51
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Guiblet WM, DeGiorgio M, Cheng X, Chiaromonte F, Eckert KA, Huang YF, Makova KD. Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome. Genome Res 2021; 31:1136-1149. [PMID: 34187812 PMCID: PMC8256861 DOI: 10.1101/gr.269589.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 05/24/2021] [Indexed: 12/11/2022]
Abstract
Approximately 1% of the human genome has the ability to fold into G-quadruplexes (G4s)-noncanonical strand-specific DNA structures forming at G-rich motifs. G4s regulate several key cellular processes (e.g., transcription) and have been hypothesized to participate in others (e.g., firing of replication origins). Moreover, G4s differ in their thermostability, and this may affect their function. Yet, G4s may also hinder replication, transcription, and translation and may increase genome instability and mutation rates. Therefore, depending on their genomic location, thermostability, and functionality, G4 loci might evolve under different selective pressures, which has never been investigated. Here we conducted the first genome-wide analysis of G4 distribution, thermostability, and selection. We found an overrepresentation, high thermostability, and purifying selection for G4s within genic components in which they are expected to be functional-promoters, CpG islands, and 5' and 3' UTRs. A similar pattern was observed for G4s within replication origins, enhancers, eQTLs, and TAD boundary regions, strongly suggesting their functionality. In contrast, G4s on the nontranscribed strand of exons were underrepresented, were unstable, and evolved neutrally. In general, G4s on the nontranscribed strand of genic components had lower density and were less stable than those on the transcribed strand, suggesting that the former are avoided at the RNA level. Across the genome, purifying selection was stronger at stable G4s. Our results suggest that purifying selection preserves the sequences of functional G4s, whereas nonfunctional G4s are too costly to be tolerated in the genome. Thus, G4s are emerging as fundamental, functional genomic elements.
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Affiliation(s)
- Wilfried M Guiblet
- Bioinformatics and Genomics Graduate Program, Penn State University, University Park, Pennsylvania 16802, USA
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida 33431, USA
| | - Xiaoheng Cheng
- Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA
| | - Francesca Chiaromonte
- Department of Statistics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
- Sant'Anna School of Advanced Studies, 56127 Pisa, Italy
| | - Kristin A Eckert
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
- Department of Pathology, Penn State University, College of Medicine, Hershey, Pennsylvania 17033, USA
| | - Yi-Fei Huang
- Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
| | - Kateryna D Makova
- Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
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52
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Escoda L, Castresana J. The genome of the Pyrenean desman and the effects of bottlenecks and inbreeding on the genomic landscape of an endangered species. Evol Appl 2021; 14:1898-1913. [PMID: 34295371 PMCID: PMC8288019 DOI: 10.1111/eva.13249] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 03/19/2021] [Accepted: 04/27/2021] [Indexed: 01/23/2023] Open
Abstract
The Pyrenean desman (Galemys pyrenaicus) is a small semiaquatic mammal endemic to the Iberian Peninsula. Despite its limited range, this species presents a strong genetic structure due to past isolation in glacial refugia and subsequent bottlenecks. Additionally, some populations are highly fragmented today as a consequence of river barriers, causing substantial levels of inbreeding. These features make the Pyrenean desman a unique model in which to study the genomic footprints of differentiation, bottlenecks and extreme isolation in an endangered species. To understand these processes, the complete genome of the Pyrenean desman was sequenced and assembled using a Bloom filter-based approach. An analysis of the 1.83 Gb reference genome and the sequencing of five additional individuals from different evolutionary units allowed us to detect its main genomic characteristics. The population differentiation of the species was reflected in highly distinctive demographic trajectories. In addition, a severe population bottleneck during the postglacial recolonization of the eastern Pyrenees created one of the lowest genomic heterozygosity values recorded in a mammal. Moreover, isolation and inbreeding gave rise to a high proportion of runs of homozygosity (ROH). Despite these extremely low levels of genetic diversity, two key multigene families from an eco-evolutionary perspective, the major histocompatibility complex and olfactory receptor genes, showed heterozygosity excess in the majority of individuals, revealing that functional diversity can be maintained up to a certain extent. Furthermore, these two classes of genes were significantly less abundant than expected within ROH. In conclusion, the genomic landscape of each analysed Pyrenean desman turned out to be strikingly distinctive and was a clear reflection of its recent ancestry and current conservation conditions. These results may help characterize the genomic health of each individual, and can be crucial for the conservation and management of the species.
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Affiliation(s)
- Lídia Escoda
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
| | - Jose Castresana
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
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53
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Sahm A, Koch P, Horvath S, Hoffmann S. An analysis of methylome evolution in primates. Mol Biol Evol 2021; 38:4700-4714. [PMID: 34175932 PMCID: PMC8557466 DOI: 10.1093/molbev/msab189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Although the investigation of the epigenome becomes increasingly important, still little is known about the long-term evolution of epigenetic marks and systematic investigation strategies are still lacking. Here, we systematically demonstrate the transfer of classic phylogenetic methods such as maximum likelihood based on substitution models, parsimony, and distance-based to interval-scaled epigenetic data. Using a great apes blood data set, we demonstrate that DNA methylation is evolutionarily conserved at the level of individual CpGs in promotors, enhancers, and genic regions. Our analysis also reveals that this epigenomic conservation is significantly correlated with its transcription factor binding density. Binding sites for transcription factors involved in neuron differentiation and components of AP-1 evolve at a significantly higher rate at methylation than at the nucleotide level. Moreover, our models suggest an accelerated epigenomic evolution at binding sites of BRCA1, chromobox homolog protein 2, and factors of the polycomb repressor 2 complex in humans. For most genomic regions, the methylation-based reconstruction of phylogenetic trees is at par with sequence-based reconstruction. Most strikingly, phylogenetic reconstruction using methylation rates in enhancer regions was ineffective independently of the chosen model. We identify a set of phylogenetically uninformative CpG sites enriched in enhancers controlling immune-related genes.
