgary, Department of Biological Sciences, Calgary, AB T2N 1N4, Canada
| | - Hans A Hofmann
- The University of Texas at Austin, Department of Integrative Biology and Institute for Cellular and Molecular Biology, 2415 Speedway C-0990, Austin, TX 78712, USA.
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54
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Kahveci F, Alkan C. Whole-Genome Shotgun Sequence CNV Detection Using Read Depth. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2019; 1833:61-72. [PMID: 30039363 DOI: 10.1007/978-1-4939-8666-8_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
With the developments in high-throughput sequencing (HTS) technologies, researchers have gained a powerful tool to identify structural variants (SVs) in genomes with substantially less cost than before. SVs can be broadly classified into two main categories: balanced rearrangements and copy number variations (CNVs). Many algorithms have been developed to characterize CNVs using HTS data, with focus on different types and size range of variants using different read signatures. Read depth (RD) based tools are more common in characterizing large (>10 kb) CNVs since RD strategy does not rely on the fragment size and read length, which are limiting factors in read pair and split read analysis. Here we provide a guideline for a user friendly tool for detecting large segmental duplications and deletions that can also predict integer copy numbers for duplicated genes.
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Affiliation(s)
- Fatma Kahveci
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - Can Alkan
- Department of Computer Engineering, Bilkent University, Ankara, Turkey.
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55
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Huynh L, Hormozdiari F. TAD fusion score: discovery and ranking the contribution of deletions to genome structure. Genome Biol 2019; 20:60. [PMID: 30898144 PMCID: PMC6427865 DOI: 10.1186/s13059-019-1666-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 03/01/2019] [Indexed: 11/17/2022] Open
Abstract
Deletions that fuse two adjacent topologically associating domains (TADs) can cause severe developmental disorders. We provide a formal method to quantify deletions based on their potential disruption of the three-dimensional genome structure, denoted as the TAD fusion score. Furthermore, we show that deletions that cause TAD fusion are rare and under negative selection in the general population. Finally, we show that our method correctly gives higher scores to deletions reported to cause various disorders, including developmental disorders and cancer, in comparison to the deletions reported in the 1000 Genomes Project. The TAD fusion score tool is publicly available at https://github.com/HormozdiariLab/TAD-fusion-score .
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Affiliation(s)
| | - Fereydoun Hormozdiari
- Genome Center, UC Davis, Davis, USA.
- UC Davis MIND Institute, Sacramento, USA.
- Department of Biochemistry and Molecular Medicine, UC Davis, Sacramento, USA.
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56
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Maggiolini FAM, Cantsilieris S, D’Addabbo P, Manganelli M, Coe BP, Dumont BL, Sanders AD, Pang AWC, Vollger MR, Palumbo O, Palumbo P, Accadia M, Carella M, Eichler EE, Antonacci F. Genomic inversions and GOLGA core duplicons underlie disease instability at the 15q25 locus. PLoS Genet 2019; 15:e1008075. [PMID: 30917130 PMCID: PMC6436712 DOI: 10.1371/journal.pgen.1008075] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/07/2019] [Indexed: 11/19/2022] Open
Abstract
Human chromosome 15q25 is involved in several disease-associated structural rearrangements, including microdeletions and chromosomal markers with inverted duplications. Using comparative fluorescence in situ hybridization, strand-sequencing, single-molecule, real-time sequencing and Bionano optical mapping analyses, we investigated the organization of the 15q25 region in human and nonhuman primates. We found that two independent inversions occurred in this region after the fission event that gave rise to phylogenetic chromosomes XIV and XV in humans and great apes. One of these inversions is still polymorphic in the human population today and may confer differential susceptibility to 15q25 microdeletions and inverted duplications. The inversion breakpoints map within segmental duplications containing core duplicons of the GOLGA gene family and correspond to the site of an ancestral centromere, which became inactivated about 25 million years ago. The inactivation of this centromere likely released segmental duplications from recombination repression typical of centromeric regions. We hypothesize that this increased the frequency of ectopic recombination creating a hotspot of hominid inversions where dispersed GOLGA core elements now predispose this region to recurrent genomic rearrangements associated with disease.
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Affiliation(s)
| | - Stuart Cantsilieris
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Pietro D’Addabbo
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Michele Manganelli
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Bradley P. Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Beth L. Dumont
- The Jackson Laboratory, Bar Harbor, ME, United States of America
| | - Ashley D. Sanders
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, Heidelberg, Germany
| | | | - Mitchell R. Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Orazio Palumbo
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Pietro Palumbo
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Maria Accadia
- Medical Genetics Service, Hospital “Cardinale G. Panico”, Via San Pio X n°4, Tricase, LE, Italy
| | - Massimo Carella
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, United States of America
| | - Francesca Antonacci
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
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57
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Pollen AA, Bhaduri A, Andrews MG, Nowakowski TJ, Meyerson OS, Mostajo-Radji MA, Di Lullo E, Alvarado B, Bedolli M, Dougherty ML, Fiddes IT, Kronenberg ZN, Shuga J, Leyrat AA, West JA, Bershteyn M, Lowe CB, Pavlovic BJ, Salama SR, Haussler D, Eichler EE, Kriegstein AR. Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution. Cell 2019; 176:743-756.e17. [PMID: 30735633 PMCID: PMC6544371 DOI: 10.1016/j.cell.2019.01.017] [Citation(s) in RCA: 339] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 10/22/2018] [Accepted: 01/04/2019] [Indexed: 12/22/2022]
Abstract
Direct comparisons of human and non-human primate brains can reveal molecular pathways underlying remarkable specializations of the human brain. However, chimpanzee tissue is inaccessible during neocortical neurogenesis when differences in brain size first appear. To identify human-specific features of cortical development, we leveraged recent innovations that permit generating pluripotent stem cell-derived cerebral organoids from chimpanzee. Despite metabolic differences, organoid models preserve gene regulatory networks related to primary cell types and developmental processes. We further identified 261 differentially expressed genes in human compared to both chimpanzee organoids and macaque cortex, enriched for recent gene duplications, and including multiple regulators of PI3K-AKT-mTOR signaling. We observed increased activation of this pathway in human radial glia, dependent on two receptors upregulated specifically in human: INSR and ITGB8. Our findings establish a platform for systematic analysis of molecular changes contributing to human brain development and evolution.
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Affiliation(s)
- Alex A Pollen
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA.
| | - Aparna Bhaduri
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA
| | - Madeline G Andrews
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA
| | - Tomasz J Nowakowski
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; Department of Anatomy, UCSF, San Francisco, CA, USA
| | - Olivia S Meyerson
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA
| | - Mohammed A Mostajo-Radji
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA
| | - Elizabeth Di Lullo
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA
| | - Beatriz Alvarado
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA
| | - Melanie Bedolli
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA
| | - Max L Dougherty
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ian T Fiddes
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Zev N Kronenberg
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Joe Shuga
- New Technologies, Fluidigm, South San Francisco, CA, USA
| | - Anne A Leyrat
- New Technologies, Fluidigm, South San Francisco, CA, USA
| | - Jay A West
- New Technologies, Fluidigm, South San Francisco, CA, USA
| | - Marina Bershteyn
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA
| | - Craig B Lowe
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Bryan J Pavlovic
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA
| | - Sofie R Salama
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - David Haussler
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA; Howard Hughes Medical Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Arnold R Kriegstein
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA.
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58
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Abstract
Noncoding DNA sequences play crucial roles in gene regulation, including via three-dimensional genome organization where they define chromatin boundaries and segment the genome into a sequence of insulated neighborhoods. However, the relative importance of noncoding DNA elements, particularly in comparison with protein-coding DNA sequences, remains more poorly characterized. Here, we systematically test if chromatin boundary disruptions are under purifying selection. Our analyses uncover a genomewide depletion of structural variants that would have the potential to alter chromatin structure. This in turn has implications for predicting not only which variants are likely pathogenic in clinical genetics settings, but also which are likely key innovations in primate evolution, and argues for expanding the current gene-centric paradigm for interpreting structural variants. The potential impact of structural variants includes not only the duplication or deletion of coding sequences, but also the perturbation of noncoding DNA regulatory elements and structural chromatin features, including topological domains (TADs). Structural variants disrupting TAD boundaries have been implicated both in cancer and developmental disease; this likely occurs via “enhancer hijacking,” whereby removal of the TAD boundary exposes enhancers to new target transcription start sites (TSSs). With this functional role, we hypothesized that boundaries would display evidence for negative selection. Here we demonstrate that the chromatin landscape constrains structural variation both within healthy humans and across primate evolution. In contrast, in patients with developmental delay, variants occur remarkably uniformly across genomic features, suggesting a potentially broad role for enhancer hijacking in human disease.
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59
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Tucci S, Vohr SH, McCoy RC, Vernot B, Robinson MR, Barbieri C, Nelson BJ, Fu W, Purnomo GA, Sudoyo H, Eichler EE, Barbujani G, Visscher PM, Akey JM, Green RE. Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science 2018; 361:511-516. [PMID: 30072539 DOI: 10.1126/science.aar8486] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 06/22/2018] [Indexed: 12/21/2022]
Abstract
Flores Island, Indonesia, was inhabited by the small-bodied hominin species Homo floresiensis, which has an unknown evolutionary relationship to modern humans. This island is also home to an extant human pygmy population. Here we describe genome-scale single-nucleotide polymorphism data and whole-genome sequences from a contemporary human pygmy population living on Flores near the cave where H. floresiensis was found. The genomes of Flores pygmies reveal a complex history of admixture with Denisovans and Neanderthals but no evidence for gene flow with other archaic hominins. Modern individuals bear the signatures of recent positive selection encompassing the FADS (fatty acid desaturase) gene cluster, likely related to diet, and polygenic selection acting on standing variation that contributed to their short-stature phenotype. Thus, multiple independent instances of hominin insular dwarfism occurred on Flores.
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Affiliation(s)
- Serena Tucci
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Lewis-Sigler Institute, Princeton University, Princeton, NJ, USA.,Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy
| | - Samuel H Vohr
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Rajiv C McCoy
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Lewis-Sigler Institute, Princeton University, Princeton, NJ, USA
| | - Benjamin Vernot
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthew R Robinson
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Génopode, Quatier Sorge, Lausanne, Switzerland
| | - Chiara Barbieri
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland
| | - Brad J Nelson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Wenqing Fu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Gludhug A Purnomo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.,Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Guido Barbujani
- Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Joshua M Akey
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA. .,Lewis-Sigler Institute, Princeton University, Princeton, NJ, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA.
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60
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Numanagić I, Gökkaya AS, Zhang L, Berger B, Alkan C, Hach F. Fast characterization of segmental duplications in genome assemblies. Bioinformatics 2018; 34:i706-i714. [PMID: 30423092 PMCID: PMC6129265 DOI: 10.1093/bioinformatics/bty586] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Motivation Segmental duplications (SDs) or low-copy repeats, are segments of DNA > 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common cause of genomic structural variation and several are associated with diseases of genomic origin including schizophrenia and autism. Despite their functional importance, SDs present one of the major hurdles for de novo genome assembly due to the ambiguity they cause in building and traversing both state-of-the-art overlap-layout-consensus and de Bruijn graphs. This causes SD regions to be misassembled, collapsed into a unique representation, or completely missing from assembled reference genomes for various organisms. In turn, this missing or incorrect information limits our ability to fully understand the evolution and the architecture of the genomes. Despite the essential need to accurately characterize SDs in assemblies, there has been only one tool that was developed for this purpose, called Whole-Genome Assembly Comparison (WGAC); its primary goal is SD detection. WGAC is comprised of several steps that employ different tools and custom scripts, which makes this strategy difficult and time consuming to use. Thus there is still a need for algorithms to characterize within-assembly SDs quickly, accurately, and in a user friendly manner. Results Here we introduce SEgmental Duplication Evaluation Framework (SEDEF) to rapidly detect SDs through sophisticated filtering strategies based on Jaccard similarity and local chaining. We show that SEDEF accurately detects SDs while maintaining substantial speed up over WGAC that translates into practical run times of minutes instead of weeks. Notably, our algorithm captures up to 25% 'pairwise error' between segments, whereas previous studies focused on only 10%, allowing us to more deeply track the evolutionary history of the genome. Availability and implementation SEDEF is available at https://github.com/vpc-ccg/sedef.