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Affiliation(s)
- Arne Sahm
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Philipp Koch
- Core Facility Life Science Computing, Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
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54
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Fountain ED, Zhou LC, Karklus A, Liu QX, Meyers J, Fontanilla IKC, Rafael EF, Yu JY, Zhang Q, Zhu XL, Pei EL, Yuan YH, Banes GL. Cross-Species Application of Illumina iScan Microarrays for Cost-Effective, High-Throughput SNP Discovery. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.629252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microarrays can be a cost-effective alternative to high-throughput sequencing for discovering novel single-nucleotide polymorphisms (SNPs). Illumina’s iScan platform dominates the market, but their commercial microarray products are designed for model organisms. Further, the platform outputs data in a proprietary format. This cannot be easily converted to human-readable genotypes or be merged with pre-existing data. To address this, we present and validate a novel pipeline to facilitate data analysis from cross-species application of Illumina microarrays. This facilitates the generation of a compatible VCF from iScan data and the merging of this with a second VCF comprising genotypes derived from other samples and sources. Our pipeline includes a custom script, iScanVCFMerge (presented as a Python package), which we validate using iScan data from three great ape genera. We conclude that cross-species application of microarrays can be a rapid, cost-effective approach for SNP discovery in non-model organisms. Our pipeline surmounts the common challenges of integrating iScan genotypes with pre-existing data.
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55
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Kuhlwilm M, Fontsere C, Han S, Alvarez-Estape M, Marques-Bonet T. HuConTest: Testing Human Contamination in Great Ape Samples. Genome Biol Evol 2021; 13:6284962. [PMID: 34038549 PMCID: PMC8247554 DOI: 10.1093/gbe/evab117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2021] [Indexed: 12/20/2022] Open
Abstract
Modern human contamination is a common problem in ancient DNA studies. We provide evidence that this issue is also present in studies in great apes, which are our closest living relatives, for example in noninvasive samples. Here, we present a simple method to detect human contamination in short-read sequencing data from different species: HuConTest. We demonstrate its feasibility using blood and tissue samples from these species. This test is particularly useful for more complex samples (such as museum and noninvasive samples) which have smaller amounts of endogenous DNA, as we show here.
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Affiliation(s)
- Martin Kuhlwilm
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Claudia Fontsere
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Sojung Han
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Marina Alvarez-Estape
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Cerdanyola del Vallès, Barcelona, Spain
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56
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Hartley GA, Okhovat M, O'Neill RJ, Carbone L. Comparative analyses of gibbon centromeres reveal dynamic genus specific shifts in repeat composition. Mol Biol Evol 2021; 38:3972-3992. [PMID: 33983366 PMCID: PMC8382927 DOI: 10.1093/molbev/msab148] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Centromeres are functionally conserved chromosomal loci essential for proper chromosome segregation during cell division, yet they show high sequence diversity across species. Despite their variation, a near universal feature of centromeres is the presence of repetitive sequences, such as DNA satellites and transposable elements (TEs). Because of their rapidly evolving karyotypes, gibbons represent a compelling model to investigate divergence of functional centromere sequences across short evolutionary timescales. In this study, we use ChIP-seq, RNA-seq, and fluorescence in situ hybridization to comprehensively investigate the centromeric repeat content of the four extant gibbon genera (Hoolock, Hylobates, Nomascus, and Siamang). In all gibbon genera, we find that CENP-A nucleosomes and the DNA-proteins that interface with the inner kinetochore preferentially bind retroelements of broad classes rather than satellite DNA. A previously identified gibbon-specific composite retrotransposon, LAVA, known to be expanded within the centromere regions of one gibbon genus (Hoolock), displays centromere- and species-specific sequence differences, potentially as a result of its co-option to a centromeric function. When dissecting centromere satellite composition, we discovered the presence of the retroelement-derived macrosatellite SST1 in multiple centromeres of Hoolock, whereas alpha-satellites represent the predominate satellite in the other genera, further suggesting an independent evolutionary trajectory for Hoolock centromeres. Finally, using de novo assembly of centromere sequences, we determined that transcripts originating from gibbon centromeres recapitulate the species-specific TE composition. Combined, our data reveal dynamic shifts in the repeat content that define gibbon centromeres and coincide with the extensive karyotypic diversity within this lineage.
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Affiliation(s)
- Gabrielle A Hartley
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269
| | - Mariam Okhovat
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, 97239
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269.,Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269.,Department of Genomics and Genome Sciences, UConn Health, Farmington, CT, 06030
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, 97239.,Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, 97006.,Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, 97239.,Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, 97239
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57
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Mathyer ME, Brettmann EA, Schmidt AD, Goodwin ZA, Oh IY, Quiggle AM, Tycksen E, Ramakrishnan N, Matkovich SJ, Guttman-Yassky E, Edwards JR, de Guzman Strong C. Selective sweep for an enhancer involucrin allele identifies skin barrier adaptation out of Africa. Nat Commun 2021; 12:2557. [PMID: 33963188 PMCID: PMC8105351 DOI: 10.1038/s41467-021-22821-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/30/2021] [Indexed: 02/03/2023] Open
Abstract
The genetic modules that contribute to human evolution are poorly understood. Here we investigate positive selection in the Epidermal Differentiation Complex locus for skin barrier adaptation in diverse HapMap human populations (CEU, JPT/CHB, and YRI). Using Composite of Multiple Signals and iSAFE, we identify selective sweeps for LCE1A-SMCP and involucrin (IVL) haplotypes associated with human migration out-of-Africa, reaching near fixation in European populations. CEU-IVL is associated with increased IVL expression and a known epidermis-specific enhancer. CRISPR/Cas9 deletion of the orthologous mouse enhancer in vivo reveals a functional requirement for the enhancer to regulate Ivl expression in cis. Reporter assays confirm increased regulatory and additive enhancer effects of CEU-specific polymorphisms identified at predicted IRF1 and NFIC binding sites in the IVL enhancer (rs4845327) and its promoter (rs1854779). Together, our results identify a selective sweep for a cis regulatory module for CEU-IVL, highlighting human skin barrier evolution for increased IVL expression out-of-Africa.
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Affiliation(s)
- Mary Elizabeth Mathyer
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Erin A. Brettmann
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Alina D. Schmidt
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Zane A. Goodwin
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Inez Y. Oh
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Ashley M. Quiggle
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Eric Tycksen
- grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Natasha Ramakrishnan
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Scot J. Matkovich
- grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Emma Guttman-Yassky
- grid.59734.3c0000 0001 0670 2351Department of Dermatology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029 USA
| | - John R. Edwards
- grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Cristina de Guzman Strong
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
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58
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Mao Y, Catacchio CR, Hillier LW, Porubsky D, Li R, Sulovari A, Fernandes JD, Montinaro F, Gordon DS, Storer JM, Haukness M, Fiddes IT, Murali SC, Dishuck PC, Hsieh P, Harvey WT, Audano PA, Mercuri L, Piccolo I, Antonacci F, Munson KM, Lewis AP, Baker C, Underwood JG, Hoekzema K, Huang TH, Sorensen M, Walker JA, Hoffman J, Thibaud-Nissen F, Salama SR, Pang AWC, Lee J, Hastie AR, Paten B, Batzer MA, Diekhans M, Ventura M, Eichler EE. A high-quality bonobo genome refines the analysis of hominid evolution. Nature 2021; 594:77-81. [PMID: 33953399 PMCID: PMC8172381 DOI: 10.1038/s41586-021-03519-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 04/07/2021] [Indexed: 12/17/2022]
Abstract
The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation1,2. Here we describe a fully annotated, high-quality bonobo genome assembly, which was constructed without guidance from reference genomes by applying a multiplatform genomics approach. We generate a bonobo genome assembly in which more than 98% of genes are completely annotated and 99% of the gaps are closed, including the resolution of about half of the segmental duplications and almost all of the full-length mobile elements. We compare the bonobo genome to those of other great apes1,3–5 and identify more than 5,569 fixed structural variants that specifically distinguish the bonobo and chimpanzee lineages. We focus on genes that have been lost, changed in structure or expanded in the last few million years of bonobo evolution. We produce a high-resolution map of incomplete lineage sorting and estimate that around 5.1% of the human genome is genetically closer to chimpanzee or bonobo and that more than 36.5% of the genome shows incomplete lineage sorting if we consider a deeper phylogeny including gorilla and orangutan. We also show that 26% of the segments of incomplete lineage sorting between human and chimpanzee or human and bonobo are non-randomly distributed and that genes within these clustered segments show significant excess of amino acid replacement compared to the rest of the genome. A high-quality bonobo genome assembly provides insights into incomplete lineage sorting in hominids and its relevance to gene evolution and the genetic relationship among living hominids.
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Affiliation(s)
- Yafei Mao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - LaDeana W Hillier
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ruiyang Li
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Jason D Fernandes
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Francesco Montinaro
- Department of Biology, University of Bari, Bari, Italy.,Estonian Biocentre, Institute of Genomics, Tartu, Estonia
| | - David S Gordon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | | | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Ian T Fiddes
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Shwetha Canchi Murali
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Philip C Dishuck
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - PingHsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Peter A Audano
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | | | | | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Tzu-Hsueh Huang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Melanie Sorensen
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Jerilyn A Walker
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Jinna Hoffman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Sofie R Salama
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - Joyce Lee
- Bionano Genomics, San Diego, CA, USA
| | | | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Mario Ventura
- Department of Biology, University of Bari, Bari, Italy.
| | - 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.
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59
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Nakamura T, Fujiwara K, Saitou M, Tsukiyama T. Non-human primates as a model for human development. Stem Cell Reports 2021; 16:1093-1103. [PMID: 33979596 PMCID: PMC8185448 DOI: 10.1016/j.stemcr.2021.03.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 12/12/2022] Open
Abstract
Human development has been studied for over a century, but the molecular mechanisms underlying human embryogenesis remain largely unknown due to technical difficulties and ethical issues. Accordingly, mice have been used as a model for mammalian development and studied extensively to infer human biology based on the conservation of fundamental processes between the two species. As research has progressed, however, species-specific differences in characteristics between rodents and primates have become apparent. Non-human primates (NHPs) have also been used for biomedical research, and are now attracting attention as a model for human development. Here, we summarize primate species from the evolutionary and genomic points of view. Then we review the current issues and progress in gene modification technology for NHPs. Finally, we discuss recent studies on the early embryogenesis of primates and future perspectives.
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Affiliation(s)
- Tomonori Nakamura
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; The Hakubi Center for Advanced Research, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Kohei Fujiwara
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Tomoyuki Tsukiyama
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; Research Center for Animal Life Science, Shiga University of Medical Science, Seta-Tsukinowa-cho, Otsu, Shiga 520-2192, Japan.
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60
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Yalcindag E, Stuart P, Hasegawa H, Streit A, Doležalová J, Morrogh-Bernard H, Cheyne SM, Nurcahyo W, Foitová I. Genetic characterization of nodular worm infections in Asian Apes. Sci Rep 2021; 11:7226. [PMID: 33790353 PMCID: PMC8012698 DOI: 10.1038/s41598-021-86518-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/16/2021] [Indexed: 11/09/2022] Open
Abstract
Parasitic nematodes of Oesophagostomum spp., commonly known, as 'nodular worms' are emerging as the most widely distributed and prevalent zoonotic nematodes. Oesophagostomum infections are well documented in African non-human primates; however, the taxonomy, distribution and transmission of Oesophagostomum in Asian non-human primates are not adequately studied. To better understand which Oesophagostomum species infect Asian non-human primates and determine their phylogeny we analysed 55 faecal samples from 50 orangutan and 5 gibbon individuals from Borneo and Sumatra. Both microscopy and molecular results revealed that semi-wild animals had higher Oesophagostomum infection prevalence than free ranging animals. Based on sequence genotyping analysis targeting the Internal transcribed spacer 2 of rDNA, we report for the first time the presence of O. aculeatum in Sumatran apes. Population genetic analysis shows that there is significant genetic differentiation between Bornean and Sumatran O. aculeatum populations. Our results clearly reveal that O. aculeatum in free-ranging animals have a higher genetic variation than those in semi-wild animals, demonstrating that O. aculeatum is circulating naturally in wildlife and zoonotic transmission is possible. Further studies should be conducted to better understand the epidemiology and dynamics of Oesophagostomum transmission between humans, non-human primates and other wild species and livestock in Southeast Asia.
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Affiliation(s)
- Erhan Yalcindag
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Peter Stuart
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
- Department of Biological and Pharmaceutical Sciences, Munster Technological University, Tralee, Co. Kerry, Ireland
| | - Hideo Hasegawa
- Department of Biomedicine, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama, Yufu, Oita, 879-5593, Japan
| | - Adrian Streit
- Department Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Jana Doležalová
- Department of Physiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Brno, Palackého tř. 1, Brno, Czech Republic
| | - Helen Morrogh-Bernard
- Borneo Nature Foundation, Palangkaraya, Central Kalimantan, Indonesia
- Department of Humanities and Social Sciences, Oxford Brookes University, Oxford, UK
| | - Susan M Cheyne
- Department of Humanities and Social Sciences, Oxford Brookes University, Oxford, UK
| | - Wisnu Nurcahyo
- Department of Parasitology, Faculty of Veterinary Medicine, Gadjah Mada University, Yogyakarta, Indonesia
| | - Ivona Foitová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic.