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Affiliation(s)
- Ibrahim Numanagić
- Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alim S Gökkaya
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - Lillian Zhang
- Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Can Alkan
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - Faraz Hach
- Vancouver Prostate Centre, Vancouver, Canada
- Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
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61
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Pendleton AL, Shen F, Taravella AM, Emery S, Veeramah KR, Boyko AR, Kidd JM. Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication. BMC Biol 2018; 16:64. [PMID: 29950181 PMCID: PMC6022502 DOI: 10.1186/s12915-018-0535-2] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/23/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Domesticated from gray wolves between 10 and 40 kya in Eurasia, dogs display a vast array of phenotypes that differ from their ancestors, yet mirror other domesticated animal species, a phenomenon known as the domestication syndrome. Here, we use signatures persisting in dog genomes to identify genes and pathways possibly altered by the selective pressures of domestication. RESULTS Whole-genome SNP analyses of 43 globally distributed village dogs and 10 wolves differentiated signatures resulting from domestication rather than breed formation. We identified 246 candidate domestication regions containing 10.8 Mb of genome sequence and 429 genes. The regions share haplotypes with ancient dogs, suggesting that the detected signals are not the result of recent selection. Gene enrichments highlight numerous genes linked to neural crest and central nervous system development as well as neurological function. Read depth analysis suggests that copy number variation played a minor role in dog domestication. CONCLUSIONS Our results identify genes that act early in embryogenesis and can confer phenotypes distinguishing domesticated dogs from wolves, such as tameness, smaller jaws, floppy ears, and diminished craniofacial development as the targets of selection during domestication. These differences reflect the phenotypes of the domestication syndrome, which can be explained by alterations in the migration or activity of neural crest cells during development. We propose that initial selection during early dog domestication was for behavior, a trait influenced by genes which act in the neural crest, which secondarily gave rise to the phenotypes of modern dogs.
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Affiliation(s)
- Amanda L Pendleton
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Feichen Shen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Angela M Taravella
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sarah Emery
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Adam R Boyko
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, 14853, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.
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62
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The chromatin basis of neurodevelopmental disorders: Rethinking dysfunction along the molecular and temporal axes. Prog Neuropsychopharmacol Biol Psychiatry 2018; 84:306-327. [PMID: 29309830 DOI: 10.1016/j.pnpbp.2017.12.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 12/19/2017] [Accepted: 12/24/2017] [Indexed: 12/13/2022]
Abstract
The complexity of the human brain emerges from a long and finely tuned developmental process orchestrated by the crosstalk between genome and environment. Vis à vis other species, the human brain displays unique functional and morphological features that result from this extensive developmental process that is, unsurprisingly, highly vulnerable to both genetically and environmentally induced alterations. One of the most striking outcomes of the recent surge of sequencing-based studies on neurodevelopmental disorders (NDDs) is the emergence of chromatin regulation as one of the two domains most affected by causative mutations or Copy Number Variations besides synaptic function, whose involvement had been largely predicted for obvious reasons. These observations place chromatin dysfunction at the top of the molecular pathways hierarchy that ushers in a sizeable proportion of NDDs and that manifest themselves through synaptic dysfunction and recurrent systemic clinical manifestation. Here we undertake a conceptual investigation of chromatin dysfunction in NDDs with the aim of systematizing the available evidence in a new framework: first, we tease out the developmental vulnerabilities in human corticogenesis as a structuring entry point into the causation of NDDs; second, we provide a much needed clarification of the multiple meanings and explanatory frameworks revolving around "epigenetics", highlighting those that are most relevant for the analysis of these disorders; finally we go in-depth into paradigmatic examples of NDD-causing chromatin dysregulation, with a special focus on human experimental models and datasets.
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63
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Catacchio CR, Maggiolini FAM, D'Addabbo P, Bitonto M, Capozzi O, Lepore Signorile M, Miroballo M, Archidiacono N, Eichler EE, Ventura M, Antonacci F. Inversion variants in human and primate genomes. Genome Res 2018; 28:910-920. [PMID: 29776991 PMCID: PMC5991517 DOI: 10.1101/gr.234831.118] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/26/2018] [Indexed: 02/06/2023]
Abstract
For many years, inversions have been proposed to be a direct driving force in speciation since they suppress recombination when heterozygous. Inversions are the most common large-scale differences among humans and great apes. Nevertheless, they represent large events easily distinguishable by classical cytogenetics, whose resolution, however, is limited. Here, we performed a genome-wide comparison between human, great ape, and macaque genomes using the net alignments for the most recent releases of genome assemblies. We identified a total of 156 putative inversions, between 103 kb and 91 Mb, corresponding to 136 human loci. Combining literature, sequence, and experimental analyses, we analyzed 109 of these loci and found 67 regions inverted in one or multiple primates, including 28 newly identified inversions. These events overlap with 81 human genes at their breakpoints, and seven correspond to sites of recurrent rearrangements associated with human disease. This work doubles the number of validated primate inversions larger than 100 kb, beyond what was previously documented. We identified 74 sites of errors, where the sequence has been assembled in the wrong orientation, in the reference genomes analyzed. Our data serve two purposes: First, we generated a map of evolutionary inversions in these genomes representing a resource for interrogating differences among these species at a functional level; second, we provide a list of misassembled regions in these primate genomes, involving over 300 Mb of DNA and 1978 human genes. Accurately annotating these regions in the genome references has immediate applications for evolutionary and biomedical studies on primates.
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Affiliation(s)
| | | | - Pietro D'Addabbo
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
| | - Miriana Bitonto
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
| | - Oronzo Capozzi
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
| | | | - Mattia Miroballo
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
| | | | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| | - Mario Ventura
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
| | - Francesca Antonacci
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
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64
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Elhaik E, Yusuf L, Anderson AIJ, Pirooznia M, Arnellos D, Vilshansky G, Ercal G, Lu Y, Webster T, Baird ML, Esposito U. The Diversity of REcent and Ancient huMan (DREAM): A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine. Genome Biol Evol 2018; 9:3225-3237. [PMID: 29165562 PMCID: PMC5726468 DOI: 10.1093/gbe/evx237] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2017] [Indexed: 12/11/2022] Open
Abstract
The human population displays wide variety in demographic history, ancestry, content of DNA derived from hominins or ancient populations, adaptation, traits, copy number variation, drug response, and more. These polymorphisms are of broad interest to population geneticists, forensics investigators, and medical professionals. Historically, much of that knowledge was gained from population survey projects. Although many commercial arrays exist for genome-wide single-nucleotide polymorphism genotyping, their design specifications are limited and they do not allow a full exploration of biodiversity. We thereby aimed to design the Diversity of REcent and Ancient huMan (DREAM)—an all-inclusive microarray that would allow both identification of known associations and exploration of standing questions in genetic anthropology, forensics, and personalized medicine. DREAM includes probes to interrogate ancestry informative markers obtained from over 450 human populations, over 200 ancient genomes, and 10 archaic hominins. DREAM can identify 94% and 61% of all known Y and mitochondrial haplogroups, respectively, and was vetted to avoid interrogation of clinically relevant markers. To demonstrate its capabilities, we compared its FST distributions with those of the 1000 Genomes Project and commercial arrays. Although all arrays yielded similarly shaped (inverse J) FST distributions, DREAM’s autosomal and X-chromosomal distributions had the highest mean FST, attesting to its ability to discern subpopulations. DREAM performances are further illustrated in biogeographical, identical by descent, and copy number variation analyses. In summary, with approximately 800,000 markers spanning nearly 2,000 genes, DREAM is a useful tool for genetic anthropology, forensic, and personalized medicine studies.
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Affiliation(s)
- Eran Elhaik
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom
| | - Leeban Yusuf
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom
| | | | - Mehdi Pirooznia
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University
| | - Dimitrios Arnellos
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom.,Department of Biology, Lund University, Sweden
| | | | - Gunes Ercal
- Department of Computer Science, Southern Illinois University Edwardsville
| | - Yontao Lu
- Thermo Fisher Scientific, Santa Clara, California
| | | | | | - Umberto Esposito
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom
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65
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Janiak MC. No Evidence of Copy Number Variation in Acidic Mammalian Chitinase Genes (CHIA) in New World and Old World Monkeys. INT J PRIMATOL 2018. [DOI: 10.1007/s10764-018-0037-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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66
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Abstract
The noncoding portion of the genome, including microRNAs, has been fertile evolutionary soil for cortical development in primates. A major contribution to cortical expansion in primates is the generation of novel precursor cell populations. Because miRNA expression profiles track closely with cell identity, it is likely that numerous novel microRNAs have contributed to cellular diversity in the brain. The tools to determine the genomic context within which novel microRNAs emerge and how they become integrated into molecular circuitry are now in hand.
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Affiliation(s)
- Kenneth S Kosik
- Neuroscience Research Institute and Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106, USA;
| | - Tomasz Nowakowski
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, California 94143, USA.,Department of Anatomy, University of California, San Francisco, California 94158, USA
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67
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Byrne G, Ahmad-Villiers S, Du Z, McGregor C. B4GALNT2 and xenotransplantation: A newly appreciated xenogeneic antigen. Xenotransplantation 2018; 25:e12394. [PMID: 29604134 PMCID: PMC6158069 DOI: 10.1111/xen.12394] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 03/08/2018] [Accepted: 03/13/2018] [Indexed: 12/20/2022]
Abstract
Analysis of non‐Gal antibody induced after pig‐to‐baboon cardiac xenotransplantation identified the glycan produced by porcine beta‐1,4‐N‐acetyl‐galactosaminyltransferase 2 (B4GALNT2) as an immunogenic xenotransplantation antigen. The porcine B4GALNT2 enzyme is homologous to the human enzyme, which synthesizes the human SDa blood group antigen. Most humans produce low levels of anti‐SDa IgM which polyagglutinates red blood cells from rare individuals with high levels of SDa expression. The SDa glycan is also present on GM2 gangliosides. Clinical GM2 vaccination studies for melanoma patients suggest that a human antibody response to SDa can be induced. Expression of porcine B4GALNT2 in human HEK293 cells results in increased binding of anti‐SDa antibody and increased binding of Dolichos biflorus agglutinin (DBA), a lectin commonly used to detect SDa. In pigs, B4GALNT2 is expressed by vascular endothelial cells and endothelial cells from a wide variety of pig backgrounds stain with DBA, suggesting that porcine vascular expression of B4GALNT2 is not polymorphic. Mutations in B4GALNT2 have been engineered in mice and pigs. In both species, the B4GALNT2‐KO animals are apparently normal and no longer show evidence of SDa antigen expression. Pig tissues with a mutation in B4GALNT2, added to a background of alpha‐1,3‐galactosyltransferase deficient (GGTA1‐KO) and cytidine monophosphate‐N‐acetylneuraminic acid hydroxylase deficient (CMAH‐KO), show reduced antibody binding, confirming the presence of B4GALNT2‐dependent antibodies in both humans and non‐human primates. Preclinical xenotransplantation using B4GALNT2‐deficient donors has recently been reported. Elimination of this source of immunogenic pig antigen should minimize acute injury by preformed anti‐pig antibody and eliminate an induced clinical immune response to this newly appreciated xenotransplantation antigen.