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61
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Navarro AP, Cheeseman IM. Kinetochore assembly throughout the cell cycle. Semin Cell Dev Biol 2021; 117:62-74. [PMID: 33753005 DOI: 10.1016/j.semcdb.2021.03.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 11/29/2022]
Abstract
The kinetochore plays an essential role in facilitating chromosome segregation during cell division. This massive protein complex assembles onto the centromere of chromosomes and enables their attachment to spindle microtubules during mitosis. The kinetochore also functions as a signaling hub to regulate cell cycle progression, and is crucial to ensuring the fidelity of chromosome segregation. Despite the fact that kinetochores are large and robust molecular assemblies, they are also highly dynamic structures that undergo structural and organizational changes throughout the cell cycle. This review will highlight our current understanding of kinetochore structure and function, focusing on the dynamic processes that underlie kinetochore assembly.
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Affiliation(s)
- Alexandra P Navarro
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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62
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Sacrum morphology supports taxonomic heterogeneity of "Australopithecus africanus" at Sterkfontein Member 4. Commun Biol 2021; 4:347. [PMID: 33731844 PMCID: PMC7969745 DOI: 10.1038/s42003-021-01850-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/12/2021] [Indexed: 12/14/2022] Open
Abstract
The presence of multiple Australopithecus species at Sterkfontein Member 4, South Africa (2.07–2.61 Ma), is highly contentious, and quantitative assessments of craniodental and postcranial variability remain inconclusive. Using geometric morphometrics, we compared the sacrum of the small-bodied, presumed female subadult Australopithecus africanus skeleton Sts 14 to the large, alleged male adult StW 431 against a geographically diverse sample of modern humans, and two species of Pan, Gorilla, and Pongo. The probabilities of sampling morphologies as distinct as Sts 14 and StW 431 from a single species ranged from 1.3 to 2.5% for the human sample, and from 0.0 to 4.5% for the great apes, depending on the species and the analysis. Sexual dimorphism and developmental or geologic age could not adequately explain the differences between StW 431 and Sts 14, suggesting that they are unlikely to be conspecific. This supports earlier claims of taxonomic heterogeneity at Sterkfontein Member 4. Fornai et al. present a geometric morphometric study of the sacrum in two alleged Australopithecus africanus specimens from Sterkfontein Member 4, South Africa. By comparing the two fossil hominins to a diverse sample of modern humans and great apes, the authors conclude that the observed morphological differences are unlikely to occur within a single species, supporting earlier claims of taxonomic heterogeneity within the Australopithecus africanus hypodigm.
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63
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Ayoola AO, Zhang BL, Meisel RP, Nneji LM, Shao Y, Morenikeji OB, Adeola AC, Ng’ang’a SI, Ogunjemite BG, Okeyoyin AO, Roos C, Wu DD. Population Genomics Reveals Incipient Speciation, Introgression, and Adaptation in the African Mona Monkey (Cercopithecus mona). Mol Biol Evol 2021; 38:876-890. [PMID: 32986826 PMCID: PMC7947840 DOI: 10.1093/molbev/msaa248] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Guenons (tribe Cercopithecini) are the most widely distributed nonhuman primate in the tropical forest belt of Africa and show considerable phenotypic, taxonomic, and ecological diversity. However, genomic information for most species within this group is still lacking. Here, we present a high-quality de novo genome (total 2.90 Gb, contig N50 equal to 22.7 Mb) of the mona monkey (Cercopithecus mona), together with genome resequencing data of 13 individuals sampled across Nigeria. Our results showed differentiation between populations from East and West of the Niger River ∼84 ka and potential ancient introgression in the East population from other mona group species. The PTPRK, FRAS1, BNC2, and EDN3 genes related to pigmentation displayed signals of introgression in the East population. Genomic scans suggest that immunity genes such as AKT3 and IL13 (possibly involved in simian immunodeficiency virus defense), and G6PD, a gene involved in malaria resistance, are under positive natural selection. Our study gives insights into differentiation, natural selection, and introgression in guenons.
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Affiliation(s)
- Adeola Oluwakemi Ayoola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, Houston, TX
| | - Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Olanrewaju B Morenikeji
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY
- Department of Biology, Hamilton College, Clinton, NY
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Said I Ng’ang’a
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Babafemi G Ogunjemite
- Department of Ecotourism and Wildlife Management, Federal University of Technology, Akure, Nigeria
| | - Agboola O Okeyoyin
- National Park Service Headquarters, Federal Capital Territory, Abuja, Nigeria
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
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64
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Abstract
The great apes play an important role as model organisms. They are our closest living relatives, allowing us to identify the genetic basis of phenotypic traits that we think of as characteristically human. However, the most significant asset of great apes as model organisms is that they share with humans most of their genetic makeup. This means that we can extend our vast knowledge of the human genome, its genes, and the associated phenotypes to these species. Comparative genomic studies of humans and apes thus reveal how very similar genomes react when exposed to different population genetic regimes. In this way, each species represents a natural experiment, where a genome highly similar to the human one, is differently exposed to the evolutionary forces of demography, population structure, selection, recombination, and admixture/hybridization. The initial sequencing of reference genomes for chimpanzee, orangutan, gorilla, the bonobo, each provided new insights and a second generation of sequencing projects has provided diversity data for all the great apes. In this chapter, we will outline some of the findings that population genomic analysis of great apes has provided, and how comparative studies have helped us understand how the fundamental forces in evolution have contributed to shaping the genomes and the genetic diversity of the great apes.
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Affiliation(s)
- David Castellano
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, Aarhus C, Denmark
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65
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Endo S, Motomura K, Tsuhako M, Kakazu Y, Nakamura M, M. Otaki J. Search for Human-Specific Proteins Based on Availability Scores of Short Constituent Sequences: Identification of a WRWSH Protein in Human Testis. Comput Biol Chem 2020. [DOI: 10.5772/intechopen.89653] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Little is known about protein sequences unique in humans. Here, we performed alignment-free sequence comparisons based on the availability (frequency bias) of short constituent amino acid (aa) sequences (SCSs) in proteins to search for human-specific proteins. Focusing on 5-aa SCSs (pentats), exhaustive comparisons of availability scores among the human proteome and other nine mammalian proteomes in the nonredundant (nr) database identified a candidate protein containing WRWSH, here called FAM75, as human-specific. Examination of various human genome sequences revealed that FAM75 had genomic DNA sequences for either WRWSH or WRWSR due to a single nucleotide polymorphism (SNP). FAM75 and its related protein FAM205A were found to be produced through alternative splicing. The FAM75 transcript was found only in humans, but the FAM205A transcript was also present in other mammals. In humans, both FAM75 and FAM205A were expressed specifically in testis at the mRNA level, and they were immunohistochemically located in cells in seminiferous ducts and in acrosomes in spermatids at the protein level, suggesting their possible function in sperm development and fertilization. This study highlights a practical application of SCS-based methods for protein searches and suggests possible contributions of SNP variants and alternative splicing of FAM75 to human evolution.