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Affiliation(s)
- Guerard Byrne
- Institute of Cardiovascular Science, University College London, London, UK.,Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | | | - Zeji Du
- Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Christopher McGregor
- Institute of Cardiovascular Science, University College London, London, UK.,Department of Surgery, Mayo Clinic, Rochester, MN, USA
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68
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Levchenko A, Kanapin A, Samsonova A, Gainetdinov RR. Human Accelerated Regions and Other Human-Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development. Genome Biol Evol 2018; 10:166-188. [PMID: 29149249 PMCID: PMC5767953 DOI: 10.1093/gbe/evx240] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2017] [Indexed: 12/24/2022] Open
Abstract
The review discusses, in a format of a timeline, the studies of different types of genetic variants, present in Homo sapiens, but absent in all other primate, mammalian, or vertebrate species, tested so far. The main characteristic of these variants is that they are found in regions of high evolutionary conservation. These sequence variations include single nucleotide substitutions (called human accelerated regions), deletions, and segmental duplications. The rationale for finding such variations in the human genome is that they could be responsible for traits, specific to our species, of which the human brain is the most remarkable. As became obvious, the vast majority of human-specific single nucleotide substitutions are found in noncoding, likely regulatory regions. A number of genes, associated with these human-specific alleles, often through novel enhancer activity, were in fact shown to be implicated in human-specific development of certain brain areas, including the prefrontal cortex. Human-specific deletions may remove regulatory sequences, such as enhancers. Segmental duplications, because of their large size, create new coding sequences, like new functional paralogs. Further functional study of these variants will shed light on evolution of our species, as well as on the etiology of neurodevelopmental disorders.
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Affiliation(s)
- Anastasia Levchenko
- Institute of Translational Biomedicine, Saint Petersburg State University, Russia
| | - Alexander Kanapin
- Institute of Translational Biomedicine, Saint Petersburg State University, Russia
- Department of Oncology, University of Oxford, United Kingdom
| | - Anastasia Samsonova
- Institute of Translational Biomedicine, Saint Petersburg State University, Russia
- Department of Oncology, University of Oxford, United Kingdom
| | - Raul R Gainetdinov
- Institute of Translational Biomedicine, Saint Petersburg State University, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, Russia
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69
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Abstract
Humans are a remarkable species, especially because of the remarkable properties of their brain. Since the split from the chimpanzee lineage, the human brain has increased three-fold in size and has acquired abilities for vocal learning, language and intense cooperation. To better understand the molecular basis of these changes is of great biological and biomedical interest. However, all the about 16 million fixed genetic changes that occurred during human evolution are fully correlated with all molecular, cellular, anatomical and behavioral changes that occurred during this time. Hence, as humans and chimpanzees cannot be crossed or genetically manipulated, no direct evidence for linking particular genetic and molecular changes to human brain evolution can be obtained. Here, I sketch a framework how indirect evidence can be obtained and review findings related to the molecular basis of human cognition, vocal learning and brain size. In particular, I discuss how a comprehensive comparative approach, leveraging cellular systems and genomic technologies, could inform the evolution of our brain in the future.
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Affiliation(s)
- Wolfgang Enard
- Department of Biology II, Ludwig Maximilian University Munich, Grosshaderner Str. 2, D-82152 Martinsried, Germany.
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70
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Serres-Armero A, Povolotskaya IS, Quilez J, Ramirez O, Santpere G, Kuderna LFK, Hernandez-Rodriguez J, Fernandez-Callejo M, Gomez-Sanchez D, Freedman AH, Fan Z, Novembre J, Navarro A, Boyko A, Wayne R, Vilà C, Lorente-Galdos B, Marques-Bonet T. Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing. BMC Genomics 2017; 18:977. [PMID: 29258433 PMCID: PMC5735816 DOI: 10.1186/s12864-017-4318-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 11/17/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Whole genome re-sequencing data from dogs and wolves are now commonly used to study how natural and artificial selection have shaped the patterns of genetic diversity. Single nucleotide polymorphisms, microsatellites and variants in mitochondrial DNA have been interrogated for links to specific phenotypes or signals of domestication. However, copy number variation (CNV), despite its increasingly recognized importance as a contributor to phenotypic diversity, has not been extensively explored in canids. RESULTS Here, we develop a new accurate probabilistic framework to create fine-scale genomic maps of segmental duplications (SDs), compare patterns of CNV across groups and investigate their role in the evolution of the domestic dog by using information from 34 canine genomes. Our analyses show that duplicated regions are enriched in genes and hence likely possess functional importance. We identify 86 loci with large CNV differences between dogs and wolves, enriched in genes responsible for sensory perception, immune response, metabolic processes, etc. In striking contrast to the observed loss of nucleotide diversity in domestic dogs following the population bottlenecks that occurred during domestication and breed creation, we find a similar proportion of CNV loci in dogs and wolves, suggesting that other dynamics are acting to particularly select for CNVs with potentially functional impacts. CONCLUSIONS This work is the first comparison of genome wide CNV patterns in domestic and wild canids using whole-genome sequencing data and our findings contribute to study the impact of novel kinds of genetic changes on the evolution of the domestic dog.
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Affiliation(s)
- Aitor Serres-Armero
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Inna S Povolotskaya
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Javier Quilez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Oscar Ramirez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,Vetgenomics, 08193, Barcelona, Spain
| | - Gabriel Santpere
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Lukas F K Kuderna
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Jessica Hernandez-Rodriguez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Marcos Fernandez-Callejo
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Daniel Gomez-Sanchez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Adam H Freedman
- UCLA, Department of Ecology and Evolutionary Biology, Los Angeles, CA, 90095, USA
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - John Novembre
- UCLA, Department of Ecology and Evolutionary Biology, Los Angeles, CA, 90095, USA
| | - Arcadi Navarro
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Catalonia, Spain
| | - Adam Boyko
- Cornell University, Department of Biological Statistics and Computational Biology, New York, NY, 14853, USA
| | - Robert Wayne
- UCLA, Department of Ecology and Evolutionary Biology, Los Angeles, CA, 90095, USA
| | - Carles Vilà
- Estación Biológica de Doñana EBD-CSIC, Department of Integrative Ecology, 41092, Sevilla, Spain
| | - Belen Lorente-Galdos
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain. .,Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.
| | - Tomas Marques-Bonet
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain. .,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Catalonia, Spain.
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71
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Solis-Moruno M, de Manuel M, Hernandez-Rodriguez J, Fontsere C, Gomara-Castaño A, Valsera-Naranjo C, Crailsheim D, Navarro A, Llorente M, Riera L, Feliu-Olleta O, Marques-Bonet T. Potential damaging mutation in LRP5 from genome sequencing of the first reported chimpanzee with the Chiari malformation. Sci Rep 2017; 7:15224. [PMID: 29123202 PMCID: PMC5680330 DOI: 10.1038/s41598-017-15544-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/30/2017] [Indexed: 12/29/2022] Open
Abstract
The genus Pan is the closest related to humans (Homo sapiens) and it includes two species: Pan troglodytes (chimpanzees) and Pan paniscus (bonobos). Different characteristics, some of biomedical aspect, separate them from us. For instance, some common human medical conditions are rare in chimpanzees (menopause, Alzheimer disease) although it is unclear to which extent longevity plays an active role in these differences. However, both humans and chimpanzees present similar pathologies, thus, understanding traits in chimpanzees can help unravel the molecular basis of human conditions. Here, we sequenced the genome of Nico, a central chimpanzee diagnosed with a particular biomedical condition, the Chiari malformation. We performed a variant calling analysis comparing his genome to 25 whole genomes from healthy individuals (bonobos and chimpanzees), and after predicting the effects of the genetic variants, we looked for genes within the OMIM database. We found a novel, private, predicted as damaging mutation in Nico in LRP5, a gene related to bone density alteration pathologies, and we suggest a link between this mutation and his Chiari malformation as previously shown in humans. Our results reinforce the idea that a comparison between humans and chimpanzees can be established in this genetic frame of common diseases.
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Affiliation(s)
- Manuel Solis-Moruno
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain.
| | - Marc de Manuel
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Jessica Hernandez-Rodriguez
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Claudia Fontsere
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Alba Gomara-Castaño
- Fundació Mona, Carretera C-25, s/n, Riudellots de la Selva, 17457, Girona, Spain
| | | | - Dietmar Crailsheim
- Fundació Mona, Carretera C-25, s/n, Riudellots de la Selva, 17457, Girona, Spain
| | - Arcadi Navarro
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, Barcelona, 08010, Spain
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona, 08028, Spain
| | - Miquel Llorente
- Fundació Mona, Carretera C-25, s/n, Riudellots de la Selva, 17457, Girona, Spain
| | - Laura Riera
- Fundació Mona, Carretera C-25, s/n, Riudellots de la Selva, 17457, Girona, Spain
| | - Olga Feliu-Olleta
- Fundació Mona, Carretera C-25, s/n, Riudellots de la Selva, 17457, Girona, Spain
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain.
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, Barcelona, 08010, Spain.
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona, 08028, Spain.
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72
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Prüfer K, de Filippo C, Grote S, Mafessoni F, Korlević P, Hajdinjak M, Vernot B, Skov L, Hsieh P, Peyrégne S, Reher D, Hopfe C, Nagel S, Maricic T, Fu Q, Theunert C, Rogers R, Skoglund P, Chintalapati M, Dannemann M, Nelson BJ, Key FM, Rudan P, Kućan Ž, Gušić I, Golovanova LV, Doronichev VB, Patterson N, Reich D, Eichler EE, Slatkin M, Schierup MH, Andrés AM, Kelso J, Meyer M, Pääbo S. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science 2017; 358:655-658. [PMID: 28982794 PMCID: PMC6185897 DOI: 10.1126/science.aao1887] [Citation(s) in RCA: 310] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/27/2017] [Indexed: 12/30/2022]
Abstract
To date, the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, to ~30-fold genomic coverage. She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10 to 20% more Neandertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.
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Affiliation(s)
- Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
| | - Cesare de Filippo
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Steffi Grote
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Fabrizio Mafessoni
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Petra Korlević
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Mateja Hajdinjak
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Benjamin Vernot
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Laurits Skov
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Pinghsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Stéphane Peyrégne
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - David Reher
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Charlotte Hopfe
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Sarah Nagel
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Tomislav Maricic
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Christoph Theunert
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Rebekah Rogers
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Pontus Skoglund
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Michael Dannemann
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Felix M Key
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Pavao Rudan
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Željko Kućan
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Ivan Gušić
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | | | | | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David Reich
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Aida M Andrés
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
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73
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Abstract
What made us human? Gene expression changes clearly played a significant part in human evolution, but pinpointing the causal regulatory mutations is hard. Comparative genomics enabled the identification of human accelerated regions (HARs) and other human-specific genome sequences. The major challenge in the past decade has been to link diverged sequences to uniquely human biology. This review discusses approaches to this problem, progress made at the molecular level, and prospects for moving towards genetic causes for uniquely human biology.
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Affiliation(s)
- Lucía F Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, 94158, USA. .,Department of Epidemiology & Biostatistics, Institute for Human Genetics, Institute for Computational Health Sciences, University of California, San Francisco, CA, 94158, USA.
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74
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Astling DP, Heft IE, Jones KL, Sikela JM. High resolution measurement of DUF1220 domain copy number from whole genome sequence data. BMC Genomics 2017; 18:614. [PMID: 28807002 PMCID: PMC5556342 DOI: 10.1186/s12864-017-3976-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 07/31/2017] [Indexed: 11/10/2022] Open
Abstract
Background DUF1220 protein domains found primarily in Neuroblastoma BreakPoint Family (NBPF) genes show the greatest human lineage-specific increase in copy number of any coding region in the genome. There are 302 haploid copies of DUF1220 in hg38 (~160 of which are human-specific) and the majority of these can be divided into 6 different subtypes (referred to as clades). Copy number changes of specific DUF1220 clades have been associated in a dose-dependent manner with brain size variation (both evolutionarily and within the human population), cognitive aptitude, autism severity, and schizophrenia severity. However, no published methods can directly measure copies of DUF1220 with high accuracy and no method can distinguish between domains within a clade. Results Here we describe a novel method for measuring copies of DUF1220 domains and the NBPF genes in which they are found from whole genome sequence data. We have characterized the effect that various sequencing and alignment parameters and strategies have on the accuracy and precision of the method and defined the parameters that lead to optimal DUF1220 copy number measurement and resolution. We show that copy number estimates obtained using our read depth approach are highly correlated with those generated by ddPCR for three representative DUF1220 clades. By simulation, we demonstrate that our method provides sufficient resolution to analyze DUF1220 copy number variation at three levels: (1) DUF1220 clade copy number within individual genes and groups of genes (gene-specific clade groups) (2) genome wide DUF1220 clade copies and (3) gene copy number for DUF1220-encoding genes. Conclusions To our knowledge, this is the first method to accurately measure copies of all six DUF1220 clades and the first method to provide gene specific resolution of these clades. This allows one to discriminate among the ~300 haploid human DUF1220 copies to an extent not possible with any other method. The result is a greatly enhanced capability to analyze the role that these sequences play in human variation and disease. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3976-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David P Astling
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ilea E Heft
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Kenneth L Jones
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - James M Sikela
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA.
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75
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Sousa AMM, Meyer KA, Santpere G, Gulden FO, Sestan N. Evolution of the Human Nervous System Function, Structure, and Development. Cell 2017; 170:226-247. [PMID: 28708995 DOI: 10.1016/j.cell.2017.06.036] [Citation(s) in RCA: 237] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 04/21/2017] [Accepted: 06/22/2017] [Indexed: 12/22/2022]
Abstract
The nervous system-in particular, the brain and its cognitive abilities-is among humans' most distinctive and impressive attributes. How the nervous system has changed in the human lineage and how it differs from that of closely related primates is not well understood. Here, we consider recent comparative analyses of extant species that are uncovering new evidence for evolutionary changes in the size and the number of neurons in the human nervous system, as well as the cellular and molecular reorganization of its neural circuits. We also discuss the developmental mechanisms and underlying genetic and molecular changes that generate these structural and functional differences. As relevant new information and tools materialize at an unprecedented pace, the field is now ripe for systematic and functionally relevant studies of the development and evolution of human nervous system specializations.
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Affiliation(s)
- André M M Sousa
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Kyle A Meyer
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Gabriel Santpere
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Forrest O Gulden
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA; Department of Genetics, Yale School of Medicine, New Haven, CT, USA; Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA; Section of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA; Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT, USA; Yale Child Study Center, Yale School of Medicine, New Haven, CT, USA; Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA.
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76
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Ma R, Deng L, Xia Y, Wei X, Cao Y, Guo R, Zhang R, Guo J, Liang D, Wu L. A clear bias in parental origin of de novo pathogenic CNVs related to intellectual disability, developmental delay and multiple congenital anomalies. Sci Rep 2017; 7:44446. [PMID: 28322228 PMCID: PMC5359547 DOI: 10.1038/srep44446] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/08/2017] [Indexed: 12/28/2022] Open
Abstract
Copy number variation (CNV) is of great significance in human evolution and disorders. Through tracing the parent-of-origin of de novo pathogenic CNVs, we are expected to investigate the relative contributions of germline genomic stability on reproductive health. In our study, short tandem repeat (STR) and single nucleotide polymorphism (SNP) were used to determine the parent-of-origin of 87 de novo pathogenic CNVs found in unrelated patients with intellectual disability (ID), developmental delay (DD) and multiple congenital anomalies (MCA). The results shown that there was a significant difference on the distribution of the parent-of-origin for different CNVs types (Chi-square test, p = 4.914 × 10−3). An apparently paternal bias existed in deletion CNVs and a maternal bias in duplication CNVs, indicating that the relative contribution of paternal germline variations is greater than that of maternal to the origin of deletions, and vice versa to the origin of duplications. By analyzing the sequences flanking the breakpoints, we also confirmed that non-allelic homologous recombination (NAHR) served as the major mechanism for the formation of recurrent CNVs whereas non-SDs-based mechanisms played a part in generating rare non-recurrent CNVs and might relate to the paternal germline bias in deletion CNVs.
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Affiliation(s)
- Ruiyu Ma
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, P.R. China
| | - Linbei Deng
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, P.R. China
| | - Yan Xia
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, P.R. China
| | - Xianda Wei
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, P.R. China
| | - Yingxi Cao
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, P.R. China
| | - Ruolan Guo
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, P.R. China
| | - Rui Zhang
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, P.R. China
| | - Jing Guo
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, P.R. China
| | - Desheng Liang
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, P.R. China
| | - Lingqian Wu
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, P.R. China
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77
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Dougherty ML, Nuttle X, Penn O, Nelson BJ, Huddleston J, Baker C, Harshman L, Duyzend MH, Ventura M, Antonacci F, Sandstrom R, Dennis MY, Eichler EE. The birth of a human-specific neural gene by incomplete duplication and gene fusion. Genome Biol 2017; 18:49. [PMID: 28279197 PMCID: PMC5345166 DOI: 10.1186/s13059-017-1163-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/27/2017] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Gene innovation by duplication is a fundamental evolutionary process but is difficult to study in humans due to the large size, high sequence identity, and mosaic nature of segmental duplication blocks. The human-specific gene hydrocephalus-inducing 2, HYDIN2, was generated by a 364 kbp duplication of 79 internal exons of the large ciliary gene HYDIN from chromosome 16q22.2 to chromosome 1q21.1. Because the HYDIN2 locus lacks the ancestral promoter and seven terminal exons of the progenitor gene, we sought to characterize transcription at this locus by coupling reverse transcription polymerase chain reaction and long-read sequencing. RESULTS 5' RACE indicates a transcription start site for HYDIN2 outside of the duplication and we observe fusion transcripts spanning both the 5' and 3' breakpoints. We observe extensive splicing diversity leading to the formation of altered open reading frames (ORFs) that appear to be under relaxed selection. We show that HYDIN2 adopted a new promoter that drives an altered pattern of expression, with highest levels in neural tissues. We estimate that the HYDIN duplication occurred ~3.2 million years ago and find that it is nearly fixed (99.9%) for diploid copy number in contemporary humans. Examination of 73 chromosome 1q21 rearrangement patients reveals that HYDIN2 is deleted or duplicated in most cases. CONCLUSIONS Together, these data support a model of rapid gene innovation by fusion of incomplete segmental duplications, altered tissue expression, and potential subfunctionalization or neofunctionalization of HYDIN2 early in the evolution of the Homo lineage.
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Affiliation(s)
- Max L Dougherty
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
| | - Xander Nuttle
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
| | - Osnat Penn
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
| | - John Huddleston
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
| | - Lana Harshman
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
| | - Michael H Duyzend
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
| | - Mario Ventura
- Department of Biology, University of Bari, Bari, 70121, Italy
| | | | | | - Megan Y Dennis
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, 95616, CA, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
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78
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Dennis MY, Harshman L, Nelson BJ, Penn O, Cantsilieris S, Huddleston J, Antonacci F, Penewit K, Denman L, Raja A, Baker C, Mark K, Malig M, Janke N, Espinoza C, Stessman HAF, Nuttle X, Hoekzema K, Lindsay-Graves TA, Wilson RK, Eichler EE. The evolution and population diversity of human-specific segmental duplications. Nat Ecol Evol 2017; 1:69. [PMID: 28580430 PMCID: PMC5450946 DOI: 10.1038/s41559-016-0069] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Segmental duplications contribute to human evolution, adaptation and genomic instability but are often poorly characterized. We investigate the evolution, genetic variation and coding potential of human-specific segmental duplications (HSDs). We identify 218 HSDs based on analysis of 322 deeply sequenced archaic and contemporary hominid genomes. We sequence 550 human and nonhuman primate genomic clones to reconstruct the evolution of the largest, most complex regions with protein-coding potential (n=80 genes/33 gene families). We show that HSDs are non-randomly organized, associate preferentially with ancestral ape duplications termed “core duplicons”, and evolved primarily in an interspersed inverted orientation. In addition to Homo sapiens-specific gene expansions (e.g., TCAF1/2), we highlight ten gene families (e.g., ARHGAP11B and SRGAP2C) where copy number never returns to the ancestral state, there is evidence of mRNA splicing, and no common gene-disruptive mutations are observed in the general population. Such duplicates are candidates for the evolution of human-specific adaptive traits.
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Affiliation(s)
- Megan Y Dennis
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, USA.,Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Lana Harshman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Osnat Penn
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Stuart Cantsilieris
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - John Huddleston
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Francesca Antonacci
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", Bari 70125, Italy
| | - Kelsi Penewit
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Laura Denman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Archana Raja
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Kenneth Mark
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Maika Malig
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Nicolette Janke
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Claudia Espinoza
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Holly A F Stessman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Xander Nuttle
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Tina A Lindsay-Graves
- McDonnell Genome Institute at Washington University, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Richard K Wilson
- McDonnell Genome Institute at Washington University, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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79
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Gschwind AR, Singh A, Certa U, Reymond A, Heckel T. Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis. BMC Genomics 2017; 18:144. [PMID: 28183275 PMCID: PMC5301398 DOI: 10.1186/s12864-017-3531-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 02/01/2017] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Copy number variations (CNVs) are a significant source of genetic diversity and commonly found in mammalian genomes. We have generated a genome-wide CNV map for Cynomolgus monkeys (Macaca fascicularis). This crab-eating macaque is the closest animal model to humans that is used in biomedical research. RESULTS We show that Cynomolgus monkey CNVs are in general much smaller in size than gene loci and are specific to the population of origin. Genome-wide expression data from five vitally important organs demonstrates that CNVs in close proximity to transcription start sites associate strongly with expression changes. Among these eQTL genes we find an overrepresentation of genes involved in metabolism, receptor activity, and transcription. CONCLUSION These results provide evidence that CNVs shape tissue transcriptomes in monkey populations, potentially offering an adaptive advantage. We suggest that this genetic diversity should be taken into account when using Cynomolgus macaques as models.
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Affiliation(s)
- Andreas R Gschwind
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics SIB, Lausanne, Switzerland
| | - Anjali Singh
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Ulrich Certa
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
| | - Tobias Heckel
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland.