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66
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Fontsere C, Alvarez-Estape M, Lester J, Arandjelovic M, Kuhlwilm M, Dieguez P, Agbor A, Angedakin S, Ayuk Ayimisin E, Bessone M, Brazzola G, Deschner T, Eno-Nku M, Granjon AC, Head J, Kadam P, Kalan AK, Kambi M, Langergraber K, Lapuente J, Maretti G, Jayne Ormsby L, Piel A, Robbins MM, Stewart F, Vergnes V, Wittig RM, Kühl HS, Marques-Bonet T, Hughes DA, Lizano E. Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments. Mol Ecol Resour 2020; 21:745-761. [PMID: 33217149 DOI: 10.1111/1755-0998.13300] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 10/15/2020] [Accepted: 11/13/2020] [Indexed: 11/30/2022]
Abstract
Noninvasive samples as a source of DNA are gaining interest in genomic studies of endangered species. However, their complex nature and low endogenous DNA content hamper the recovery of good quality data. Target capture has become a productive method to enrich the endogenous fraction of noninvasive samples, such as faeces, but its sensitivity has not yet been extensively studied. Coping with faecal samples with an endogenous DNA content below 1% is a common problem when prior selection of samples from a large collection is not possible. However, samples classified as unfavourable for target capture sequencing might be the only representatives of unique specific geographical locations, or to answer the question of interest. To explore how library complexity may be increased without repeating DNA extractions and generating new libraries, in this study we captured the exome of 60 chimpanzees (Pan troglodytes) using faecal samples with very low proportions of endogenous content (<1%). Our results indicate that by performing additional hybridizations of the same libraries, the molecular complexity can be maintained to achieve higher coverage. Also, whenever possible, the starting DNA material for capture should be increased. Finally, we specifically calculated the sequencing effort needed to avoid exhausting the library complexity of enriched faecal samples with low endogenous DNA content. This study provides guidelines, schemes and tools for laboratories facing the challenges of working with noninvasive samples containing extremely low amounts of endogenous DNA.
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Affiliation(s)
- Claudia Fontsere
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Marina Alvarez-Estape
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Jack Lester
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mimi Arandjelovic
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Martin Kuhlwilm
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Paula Dieguez
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anthony Agbor
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Samuel Angedakin
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Mattia Bessone
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Gregory Brazzola
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tobias Deschner
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | | | - Josephine Head
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Parag Kadam
- School of Biological and Environmental Sciences, Liverpool John Moores University, James Parsons Building, Liverpool, UK
| | - Ammie K Kalan
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mohamed Kambi
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kevin Langergraber
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Institute of Human Origins, Arizona State University, Tempe, AZ, USA
| | - Juan Lapuente
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Comoé Chimpanzee Conservation Project, Kakpin, Comoé National Park, Ivory Coast, Côte d'Ivoire
| | - Giovanna Maretti
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Lucy Jayne Ormsby
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alex Piel
- Department of Anthropology, University College London, London, UK
| | - Martha M Robbins
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Fiona Stewart
- School of Biological and Environmental Sciences, Liverpool John Moores University, James Parsons Building, Liverpool, UK.,Department of Anthropology, University College London, London, UK
| | | | - Roman M Wittig
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
| | - Hjalmar S Kühl
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - David A Hughes
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Esther Lizano
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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67
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Kuang W, Hu J, Wu H, Fen X, Dai Q, Fu Q, Xiao W, Frantz L, Roos C, Nadler T, Irwin DM, Zhou L, Yang X, Yu L. Genetic Diversity, Inbreeding Level, and Genetic Load in Endangered Snub-Nosed Monkeys ( Rhinopithecus). Front Genet 2020; 11:615926. [PMID: 33384722 PMCID: PMC7770136 DOI: 10.3389/fgene.2020.615926] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 11/17/2020] [Indexed: 11/16/2022] Open
Abstract
The snub-nosed monkey genus (Rhinopithecus) comprises five closely related species (R. avunculus, R. bieti, R. brelichi, R. roxellana, and R. strykeri). All are among the world's rarest and most endangered primates. However, the genomic impact associated with their population decline remains unknown. We analyzed population genomic data of all five snub-nosed monkey species to assess their genetic diversity, inbreeding level, and genetic load. For R. roxellana, R. bieti, and R. strykeri, population size is positively correlated with genetic diversity and negatively correlated with levels of inbreeding. Other species, however, which possess small population sizes, such as R. brelichi and R. avunculus, show high levels of genetic diversity and low levels of genomic inbreeding. Similarly, in the three populations of R. roxellana, the Shennongjia population, which possesses the lowest population size, displays a higher level of genetic diversity and lower level of genomic inbreeding. These findings suggest that although R. brelichi and R. avunculus and the Shennongjia population might be at risk, it possess significant genetic diversity and could thus help strengthen their long-term survival potential. Intriguingly, R. roxellana with large population size possess high genetic diversity and low level of genetic load, but they show the highest recent inbreeding level compared with the other snub-nosed monkeys. This suggests that, despite its large population size, R. roxellana has likely been experiencing recent inbreeding, which has not yet affected its mutational load and fitness. Analyses of homozygous-derived deleterious mutations identified in all snub-nosed monkey species indicate that these mutations are affecting immune, especially in smaller population sizes, indicating that the long-term consequences of inbreeding may be resulting in an overall reduction of immune capability in the snub-nosed monkeys, which could provide a dramatic effect on their long-term survival prospects. Altogether, our study provides valuable information concerning the genomic impact of population decline of the snub-nosed monkeys. We revealed multiple counterintuitive and unexpected patterns of genetic diversity in small and large population, which will be essential for conservation management of these endangered species.