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80
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Romero V, Hosomichi K, Nakaoka H, Shibata H, Inoue I. Structure and evolution of the filaggrin gene repeated region in primates. BMC Evol Biol 2017; 17:10. [PMID: 28077068 PMCID: PMC5225520 DOI: 10.1186/s12862-016-0851-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 12/12/2016] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The evolutionary dynamics of repeat sequences is quite complex, with some duplicates never having differentiated from each other. Two models can explain the complex evolutionary process for repeated genes-concerted and birth-and-death, of which the latter is driven by duplications maintained by selection. Copy number variations caused by random duplications and losses in repeat regions may modulate molecular pathways and therefore affect phenotypic characteristics in a population, resulting in individuals that are able to adapt to new environments. In this study, we investigated the filaggrin gene (FLG), which codes for filaggrin-an important component of the outer layers of mammalian skin-and contains tandem repeats that exhibit copy number variation between and within species. To examine which model best fits the evolutionary pathway for the complete tandem repeats within a single exon of FLG, we determined the repeat sequences in crab-eating macaque (Macaca fascicularis), orangutan (Pongo abelii), gorilla (Gorilla gorilla), and chimpanzee (Pan troglodytes) and compared these with the sequence in human (Homo sapiens). RESULTS In this study we compared concerted and birth-and-death evolution models, commonly used for gene copies. We found that there is high nucleotide diversity between filaggrin repeat regions, which fits the birth-and-death model. Phylogenetic analyses also suggested that independent duplication events created the repeat sequences in crab-eating macaques and orangutans, while different duplication and loss events created the repeats in gorillas, chimpanzees, and humans. Comparison of the repeat sequences detected purifying selection within species and lineage-specific duplications across species. We also found variation in the length of the repeated region within species such as chimpanzee and crab-eating macaque. CONCLUSIONS We conclude that the copy number variation in the repeat sequences of FLG between primates may be a consequence of species-specific divergence and expansion.
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Affiliation(s)
- Vanessa Romero
- Department of Genetics, School of Life Sciences, Graduate University for Advanced Studies (SOKENDAI), Mishima, 411-8540, Japan.,Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Kazuyoshi Hosomichi
- Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan.,Present address: Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, 920-8640, Japan
| | - Hirofumi Nakaoka
- Department of Genetics, School of Life Sciences, Graduate University for Advanced Studies (SOKENDAI), Mishima, 411-8540, Japan.,Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Ituro Inoue
- Department of Genetics, School of Life Sciences, Graduate University for Advanced Studies (SOKENDAI), Mishima, 411-8540, Japan. .,Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan.
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81
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Cagan A, Theunert C, Laayouni H, Santpere G, Pybus M, Casals F, Prüfer K, Navarro A, Marques-Bonet T, Bertranpetit J, Andrés AM. Natural Selection in the Great Apes. Mol Biol Evol 2016; 33:3268-3283. [PMID: 27795229 PMCID: PMC5100057 DOI: 10.1093/molbev/msw215] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Natural selection is crucial for the adaptation of populations to their environments. Here, we present the first global study of natural selection in the Hominidae (humans and great apes) based on genome-wide information from population samples representing all extant species (including most subspecies). Combining several neutrality tests we create a multi-species map of signatures of natural selection covering all major types of natural selection. We find that the estimated efficiency of both purifying and positive selection varies between species and is significantly correlated with their long-term effective population size. Thus, even the modest differences in population size among the closely related Hominidae lineages have resulted in differences in their ability to remove deleterious alleles and to adapt to changing environments. Most signatures of balancing and positive selection are species-specific, with signatures of balancing selection more often being shared among species. We also identify loci with evidence of positive selection across several lineages. Notably, we detect signatures of positive selection in several genes related to brain function, anatomy, diet and immune processes. Our results contribute to a better understanding of human evolution by putting the evidence of natural selection in humans within its larger evolutionary context. The global map of natural selection in our closest living relatives is available as an interactive browser at http://tinyurl.com/nf8qmzh.
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Affiliation(s)
- Alexander Cagan
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Christoph Theunert
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA
| | - Hafid Laayouni
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Bellaterra, Barcelona, Catalonia, Spain
| | - Gabriel Santpere
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT
| | - Marc Pybus
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Ferran Casals
- Genomics Core Facility, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Arcadi Navarro
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Tomas Marques-Bonet
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Jaume Bertranpetit
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Department of Archaeology and Anthropology, Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, United Kingdom
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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Dennis MY, Eichler EE. Human adaptation and evolution by segmental duplication. Curr Opin Genet Dev 2016; 41:44-52. [PMID: 27584858 PMCID: PMC5161654 DOI: 10.1016/j.gde.2016.08.001] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/02/2016] [Accepted: 08/02/2016] [Indexed: 12/29/2022]
Abstract
Duplications are the primary force by which new gene functions arise and provide a substrate for large-scale structural variation. Analysis of thousands of genomes shows that humans and great apes have more genetic differences in content and structure over recent segmental duplications than any other euchromatic region. Novel human-specific duplicated genes, ARHGAP11B and SRGAP2C, have recently been described with a potential role in neocortical expansion and increased neuronal spine density. Large segmental duplications and the structural variants they promote are also frequently stratified between human populations with a subset being subjected to positive selection. The impact of recent duplications on human evolution and adaptation is only beginning to be realized as new technologies enhance their discovery and accurate genotyping.
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Affiliation(s)
- Megan Y Dennis
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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83
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Locatelli S, Harrigan RJ, Sesink Clee PR, Mitchell MW, McKean KA, Smith TB, Gonder MK. Why Are Nigeria-Cameroon Chimpanzees (Pan troglodytes ellioti) Free of SIVcpz Infection? PLoS One 2016; 11:e0160788. [PMID: 27505066 PMCID: PMC4978404 DOI: 10.1371/journal.pone.0160788] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/24/2016] [Indexed: 12/26/2022] Open
Abstract
Simian immunodeficiency virus (SIV) naturally infects two subspecies of chimpanzee: Pan troglodytes troglodytes from Central Africa (SIVcpzPtt) and P. t. schweinfurtii from East Africa (SIVcpzPts), but is absent in P. t. verus from West Africa and appears to be absent in P. t. ellioti inhabiting Nigeria and western Cameroon. One explanation for this pattern is that P. t. troglodytes and P. t schweinfurthii may have acquired SIVcpz after their divergence from P. t. verus and P. t. ellioti. However, all of the subspecies, except P. t. verus, still occasionally exchange migrants making the absence of SIVcpz in P. t. ellioti puzzling. Sampling of P. t. ellioti has been minimal to date, particularly along the banks of the Sanaga River, where its range abuts that of P. t. troglodytes. This study had three objectives. First, we extended the sampling of SIVcpz across the range of chimpanzees north of the Sanaga River to address whether under-sampling might account for the absence of evidence for SIVcpz infection in P. t. ellioti. Second, we investigated how environmental variation is associated with the spread and prevalence of SIVcpz in the two chimpanzee subspecies inhabiting Cameroon since environmental variation has been shown to contribute to their divergence from one another. Finally, we compared the prevalence and distribution of SIVcpz with that of Simian Foamy Virus (SFV) to examine the role of ecology and behavior in shaping the distribution of diseases in wild host populations. The dataset includes previously published results on SIVcpz infection and SFVcpz as well as newly collected data, and represents over 1000 chimpanzee fecal samples from 41 locations across Cameroon. Results revealed that none of the 181 P. t. ellioti fecal samples collected across the range of P. t. ellioti tested positive for SIVcpz. In addition, species distribution models suggest that environmental variation contributes to differences in the distribution and prevalence of SIVcpz and SFVcpz. The ecological niches of these two viruses are largely non-overlapping, although stronger statistical support for this conclusion will require more sampling. Overall this study demonstrates that SIVcpz infection is absent or very rare in P. t. ellioti, despite multiple opportunities for transmission. The reasons for its absence remain unclear, but might be explained by one or more factors, including environmental variation, viral competition, and/or local adaptation—all of which should be explored in greater detail through continued surveillance of this region.
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Affiliation(s)
- Sabrina Locatelli
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, and University of Montpellier, 34394 Montpellier, France
- Department of Biological Sciences, University at Albany – State University of New York, Albany, NY, 12222, United States of America
- * E-mail:
| | - Ryan J. Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, 621 Charles E. Young Drive South, Los Angeles, CA, 90095, United States of America
| | - Paul R. Sesink Clee
- Department of Biological Sciences, University at Albany – State University of New York, Albany, NY, 12222, United States of America
- Department of Biology, Drexel University, Philadelphia, PA, 19104, United States of America
| | - Matthew W Mitchell
- Department of Biological Sciences, University at Albany – State University of New York, Albany, NY, 12222, United States of America
- Department of Biology, Drexel University, Philadelphia, PA, 19104, United States of America
| | - Kurt A. McKean
- Department of Biological Sciences, University at Albany – State University of New York, Albany, NY, 12222, United States of America
| | - Thomas B. Smith
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, 621 Charles E. Young Drive South, Los Angeles, CA, 90095, United States of America
| | - Mary Katherine Gonder
- Department of Biological Sciences, University at Albany – State University of New York, Albany, NY, 12222, United States of America
- Department of Biology, Drexel University, Philadelphia, PA, 19104, United States of America
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84
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Yuan B, Liu P, Rogers J, Lupski JR. Copy number analysis of the low-copy repeats at the primate NPHP1 locus by array comparative genomic hybridization. GENOMICS DATA 2016; 8:106-9. [PMID: 27222811 PMCID: PMC4872932 DOI: 10.1016/j.gdata.2016.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 11/28/2022]
Abstract
Array comparative genomic hybridization (aCGH) has been widely used to detect copy number variants (CNVs) in both research and clinical settings. A customizable aCGH platform may greatly facilitate copy number analyses in genomic regions with higher-order complexity, such as low-copy repeats (LCRs). Here we present the aCGH analyses focusing on the 45 kb LCRs [1] at the NPHP1 region with diverse copy numbers in humans. Also, the interspecies aCGH analysis comparing human and nonhuman primates revealed dynamic copy number transitions of the human 45 kb LCR orthologues during primate evolution and therefore shed light on the origin of complexity at this locus. The original aCGH data are available at GEO under GSE73962.
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Affiliation(s)
- Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Miraca Genetics Laboratories, Houston, TX 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Miraca Genetics Laboratories, Houston, TX 77030, USA
| | - Jeffrey Rogers
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
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85
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Gordon D, Huddleston J, Chaisson MJP, Hill CM, Kronenberg ZN, Munson KM, Malig M, Raja A, Fiddes I, Hillier LW, Dunn C, Baker C, Armstrong J, Diekhans M, Paten B, Shendure J, Wilson RK, Haussler D, Chin CS, Eichler EE. Long-read sequence assembly of the gorilla genome. Science 2016; 352:aae0344. [PMID: 27034376 PMCID: PMC4920363 DOI: 10.1126/science.aae0344] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/26/2016] [Indexed: 12/24/2022]
Abstract
Accurate sequence and assembly of genomes is a critical first step for studies of genetic variation. We generated a high-quality assembly of the gorilla genome using single-molecule, real-time sequence technology and a string graph de novo assembly algorithm. The new assembly improves contiguity by two to three orders of magnitude with respect to previously released assemblies, recovering 87% of missing reference exons and incomplete gene models. Although regions of large, high-identity segmental duplications remain largely unresolved, this comprehensive assembly provides new biological insight into genetic diversity, structural variation, gene loss, and representation of repeat structures within the gorilla genome. The approach provides a path forward for the routine assembly of mammalian genomes at a level approaching that of the current quality of the human genome.
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Affiliation(s)
- David Gordon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - John Huddleston
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Mark J P Chaisson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Christopher M Hill
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Zev N Kronenberg
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Maika Malig
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Archana Raja
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Ian Fiddes
- Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, CA 95064, USA
| | - LaDeana W Hillier
- McDonnell Genome Institute, Department of Medicine, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | | | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Joel Armstrong
- Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, CA 95064, USA
| | - Mark Diekhans
- Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, CA 95064, USA
| | - Benedict Paten
- Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, CA 95064, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Richard K Wilson
- McDonnell Genome Institute, Department of Medicine, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - David Haussler
- Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, CA 95064, USA
| | - Chen-Shan Chin
- Pacific Biosciences of California, Menlo Park, CA 94025, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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86
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Bai Z, Chen J, Liao Y, Wang M, Liu R, Ge S, Wing RA, Chen M. The impact and origin of copy number variations in the Oryza species. BMC Genomics 2016; 17:261. [PMID: 27025496 PMCID: PMC4812662 DOI: 10.1186/s12864-016-2589-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 03/15/2016] [Indexed: 02/16/2023] Open
Abstract
Background Copy number variation (CNV), a complex genomic rearrangement, has been extensively studied in humans and other organisms. In plants, CNVs of several genes were found to be responsible for various important traits; however, the cause and consequence of CNVs remains largely unknown. Recently released next-generation sequencing (NGS) data provide an opportunity for a genome-wide study of CNVs in rice. Results Here, by an NGS-based approach, we generated a CNV map comprising 9,196 deletions compared to the reference genome ‘Nipponbare’. Using Oryza glaberrima as the outgroup, 80 % of the CNV events turned out to be insertions in Nipponbare. There were 2,806 annotated genes affected by these CNV events. We experimentally validated 28 functional CNV genes including OsMADS56, BPH14, OsDCL2b and OsMADS30, implying that CNVs might have contributed to phenotypic variations in rice. Most CNV genes were found to be located in non-co-linear positions by comparison to O. glaberrima. One of the origins of these non-co-linear genes was genomic duplications caused by transposon activity or double-strand break repair. Comprehensive analysis of mutation mechanisms suggested an abundance of CNVs formed by non-homologous end-joining and mobile element insertion. Conclusions This study showed the impact and origin of copy number variations in rice on a genomic scale. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2589-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zetao Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfeng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yi Liao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Meijiao Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rong Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Science, University of Arizona, Tucson, AZ, 85721, USA
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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87
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Ghenu AH, Bolker BM, Melnick DJ, Evans BJ. Multicopy gene family evolution on primate Y chromosomes. BMC Genomics 2016; 17:157. [PMID: 26925773 PMCID: PMC4772468 DOI: 10.1186/s12864-015-2187-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/02/2015] [Indexed: 12/12/2022] Open
Abstract
Background The primate Y chromosome is distinguished by a lack of inter-chromosomal recombination along most of its length, extensive gene loss, and a prevalence of repetitive elements. A group of genes on the male-specific portion of the Y chromosome known as the “ampliconic genes” are present in multiple copies that are sometimes part of palindromes, and that undergo a form of intra-chromosomal recombination called gene conversion, wherein the nucleotides of one copy are homogenized by those of another. With the aim of further understanding gene family evolution of these genes, we collected nucleotide sequence and gene copy number information for several species of papionin monkey. We then tested for evidence of gene conversion, and developed a novel statistical framework to evaluate alternative models of gene family evolution using our data combined with other information from a human, a chimpanzee, and a rhesus macaque. Results Our results (i) recovered evidence for several novel examples of gene conversion in papionin monkeys and indicate that (ii) ampliconic gene families evolve faster than autosomal gene families and than single-copy genes on the Y chromosome and that (iii) Y-linked singleton and autosomal gene families evolved faster in humans and chimps than they do in the other Old World Monkey lineages we studied. Conclusions Rapid evolution of ampliconic genes cannot be attributed solely to residence on the Y chromosome, nor to variation between primate lineages in the rate of gene family evolution. Instead other factors, such as natural selection and gene conversion, appear to play a role in driving temporal and genomic evolutionary heterogeneity in primate gene families. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2187-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana-Hermina Ghenu
- Biology Department, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada.
| | - Benjamin M Bolker
- Biology Department, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada.,Department of Mathematics & Statistics, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Don J Melnick
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 10th Floor Schermerhorn Extension, New York, 10027, USA
| | - Ben J Evans
- Biology Department, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada.
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88
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Frantz L, Meijaard E, Gongora J, Haile J, Groenen MA, Larson G. The Evolution of Suidae. Annu Rev Anim Biosci 2016; 4:61-85. [DOI: 10.1146/annurev-animal-021815-111155] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Laurent Frantz
- Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom;
| | - Erik Meijaard
- IUCN/SSC Wild Pig Specialist Group, Jakarta 15412, Indonesia
- School of Archaeology and Anthropology, The Australian National University, Canberra, ACT 0200, Australia
| | - Jaime Gongora
- Faculty of Veterinary Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - James Haile
- Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom;
| | - Martien A.M. Groenen
- Animal Breeding and Genomics Centre, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Greger Larson
- Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom;
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89
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Yuan B, Liu P, Gupta A, Beck CR, Tejomurtula A, Campbell IM, Gambin T, Simmons AD, Withers MA, Harris RA, Rogers J, Schwartz DC, Lupski JR. Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates. PLoS Genet 2015; 11:e1005686. [PMID: 26641089 PMCID: PMC4671654 DOI: 10.1371/journal.pgen.1005686] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 10/29/2015] [Indexed: 11/30/2022] Open
Abstract
Many loci in the human genome harbor complex genomic structures that can result in susceptibility to genomic rearrangements leading to various genomic disorders. Nephronophthisis 1 (NPHP1, MIM# 256100) is an autosomal recessive disorder that can be caused by defects of NPHP1; the gene maps within the human 2q13 region where low copy repeats (LCRs) are abundant. Loss of function of NPHP1 is responsible for approximately 85% of the NPHP1 cases—about 80% of such individuals carry a large recurrent homozygous NPHP1 deletion that occurs via nonallelic homologous recombination (NAHR) between two flanking directly oriented ~45 kb LCRs. Published data revealed a non-pathogenic inversion polymorphism involving the NPHP1 gene flanked by two inverted ~358 kb LCRs. Using optical mapping and array-comparative genomic hybridization, we identified three potential novel structural variant (SV) haplotypes at the NPHP1 locus that may protect a haploid genome from the NPHP1 deletion. Inter-species comparative genomic analyses among primate genomes revealed massive genomic changes during evolution. The aggregated data suggest that dynamic genomic rearrangements occurred historically within the NPHP1 locus and generated SV haplotypes observed in the human population today, which may confer differential susceptibility to genomic instability and the NPHP1 deletion within a personal genome. Our study documents diverse SV haplotypes at a complex LCR-laden human genomic region. Comparative analyses provide a model for how this complex region arose during primate evolution, and studies among humans suggest that intra-species polymorphism may potentially modulate an individual’s susceptibility to acquiring disease-associated alleles. Genomic instability due to the intrinsic sequence architecture of the genome, such as low copy repeats (LCRs), is a major contributor to de novo mutations that can occur in the process of human genome evolution. LCRs can mediate genomic rearrangements associated with genomic disorders by acting as substrates for nonallelic homologous recombination. Juvenile-onset nephronophthisis 1 is the most frequent genetic cause of renal failure in children. An LCR-mediated, homozygous common recurrent deletion encompassing NPHP1 is found in the majority of affected subjects, while heterozygous deletion representing the nephronophthisis 1 recessive carrier state is frequently observed amongst world populations. Interestingly, the human NPHP1 locus is located proximal to the head-to-head fusion site of two ancestral chromosomes that occurred in the great apes, which resulted in a reduction of chromosome number from 48 in nonhuman primates to the current 46 in humans. In this study, we characterized and provided evidence for the diverse genomic architecture at the NPHP1 locus and potential structural variant haplotypes in the human population. Furthermore, our analyses of primate genomes shed light on the massive changes of genomic architecture at the human NPHP1 locus and delineated a model for the emergence of the LCRs during primate evolution.
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Affiliation(s)
- Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Aditya Gupta
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and The UW-Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Christine R. Beck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anusha Tejomurtula
- Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ian M. Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Alexandra D. Simmons
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Marjorie A. Withers
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - R. Alan Harris
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jeffrey Rogers
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and The UW-Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children’s Hospital, Houston, Texas, United States of America
- * E-mail:
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90
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Cheeseman IH, Miller B, Tan JC, Tan A, Nair S, Nkhoma SC, De Donato M, Rodulfo H, Dondorp A, Branch OH, Mesia LR, Newton P, Mayxay M, Amambua-Ngwa A, Conway DJ, Nosten F, Ferdig MT, Anderson TJC. Population Structure Shapes Copy Number Variation in Malaria Parasites. Mol Biol Evol 2015; 33:603-20. [PMID: 26613787 PMCID: PMC4760083 DOI: 10.1093/molbev/msv282] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in seven countries in Africa, South East Asia and South America using a high-density single-nucleotide polymorphism/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500 bp to 59 kb, as well as 10,107 flanking, biallelic single-nucleotide polymorphisms. Overall, CNVs were rare, small, and skewed toward low frequency variants, consistent with the deleterious model. Relative to African and South East Asian populations, CNVs were significantly more common in South America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g., DNA helicase and three conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen.
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Affiliation(s)
- Ian H Cheeseman
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Becky Miller
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - John C Tan
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - Asako Tan
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - Shalini Nair
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Standwell C Nkhoma
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Marcos De Donato
- Lab. Genetica Molecular, IIBCAUDO, Universidad De Oriente, Cumana, Venezuela
| | - Hectorina Rodulfo
- Lab. Genetica Molecular, IIBCAUDO, Universidad De Oriente, Cumana, Venezuela
| | - Arjen Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Oralee H Branch
- Division of Parasitology, Department of Microbiology, New York University School of Medicine
| | - Lastenia Ruiz Mesia
- Laboratorio De Investigaciones De Productos Naturales Y Antiparasitarios, Universidad Nacional De La Amazonia Peruana, Iquitos, Peru
| | - Paul Newton
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Mayfong Mayxay
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR Faculty of Postgraduate Studies, University of Health Sciences, Vientiane, Lao PDR
| | | | - David J Conway
- Medical Research Council Unit, Fajara, Banjul, The Gambia Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - François Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Michael T Ferdig
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - Tim J C Anderson
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
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91
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Warren WC, Jasinska AJ, García-Pérez R, Svardal H, Tomlinson C, Rocchi M, Archidiacono N, Capozzi O, Minx P, Montague MJ, Kyung K, Hillier LW, Kremitzki M, Graves T, Chiang C, Hughes J, Tran N, Huang Y, Ramensky V, Choi OW, Jung YJ, Schmitt CA, Juretic N, Wasserscheid J, Turner TR, Wiseman RW, Tuscher JJ, Karl JA, Schmitz JE, Zahn R, O'Connor DH, Redmond E, Nisbett A, Jacquelin B, Müller-Trutwin MC, Brenchley JM, Dione M, Antonio M, Schroth GP, Kaplan JR, Jorgensen MJ, Thomas GWC, Hahn MW, Raney BJ, Aken B, Nag R, Schmitz J, Churakov G, Noll A, Stanyon R, Webb D, Thibaud-Nissen F, Nordborg M, Marques-Bonet T, Dewar K, Weinstock GM, Wilson RK, Freimer NB. The genome of the vervet (Chlorocebus aethiops sabaeus). Genome Res 2015; 25:1921-33. [PMID: 26377836 PMCID: PMC4665013 DOI: 10.1101/gr.192922.115] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/10/2015] [Indexed: 01/20/2023]
Abstract
We describe a genome reference of the African green monkey or vervet (Chlorocebus aethiops). This member of the Old World monkey (OWM) superfamily is uniquely valuable for genetic investigations of simian immunodeficiency virus (SIV), for which it is the most abundant natural host species, and of a wide range of health-related phenotypes assessed in Caribbean vervets (C. a. sabaeus), whose numbers have expanded dramatically since Europeans introduced small numbers of their ancestors from West Africa during the colonial era. We use the reference to characterize the genomic relationship between vervets and other primates, the intra-generic phylogeny of vervet subspecies, and genome-wide structural variations of a pedigreed C. a. sabaeus population. Through comparative analyses with human and rhesus macaque, we characterize at high resolution the unique chromosomal fission events that differentiate the vervets and their close relatives from most other catarrhine primates, in whom karyotype is highly conserved. We also provide a summary of transposable elements and contrast these with the rhesus macaque and human. Analysis of sequenced genomes representing each of the main vervet subspecies supports previously hypothesized relationships between these populations, which range across most of sub-Saharan Africa, while uncovering high levels of genetic diversity within each. Sequence-based analyses of major histocompatibility complex (MHC) polymorphisms reveal extremely low diversity in Caribbean C. a. sabaeus vervets, compared to vervets from putatively ancestral West African regions. In the C. a. sabaeus research population, we discover the first structural variations that are, in some cases, predicted to have a deleterious effect; future studies will determine the phenotypic impact of these variations.