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Affiliation(s)
- Weimin Kuang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Jingyang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Hong Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Xiaotian Fen
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing, China
- Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- Beijing College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing, China
- Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- Beijing College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing, China
- Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- Beijing College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Wen Xiao
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, China
| | - Laurent Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
- The Palaeogenomics and Bio-Archaeology Research Network, Department of Archaeology, University of Oxford, Oxford, United Kingdom
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | | | - David M. Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Linchun Zhou
- Lushui Management and Conservation Branch of Gaoligong Mountain National Nature Reserve, Nujiang, China
| | - Xu Yang
- Lushui Forestry and Grassland Council, Nujiang, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
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68
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Of Great Apes and Magpies: Initiations into Animal Behaviour. Animals (Basel) 2020; 10:ani10122369. [PMID: 33321971 PMCID: PMC7764213 DOI: 10.3390/ani10122369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Animal encounters have been favourite subjects for a long time and it would scarcely be novel to report such stories for their own sake, even though the ones told here are dramatic enough to stand on their own. The questions addressed in this paper are twofold. The first question is: What influence may particular and dramatic animal encounters have on the human observer and how dependent is such a response on previously held attitudes? This paper provides three cases studies of extraordinary moments that changed the lives of the human participants and turned them into advocates of the species they had encountered. The next question asked is how we can be respectful of animals without anthropomorphising them and study them in ways that help us understand their abilities and their needs rather than impose questions that mean much to the human researcher but could be irrelevant to the species? The examples given here compare and contrast species that are especially close to us (great apes) with studies of those that are distant from us in their evolution (birds) and show how different attitudes change the questions that can be asked by scientists, demonstrably leading to new and even stunning results. Abstract This paper presents three case studies of exceptional human encounters with animals. These particular examples were selected because they enabled analysis of the underlying reasons that led the human participants to respond in new ways to their animal counterparts. The question asked here is whether sudden insights into the needs and abilities of an animal arises purely from an anthropocentric position as empathy because of genetic closeness (e.g., chimpanzees) or is something else and whether new insights can be applied to other phylogenetic orders not close to us, e.g., birds, and change research questions and implicit prejudices and stereotypes. Particularly in avian species, phylogenetically distant from humans, the prejudices (anthroprocentric position) and the belief in human uniqueness (human exceptionalism) might be greater than in the reactions to primates. Interestingly, in studies of great apes, contradictory opinions and controversies about cognitive abilities, especially when compared with humans, tend to be pronounced. Species appropriateness in test designs are desirable present and future goals but here it is suggested how different experiences can also lead to different questions that explode the myth of human uniqueness and then arrive at entirely different and new results in cognitive and affective abilities of the species under investigation.
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69
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Banes GL, Fountain ED, Karklus A, Huang HM, Jang-Liaw NH, Burgess DL, Wendt J, Moehlenkamp C, Mayhew GF. Genomic targets for high-resolution inference of kinship, ancestry and disease susceptibility in orang-utans (genus: Pongo). BMC Genomics 2020; 21:873. [PMID: 33287706 PMCID: PMC7720378 DOI: 10.1186/s12864-020-07278-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 11/24/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Orang-utans comprise three critically endangered species endemic to the islands of Borneo and Sumatra. Though whole-genome sequencing has recently accelerated our understanding of their evolutionary history, the costs of implementing routine genome screening and diagnostics remain prohibitive. Capitalizing on a tri-fold locus discovery approach, combining data from published whole-genome sequences, novel whole-exome sequencing, and microarray-derived genotype data, we aimed to develop a highly informative gene-focused panel of targets that can be used to address a broad range of research questions. RESULTS We identified and present genomic co-ordinates for 175,186 SNPs and 2315 Y-chromosomal targets, plus 185 genes either known or presumed to be pathogenic in cardiovascular (N = 109) or respiratory (N = 43) diseases in humans - the primary and secondary causes of captive orang-utan mortality - or a majority of other human diseases (N = 33). As proof of concept, we designed and synthesized 'SeqCap' hybrid capture probes for these targets, demonstrating cost-effective target enrichment and reduced-representation sequencing. CONCLUSIONS Our targets are of broad utility in studies of orang-utan ancestry, admixture and disease susceptibility and aetiology, and thus are of value in addressing questions key to the survival of these species. To facilitate comparative analyses, these targets could now be standardized for future orang-utan population genomic studies. The targets are broadly compatible with commercial target enrichment platforms and can be utilized as published here to synthesize applicable probes.
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Affiliation(s)
- Graham L Banes
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, 1220 Capitol Court, Madison, WI, 53715, USA.
| | - Emily D Fountain
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, 1220 Capitol Court, Madison, WI, 53715, USA
| | - Alyssa Karklus
- School of Veterinary Medicine, University of Wisconsin-Madison, 2015 Linden Drive, Madison, WI, 53706, USA
| | - Hao-Ming Huang
- Conservation Genetics Laboratory, Conservation and Research Center, Taipei Zoo, No. 30, Section 2, Xinguang Road, Wenshan District, Taipei City, Taiwan, 11656
| | - Nian-Hong Jang-Liaw
- Conservation Genetics Laboratory, Conservation and Research Center, Taipei Zoo, No. 30, Section 2, Xinguang Road, Wenshan District, Taipei City, Taiwan, 11656
| | - Daniel L Burgess
- Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI, 53719, USA.,Polymer Forge, Inc., 504 S Rosa Rd Ste 200, Madison, WI, 53719, USA
| | - Jennifer Wendt
- Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI, 53719, USA.,Promega Corporation, 2800 Woods Hollow Rd, Fitchburg, WI, 53711, USA
| | - Cynthia Moehlenkamp
- Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI, 53719, USA.,Exact Sciences, 441 Charmany Dr, Madison, WI, 53719, USA
| | - George F Mayhew
- Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI, 53719, USA
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70
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Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression. PLoS Biol 2020; 18:e3000954. [PMID: 33270638 PMCID: PMC7738166 DOI: 10.1371/journal.pbio.3000954] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 12/15/2020] [Accepted: 11/02/2020] [Indexed: 12/17/2022] Open
Abstract
Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here, we present new reference genome assemblies for 3 Old World monkey (OWM) species: Colobus angolensis ssp. palliatus (the black and white colobus), Macaca nemestrina (southern pig-tailed macaque), and Mandrillus leucophaeus (the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place. Combining three newly sequenced primate genomes with other published genomes, this study adapts a little-known method for detecting ancient introgression to genome-scale data, revealing multiple previously unknown examples of hybridization between primate species.