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Affiliation(s)
- Wesley C Warren
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Anna J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA; Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Raquel García-Pérez
- ICREA at Institut de Biologia Evolutiva, (UPF-CSIC) and Centro Nacional de Analisis Genomico (CNAG), PRBB/PCB, 08003 Barcelona, Spain
| | - Hannes Svardal
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Chad Tomlinson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Mariano Rocchi
- Department of Biology, University of Bari, Bari 70126, Italy
| | | | - Oronzo Capozzi
- Department of Biology, University of Bari, Bari 70126, Italy
| | - Patrick Minx
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Michael J Montague
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Kim Kyung
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - LaDeana W Hillier
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Milinn Kremitzki
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Tina Graves
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Colby Chiang
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | | | - Nam Tran
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Yu Huang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Vasily Ramensky
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Oi-Wa Choi
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Yoon J Jung
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Christopher A Schmitt
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Nikoleta Juretic
- Department of Human Genetics, McGill University, Montreal QC H3A 1B1, Canada
| | | | - Trudy R Turner
- Department of Anthropology, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53705, USA; Department of Genetics Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9300 South Africa
| | - Roger W Wiseman
- Department of Laboratory Medicine and Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Jennifer J Tuscher
- Department of Laboratory Medicine and Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Julie A Karl
- Department of Laboratory Medicine and Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Jörn E Schmitz
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA
| | - Roland Zahn
- Crucell Holland B.V., 2333 CN Leiden, The Netherlands
| | - David H O'Connor
- Department of Laboratory Medicine and Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Eugene Redmond
- St. Kitts Biomedical Research Foundation, St. Kitts, West Indies
| | - Alex Nisbett
- St. Kitts Biomedical Research Foundation, St. Kitts, West Indies
| | - Béatrice Jacquelin
- Institut Pasteur, Unité de Régulation des Infections Rétrovirales, 75015 Paris, France
| | | | - Jason M Brenchley
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland 20892-9821, USA
| | | | | | | | - Jay R Kaplan
- Center for Comparative Medicine Research, Wake Forest School of Medicine, Winston-Salem 27157-1040, USA
| | - Matthew J Jorgensen
- Center for Comparative Medicine Research, Wake Forest School of Medicine, Winston-Salem 27157-1040, USA
| | - Gregg W C Thomas
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Brian J Raney
- University of California Santa Cruz, Santa Cruz, California 95060, USA
| | - Bronwen Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Juergen Schmitz
- Institute of Experimental Pathology (ZMBE), University of Münster, 48149 Münster, Germany
| | - Gennady Churakov
- Institute of Experimental Pathology (ZMBE), University of Münster, 48149 Münster, Germany; Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Angela Noll
- Institute of Experimental Pathology (ZMBE), University of Münster, 48149 Münster, Germany
| | - Roscoe Stanyon
- Department of Biology, University of Florence, 50122 Florence, Italy
| | - David Webb
- National Center for Biotechnology Information, Bethesda, Maryland 20894, USA
| | | | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Tomas Marques-Bonet
- ICREA at Institut de Biologia Evolutiva, (UPF-CSIC) and Centro Nacional de Analisis Genomico (CNAG), PRBB/PCB, 08003 Barcelona, Spain
| | - Ken Dewar
- Department of Human Genetics, McGill University, Montreal QC H3A 1B1, Canada
| | - George M Weinstock
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06001, USA
| | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Nelson B Freimer
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
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92
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Sudmant PH, Mallick S, Nelson BJ, Hormozdiari F, Krumm N, Huddleston J, Coe BP, Baker C, Nordenfelt S, Bamshad M, Jorde LB, Posukh OL, Sahakyan H, Watkins WS, Yepiskoposyan L, Abdullah MS, Bravi CM, Capelli C, Hervig T, Wee JTS, Tyler-Smith C, van Driem G, Romero IG, Jha AR, Karachanak-Yankova S, Toncheva D, Comas D, Henn B, Kivisild T, Ruiz-Linares A, Sajantila A, Metspalu E, Parik J, Villems R, Starikovskaya EB, Ayodo G, Beall CM, Di Rienzo A, Hammer MF, Khusainova R, Khusnutdinova E, Klitz W, Winkler C, Labuda D, Metspalu M, Tishkoff SA, Dryomov S, Sukernik R, Patterson N, Reich D, Eichler EE. Global diversity, population stratification, and selection of human copy-number variation. Science 2015; 349:aab3761. [PMID: 26249230 PMCID: PMC4568308 DOI: 10.1126/science.aab3761] [Citation(s) in RCA: 227] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 07/29/2015] [Indexed: 12/14/2022]
Abstract
In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.
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Affiliation(s)
- Peter H Sudmant
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Swapan Mallick
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | | | - Niklas Krumm
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - John Huddleston
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Bradley P Coe
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Carl Baker
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Susanne Nordenfelt
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA 98119, USA
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Olga L Posukh
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia. Novosibirsk State University, Novosibirsk 630090, Russia
| | - Hovhannes Sahakyan
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia. Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia
| | - W Scott Watkins
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Levon Yepiskoposyan
- Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia
| | - M Syafiq Abdullah
- Raja Isteri Pengiran Anak Saleha (RIPAS) Hospital, Bandar Seri Begawan, Brunei Darussalam
| | - Claudio M Bravi
- Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE), Centro Científico y Tecnológico-Consejo Nacional de Investigaciones Científicas y Técnicas (CCT-CONICET) and Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICPBA), La Plata B1906APO, Argentina
| | | | - Tor Hervig
- Department of Clinical Science, University of Bergen, Bergen 5021, Norway
| | | | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - George van Driem
- Institute of Linguistics, University of Bern, Bern CH-3012, Switzerland
| | | | - Aashish R Jha
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Sena Karachanak-Yankova
- Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria
| | - Draga Toncheva
- Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria
| | - David Comas
- Institut de Biologia Evolutiva [Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra (CSIC-UPF)], Departament de Ciències Experimentals i de la Salut, UPF, Barcelona 08003, Spain
| | - Brenna Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Toomas Kivisild
- Division of Biological Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK
| | - Andres Ruiz-Linares
- Department of Genetics, Evolution and Environment, University College London, WC1E 6BT, UK
| | - Antti Sajantila
- University of Helsinki, Department of Forensic Medicine, Helsinki 00014, Finland
| | - Ene Metspalu
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia. University of Tartu, Department of Evolutionary Biology, Tartu 5101, Estonia
| | - Jüri Parik
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia
| | - Richard Villems
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia
| | - Elena B Starikovskaya
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - George Ayodo
- Center for Global Health and Child Development, Kisumu 40100, Kenya
| | - Cynthia M Beall
- Department of Anthropology, Case Western Reserve University, Cleveland, OH 44106-7125, USA
| | - Anna Di Rienzo
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Michael F Hammer
- Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA
| | - Rita Khusainova
- Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia. Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia. Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia
| | - William Klitz
- Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Cheryl Winkler
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical Research, Incorporated, Frederick National Laboratory, Frederick, MD 21702, USA
| | - Damian Labuda
- Centre Hospitalier Universitaire (CHU) Sainte-Justine, Département de Pédiatrie, Université de Montréal, QC H3T 1C5, Canada
| | - Mait Metspalu
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia
| | - Sarah A Tishkoff
- Departments of Biology and Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stanislav Dryomov
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia. Department of Paleolithic Archaeology, Institute of Archaeology and Ethnography, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Rem Sukernik
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia. Altai State University, Barnaul 656000, Russia
| | - Nick Patterson
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - David Reich
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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93
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Simonti CN, Capra JA. The evolution of the human genome. Curr Opin Genet Dev 2015; 35:9-15. [PMID: 26338498 DOI: 10.1016/j.gde.2015.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/08/2015] [Accepted: 08/12/2015] [Indexed: 02/05/2023]
Abstract
Human genomes hold a record of the evolutionary forces that have shaped our species. Advances in DNA sequencing, functional genomics, and population genetic modeling have deepened our understanding of human demographic history, natural selection, and many other long-studied topics. These advances have also revealed many previously underappreciated factors that influence the evolution of the human genome, including functional modifications to DNA and histones, conserved 3D topological chromatin domains, structural variation, and heterogeneous mutation patterns along the genome. Using evolutionary theory as a lens to study these phenomena will lead to significant breakthroughs in understanding what makes us human and why we get sick.
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Affiliation(s)
- Corinne N Simonti
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37235, USA
| | - John A Capra
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37235, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37235, USA.
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94
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Abstract
The world of primate genomics is expanding rapidly in new and exciting ways owing to lowered costs and new technologies in molecular methods and bioinformatics. The primate order is composed of 78 genera and 478 species, including human. Taxonomic inferences are complex and likely a consequence of ongoing hybridization, introgression, and reticulate evolution among closely related taxa. Recently, we applied large-scale sequencing methods and extensive taxon sampling to generate a highly resolved phylogeny that affirms, reforms, and extends previous depictions of primate speciation. The next stage of research uses this phylogeny as a foundation for investigating genome content, structure, and evolution across primates. Ongoing and future applications of a robust primate phylogeny are discussed, highlighting advancements in adaptive evolution of genes and genomes, taxonomy and conservation management of endangered species, next-generation genomic technologies, and biomedicine.
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Affiliation(s)
- Jill Pecon-Slattery
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702; Current Affiliation: Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, Virginia 22630;
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95
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Gittelman RM, Hun E, Ay F, Madeoy J, Pennacchio L, Noble WS, Hawkins RD, Akey JM. Comprehensive identification and analysis of human accelerated regulatory DNA. Genome Res 2015; 25:1245-55. [PMID: 26104583 PMCID: PMC4561485 DOI: 10.1101/gr.192591.115] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/15/2015] [Indexed: 01/19/2023]
Abstract
It has long been hypothesized that changes in gene regulation have played an important role in human evolution, but regulatory DNA has been much more difficult to study compared with protein-coding regions. Recent large-scale studies have created genome-scale catalogs of DNase I hypersensitive sites (DHSs), which demark potentially functional regulatory DNA. To better define regulatory DNA that has been subject to human-specific adaptive evolution, we performed comprehensive evolutionary and population genetics analyses on over 18 million DHSs discovered in 130 cell types. We identified 524 DHSs that are conserved in nonhuman primates but accelerated in the human lineage (haDHS), and estimate that 70% of substitutions in haDHSs are attributable to positive selection. Through extensive computational and experimental analyses, we demonstrate that haDHSs are often active in brain or neuronal cell types; play an important role in regulating the expression of developmentally important genes, including many transcription factors such as SOX6, POU3F2, and HOX genes; and identify striking examples of adaptive regulatory evolution that may have contributed to human-specific phenotypes. More generally, our results reveal new insights into conserved and adaptive regulatory DNA in humans and refine the set of genomic substrates that distinguish humans from their closest living primate relatives.