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71
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Orkin JD, Kuderna LFK, Marques-Bonet T. The Diversity of Primates: From Biomedicine to Conservation Genomics. Annu Rev Anim Biosci 2020; 9:103-124. [PMID: 33197208 DOI: 10.1146/annurev-animal-061220-023138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Until now, the field of primate genomics has focused on two major themes: understanding human evolution and advancing biomedical research. We propose that it is now time for a third theme to receive attention: conservation genomics. As a result of anthropogenic effects, the majority of primate species have become threatened with extinction. A more robust primate conservation genomics will allow for genetically informed population management. Thanks to a steady decline in the cost of sequencing, it has now become feasible to sequence whole primate genomes at the population level. Furthermore, technological advances in noninvasive genomic methods have made it possible to acquire genome-scale data from noninvasive biomaterials. Here, we review recent advances in the analysis of primate diversity, with a focus on genomic data sets across the radiation.
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Affiliation(s)
- Joseph D Orkin
- Institut de Biologia Evolutiva, Pompeu Fabra University and Spanish National Research Council, 08003 Barcelona, Spain; , ,
| | - Lukas F K Kuderna
- Institut de Biologia Evolutiva, Pompeu Fabra University and Spanish National Research Council, 08003 Barcelona, Spain; , ,
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, Pompeu Fabra University and Spanish National Research Council, 08003 Barcelona, Spain; , , .,Sequencing Unit, National Genomic Analysis Center, Centre for Genomic Regulation, Barcelona Institute of Science, 08036 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autónoma de Barcelona, 08193 Barcelona, Spain
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72
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Svardal H, Salzburger W, Malinsky M. Genetic Variation and Hybridization in Evolutionary Radiations of Cichlid Fishes. Annu Rev Anim Biosci 2020; 9:55-79. [PMID: 33197206 DOI: 10.1146/annurev-animal-061220-023129] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Evolutionary radiations are responsible for much of the variation in biodiversity across taxa. Cichlid fishes are well known for spectacular evolutionary radiations, as they have repeatedly evolved into large and phenotypically diverse arrays of species. Cichlid genomes carry signatures of past events and, at the same time, are the substrate for ongoing evolution. We survey genome-wide data and the available literature covering 438 cichlid populations (412 species) across multiple radiations to synthesize information about patterns and sharing of genetic variation. Nucleotide diversity within species is low in cichlids, with 92% of surveyed populations having less diversity than the median value found in other vertebrates. Divergence within radiations is also low, and a large proportion of variation is shared among species due to incomplete lineage sorting and widespread hybridization. Population genetics therefore provides a suitable conceptual framework for evolutionary genomic studies of cichlid radiations. We focus in detail on the roles of hybridization in shaping the patterns of genetic variation and in promoting cichlid diversification.
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Affiliation(s)
- Hannes Svardal
- Department of Biology, University of Antwerp, 2020 Antwerp, Belgium; .,Naturalis Biodiversity Center, 2333 Leiden, The Netherlands
| | - Walter Salzburger
- Zoological Institute, University of Basel, 4051 Basel, Switzerland; ,
| | - Milan Malinsky
- Zoological Institute, University of Basel, 4051 Basel, Switzerland; ,
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73
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Premzl M. Comparative genomic analysis of eutherian interferon genes. Genomics 2020; 112:4749-4759. [DOI: 10.1016/j.ygeno.2020.08.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/18/2020] [Accepted: 08/25/2020] [Indexed: 01/23/2023]
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74
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Tang W, Liang P. Alu master copies serve as the drivers of differential SINE transposition in recent primate genomes. Anal Biochem 2020; 606:113825. [PMID: 32712063 DOI: 10.1016/j.ab.2020.113825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 12/25/2022]
Abstract
Alu elements, averaging ~300bp in length, are a family of primate-specific short intersperse nuclear elements (SINEs) with more than one million copies and contributing to ~11% of primate genomes. Despite mostly being shared among primates, our recent study revealed highly differential recent Alu transposition among the genomes of primates from Hominidae and Cercopithecidae families. To understand the underlying mechanism, we analyzed six primate genomes and revealed species- and lineage-specific Alu profile exclusively defined by AluY composition. Among all Alus from the 6 genomes, we identified 5401 Alu master copies with 99% being from the AluY subfamily. The numbers of Alu master copies are positively correlated to the number of AluY elements in the genomes with the baboon genome having the largest number of most recent Alu master copies at high activities, while the crab-eating macaque genome having a low number of Alu master copies with low activity. Furthermore, the expression level of Alu master copies is positively correlated with their transposition activity. Our results support the concept that Alu transposition in primate genomes is driven by a small number of master copies, the number and relative activity of which contribute to the differential Alu transposition in recent primate genomes.
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Affiliation(s)
- Wanxiangfu Tang
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, L2S 3A1, Canada
| | - Ping Liang
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, L2S 3A1, Canada.
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75
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Mudd AB, Bredeson JV, Baum R, Hockemeyer D, Rokhsar DS. Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution. Commun Biol 2020; 3:480. [PMID: 32873878 PMCID: PMC7463020 DOI: 10.1038/s42003-020-1096-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 05/06/2020] [Indexed: 01/29/2023] Open
Abstract
Closely related muntjac deer show striking karyotype differences. Here we describe chromosome-scale genome assemblies for Chinese and Indian muntjacs, Muntiacus reevesi (2n = 46) and Muntiacus muntjak vaginalis (2n = 6/7), and analyze their evolution and architecture. The genomes show extensive collinearity with each other and with other deer and cattle. We identified numerous fusion events unique to and shared by muntjacs relative to the cervid ancestor, confirming many cytogenetic observations with genome sequence. One of these M. muntjak fusions reversed an earlier fission in the cervid lineage. Comparative Hi-C analysis showed that the chromosome fusions on the M. muntjak lineage altered long-range, three-dimensional chromosome organization relative to M. reevesi in interphase nuclei including A/B compartment structure. This reshaping of multi-megabase contacts occurred without notable change in local chromatin compaction, even near fusion sites. A few genes involved in chromosome maintenance show evidence for rapid evolution, possibly associated with the dramatic changes in karyotype.
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Affiliation(s)
- Austin B Mudd
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Jessen V Bredeson
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Rachel Baum
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.