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Affiliation(s)
- Rachel M Gittelman
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Enna Hun
- Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Ferhat Ay
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Jennifer Madeoy
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Len Pennacchio
- Lawrence Berkeley National Laboratory, Genomics Division, Berkeley, California 94701, USA
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - R David Hawkins
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Joshua M Akey
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
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96
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Radke DW, Lee C. Adaptive potential of genomic structural variation in human and mammalian evolution. Brief Funct Genomics 2015; 14:358-68. [PMID: 26003631 DOI: 10.1093/bfgp/elv019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Because phenotypic innovations must be genetically heritable for biological evolution to proceed, it is natural to consider new mutation events as well as standing genetic variation as sources for their birth. Previous research has identified a number of single-nucleotide polymorphisms that underlie a subset of adaptive traits in organisms. However, another well-known class of variation, genomic structural variation, could have even greater potential to produce adaptive phenotypes, due to the variety of possible types of alterations (deletions, insertions, duplications, among others) at different genomic positions and with variable lengths. It is from these dramatic genomic alterations, and selection on their phenotypic consequences, that adaptations leading to biological diversification could be derived. In this review, using studies in humans and other mammals, we highlight examples of how phenotypic variation from structural variants might become adaptive in populations and potentially enable biological diversification. Phenotypic change arising from structural variants will be described according to their immediate effect on organismal metabolic processes, immunological response and physical features. Study of population dynamics of segregating structural variation can therefore provide a window into understanding current and historical biological diversification.
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97
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Paudel Y, Madsen O, Megens HJ, Frantz LAF, Bosse M, Crooijmans RPMA, Groenen MAM. Copy number variation in the speciation of pigs: a possible prominent role for olfactory receptors. BMC Genomics 2015; 16:330. [PMID: 25896665 PMCID: PMC4413995 DOI: 10.1186/s12864-015-1449-9] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 03/09/2015] [Indexed: 12/02/2022] Open
Abstract
Background Unraveling the genetic mechanisms associated with reduced gene flow between genetically differentiated populations is key to understand speciation. Different types of structural variations (SVs) have been found as a source of genetic diversity in a wide range of species. Previous studies provided detailed knowledge on the potential evolutionary role of SVs, especially copy number variations (CNVs), between well diverged species of e.g. primates. However, our understanding of their significance during ongoing speciation processes is limited due to the lack of CNV data from closely related species. The genus Sus (pig and its close relatives) which started to diverge ~4 Mya presents an excellent model for studying the role of CNVs during ongoing speciation. Results In this study, we identified 1408 CNV regions (CNVRs) across the genus Sus. These CNVRs encompass 624 genes and were found to evolve ~2.5 times faster than single nucleotide polymorphisms (SNPs). The majority of these copy number variable genes are olfactory receptors (ORs) known to play a prominent role in food foraging and mate recognition in Sus. Phylogenetic analyses, including novel Bayesian analysis, based on CNVRs that overlap ORs retain the well-accepted topology of the genus Sus whereas CNVRs overlapping genes other than ORs show evidence for random drift and/or admixture. Conclusion We hypothesize that inter-specific variation in copy number of ORs provided the means for rapid adaptation to different environments during the diversification of the genus Sus in the Pliocene. Furthermore, these regions might have acted as barriers preventing massive gene flow between these species during the multiple hybridization events that took place later in the Pleistocene suggesting a possible prominent role of ORs in the ongoing Sus speciation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1449-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yogesh Paudel
- Animal Breeding and Genomics Centre, Wageningen University, 6700 AH, Wageningen, The Netherlands. .,Current address: Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070, Basel, Switzerland.
| | - Ole Madsen
- Animal Breeding and Genomics Centre, Wageningen University, 6700 AH, Wageningen, The Netherlands.
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics Centre, Wageningen University, 6700 AH, Wageningen, The Netherlands.
| | - Laurent A F Frantz
- Animal Breeding and Genomics Centre, Wageningen University, 6700 AH, Wageningen, The Netherlands.
| | - Mirte Bosse
- Animal Breeding and Genomics Centre, Wageningen University, 6700 AH, Wageningen, The Netherlands.
| | - Richard P M A Crooijmans
- Animal Breeding and Genomics Centre, Wageningen University, 6700 AH, Wageningen, The Netherlands.
| | - Martien A M Groenen
- Animal Breeding and Genomics Centre, Wageningen University, 6700 AH, Wageningen, The Netherlands.
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98
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Xue Y, Prado-Martinez J, Sudmant PH, Narasimhan V, Ayub Q, Szpak M, Frandsen P, Chen Y, Yngvadottir B, Cooper DN, de Manuel M, Hernandez-Rodriguez J, Lobon I, Siegismund HR, Pagani L, Quail MA, Hvilsom C, Mudakikwa A, Eichler EE, Cranfield MR, Marques-Bonet T, Tyler-Smith C, Scally A. Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding. Science 2015; 348:242-245. [PMID: 25859046 PMCID: PMC4668944 DOI: 10.1126/science.aaa3952] [Citation(s) in RCA: 225] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 03/03/2015] [Indexed: 12/30/2022]
Abstract
Mountain gorillas are an endangered great ape subspecies and a prominent focus for conservation, yet we know little about their genomic diversity and evolutionary past. We sequenced whole genomes from multiple wild individuals and compared the genomes of all four Gorilla subspecies. We found that the two eastern subspecies have experienced a prolonged population decline over the past 100,000 years, resulting in very low genetic diversity and an increased overall burden of deleterious variation. A further recent decline in the mountain gorilla population has led to extensive inbreeding, such that individuals are typically homozygous at 34% of their sequence, leading to the purging of severely deleterious recessive mutations from the population. We discuss the causes of their decline and the consequences for their future survival.
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Affiliation(s)
- Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Javier Prado-Martinez
- Institut de Biologia Evolutiva (CSIC/UPF), Parque de Investigación Biomédica de Barcelona (PRBB), Barcelona, Catalonia 08003, Spain
| | - Peter H. Sudmant
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Vagheesh Narasimhan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA, UK
| | - Qasim Ayub
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Michal Szpak
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Peter Frandsen
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Yuan Chen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Bryndis Yngvadottir
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - David N. Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff CF14 4XN, UK
| | - Marc de Manuel
- Institut de Biologia Evolutiva (CSIC/UPF), Parque de Investigación Biomédica de Barcelona (PRBB), Barcelona, Catalonia 08003, Spain
| | - Jessica Hernandez-Rodriguez
- Institut de Biologia Evolutiva (CSIC/UPF), Parque de Investigación Biomédica de Barcelona (PRBB), Barcelona, Catalonia 08003, Spain
| | - Irene Lobon
- Institut de Biologia Evolutiva (CSIC/UPF), Parque de Investigación Biomédica de Barcelona (PRBB), Barcelona, Catalonia 08003, Spain
| | - Hans R. Siegismund
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Luca Pagani
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40134 Bologna, Italy
| | - Michael A. Quail
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Christina Hvilsom
- Research and Conservation, Copenhagen Zoo, DK-2000 Frederiksberg, Denmark
| | | | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 91895, USA
| | - Michael R. Cranfield
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, University of California, Davis, CA 95616, USA
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (CSIC/UPF), Parque de Investigación Biomédica de Barcelona (PRBB), Barcelona, Catalonia 08003, Spain
- Centro Nacional de Análisis Genómico (Parc Cientific de Barcelona), Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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99
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McManus KF, Kelley JL, Song S, Veeramah KR, Woerner AE, Stevison LS, Ryder OA, Ape Genome Project G, Kidd JM, Wall JD, Bustamante CD, Hammer MF. Inference of gorilla demographic and selective history from whole-genome sequence data. Mol Biol Evol 2014; 32:600-12. [PMID: 25534031 PMCID: PMC4327160 DOI: 10.1093/molbev/msu394] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Although population-level genomic sequence data have been gathered extensively for humans, similar data from our closest living relatives are just beginning to emerge. Examination of genomic variation within great apes offers many opportunities to increase our understanding of the forces that have differentially shaped the evolutionary history of hominid taxa. Here, we expand upon the work of the Great Ape Genome Project by analyzing medium to high coverage whole-genome sequences from 14 western lowland gorillas (Gorilla gorilla gorilla), 2 eastern lowland gorillas (G. beringei graueri), and a single Cross River individual (G. gorilla diehli). We infer that the ancestors of western and eastern lowland gorillas diverged from a common ancestor approximately 261 ka, and that the ancestors of the Cross River population diverged from the western lowland gorilla lineage approximately 68 ka. Using a diffusion approximation approach to model the genome-wide site frequency spectrum, we infer a history of western lowland gorillas that includes an ancestral population expansion of 1.4-fold around 970 ka and a recent 5.6-fold contraction in population size 23 ka. The latter may correspond to a major reduction in African equatorial forests around the Last Glacial Maximum. We also analyze patterns of variation among western lowland gorillas to identify several genomic regions with strong signatures of recent selective sweeps. We find that processes related to taste, pancreatic and saliva secretion, sodium ion transmembrane transport, and cardiac muscle function are overrepresented in genomic regions predicted to have experienced recent positive selection.
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Affiliation(s)
- Kimberly F McManus
- Department of Biology, Stanford University Department of Biomedical Informatics, Stanford University
| | - Joanna L Kelley
- Department of Genetics, Stanford University School of Biological Sciences, Washington State University
| | - Shiya Song
- Department of Computational Medicine & Bioinformatics, University of Michigan
| | | | | | - Laurie S Stevison
- Institute for Human Genetics, University of California San Francisco
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, Escondido, CA
| | | | - Jeffrey M Kidd
- Department of Computational Medicine & Bioinformatics, University of Michigan Department of Human Genetics, University of Michigan
| | - Jeffrey D Wall
- Institute for Human Genetics, University of California San Francisco
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100
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Steinberg KM, Schneider VA, Graves-Lindsay TA, Fulton RS, Agarwala R, Huddleston J, Shiryev SA, Morgulis A, Surti U, Warren WC, Church DM, Eichler EE, Wilson RK. Single haplotype assembly of the human genome from a hydatidiform mole. Genome Res 2014; 24:2066-76. [PMID: 25373144 PMCID: PMC4248323 DOI: 10.1101/gr.180893.114] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A complete reference assembly is essential for accurately interpreting individual genomes and associating variation with phenotypes. While the current human reference genome sequence is of very high quality, gaps and misassemblies remain due to biological and technical complexities. Large repetitive sequences and complex allelic diversity are the two main drivers of assembly error. Although increasing the length of sequence reads and library fragments can improve assembly, even the longest available reads do not resolve all regions. In order to overcome the issue of allelic diversity, we used genomic DNA from an essentially haploid hydatidiform mole, CHM1. We utilized several resources from this DNA including a set of end-sequenced and indexed BAC clones and 100× Illumina whole-genome shotgun (WGS) sequence coverage. We used the WGS sequence and the GRCh37 reference assembly to create an assembly of the CHM1 genome. We subsequently incorporated 382 finished BAC clone sequences to generate a draft assembly, CHM1_1.1 (NCBI AssemblyDB GCA_000306695.2). Analysis of gene, repetitive element, and segmental duplication content show this assembly to be of excellent quality and contiguity. However, comparison to assembly-independent resources, such as BAC clone end sequences and PacBio long reads, indicate misassembled regions. Most of these regions are enriched for structural variation and segmental duplication, and can be resolved in the future. This publicly available assembly will be integrated into the Genome Reference Consortium curation framework for further improvement, with the ultimate goal being a completely finished gap-free assembly.
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Affiliation(s)
| | - Valerie A Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | | | - Robert S Fulton
- The Genome Institute at Washington University, St. Louis, Missouri 63108, USA
| | - Richa Agarwala
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - John Huddleston
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| | - Sergey A Shiryev
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Aleksandr Morgulis
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Urvashi Surti
- Department of Pathology and Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Wesley C Warren
- The Genome Institute at Washington University, St. Louis, Missouri 63108, USA
| | | | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| | - Richard K Wilson
- The Genome Institute at Washington University, St. Louis, Missouri 63108, USA
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