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76
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Damert A. LINE-1 ORF1p does not determine substrate preference for human/orangutan SVA and gibbon LAVA. Mob DNA 2020; 11:27. [PMID: 32676128 PMCID: PMC7353768 DOI: 10.1186/s13100-020-00222-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/06/2020] [Indexed: 12/28/2022] Open
Abstract
Background Non-autonomous VNTR (Variable Number of Tandem Repeats) composite retrotransposons – SVA (SINE-R-VNTR-Alu) and LAVA (L1-Alu-VNTR-Alu) – are specific to hominoid primates. SVA expanded in great apes, LAVA in gibbon. Both SVA and LAVA have been shown to be mobilized by the autonomous LINE-1 (L1)-encoded protein machinery in a cell-based assay in trans. The efficiency of human SVA retrotransposition in vitro has, however, been considerably lower than would be expected based on recent pedigree-based in vivo estimates. The VNTR composite elements across hominoids – gibbon LAVA, orangutan SVA_A descendants and hominine SVA_D descendants – display characteristic structures of the 5′ Alu-like domain and the VNTR. Different partner L1 subfamilies are currently active in each of the lineages. The possibility that the lineage-specific types of VNTR composites evolved in response to evolutionary changes in their autonomous partners, particularly in the nucleic acid binding L1 ORF1-encoded protein, has not been addressed. Results Here I report the identification and functional characterization of a highly active human SVA element using an improved mneo retrotransposition reporter cassette. The modified cassette (mneoM) minimizes splicing between the VNTR of human SVAs and the neomycin phosphotransferase stop codon. SVA deletion analysis provides evidence that key elements determining its mobilization efficiency reside in the VNTR and 5′ hexameric repeats. Simultaneous removal of the 5′ hexameric repeats and part of the VNTR has an additive negative effect on mobilization rates. Taking advantage of the modified reporter cassette that facilitates robust cross-species comparison of SVA/LAVA retrotransposition, I show that the ORF1-encoded proteins of the L1 subfamilies currently active in gibbon, orangutan and human do not display substrate preference for gibbon LAVA versus orangutan SVA versus human SVA. Finally, I demonstrate that an orangutan-derived ORF1p supports only limited retrotransposition of SVA/LAVA in trans, despite being fully functional in L1 mobilization in cis. Conclusions Overall, the analysis confirms SVA as a highly active human retrotransposon and preferred substrate of the L1-encoded protein machinery. Based on the results obtained in human cells coevolution of L1 ORF1p and VNTR composites does not appear very likely. The changes in orangutan L1 ORF1p that markedly reduce its mobilization capacity in trans might explain the different SVA insertion rates in the orangutan and hominine lineages, respectively.
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Affiliation(s)
- Annette Damert
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
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77
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Adrion JR, Cole CB, Dukler N, Galloway JG, Gladstein AL, Gower G, Kyriazis CC, Ragsdale AP, Tsambos G, Baumdicker F, Carlson J, Cartwright RA, Durvasula A, Gronau I, Kim BY, McKenzie P, Messer PW, Noskova E, Ortega-Del Vecchyo D, Racimo F, Struck TJ, Gravel S, Gutenkunst RN, Lohmueller KE, Ralph PL, Schrider DR, Siepel A, Kelleher J, Kern AD. A community-maintained standard library of population genetic models. eLife 2020; 9:e54967. [PMID: 32573438 PMCID: PMC7438115 DOI: 10.7554/elife.54967] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 06/15/2020] [Indexed: 12/18/2022] Open
Abstract
The explosion in population genomic data demands ever more complex modes of analysis, and increasingly, these analyses depend on sophisticated simulations. Recent advances in population genetic simulation have made it possible to simulate large and complex models, but specifying such models for a particular simulation engine remains a difficult and error-prone task. Computational genetics researchers currently re-implement simulation models independently, leading to inconsistency and duplication of effort. This situation presents a major barrier to empirical researchers seeking to use simulations for power analyses of upcoming studies or sanity checks on existing genomic data. Population genetics, as a field, also lacks standard benchmarks by which new tools for inference might be measured. Here, we describe a new resource, stdpopsim, that attempts to rectify this situation. Stdpopsim is a community-driven open source project, which provides easy access to a growing catalog of published simulation models from a range of organisms and supports multiple simulation engine backends. This resource is available as a well-documented python library with a simple command-line interface. We share some examples demonstrating how stdpopsim can be used to systematically compare demographic inference methods, and we encourage a broader community of developers to contribute to this growing resource.
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Affiliation(s)
- Jeffrey R Adrion
- Department of Biology and Institute of Ecology and Evolution, University of OregonEugeneUnited States
| | - Christopher B Cole
- Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
| | - Noah Dukler
- Simons Center for Quantitative Biology, Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Jared G Galloway
- Department of Biology and Institute of Ecology and Evolution, University of OregonEugeneUnited States
| | - Ariella L Gladstein
- Department of Genetics, University of North Carolina at Chapel HillChapel HillUnited States
| | - Graham Gower
- Lundbeck GeoGenetics Centre, Globe Institute, University of CopenhagenCopenhagenDenmark
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los AngelesLos AngelesUnited States
| | | | - Georgia Tsambos
- Melbourne Integrative Genomics, School of Mathematics and Statistics, University of MelbourneMelbourneAustralia
| | - Franz Baumdicker
- Department of Mathematical Stochastics, University of FreiburgFreiburgGermany
| | - Jedidiah Carlson
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Reed A Cartwright
- The Biodesign Institute and The School of Life Sciences, Arizona State UniversityTempeUnited States
| | - Arun Durvasula
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Ilan Gronau
- The Efi Arazi School of Computer Science, Herzliya Interdisciplinary CenterHerzliyaIsrael
| | - Bernard Y Kim
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Patrick McKenzie
- Department of Ecology, Evolution, and Environmental Biology, Columbia UniversityNew YorkUnited States
| | - Philipp W Messer
- Department of Computational BiologyCornell UniversityIthacaUnited States
| | - Ekaterina Noskova
- Computer Technologies Laboratory, ITMO UniversitySaint PetersburgRussian Federation
| | - Diego Ortega-Del Vecchyo
- International Laboratory for Human Genome Research, National Autonomous University of MexicoJuriquillaMexico
| | - Fernando Racimo
- Lundbeck GeoGenetics Centre, Globe Institute, University of CopenhagenCopenhagenDenmark
| | - Travis J Struck
- Departmentof Molecular and Cellular Biology, University of ArizonaTucsonUnited States
| | - Simon Gravel
- Department of Human Genetics, McGill UniversityMontrealCanada
| | - Ryan N Gutenkunst
- Departmentof Molecular and Cellular Biology, University of ArizonaTucsonUnited States
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los AngelesLos AngelesUnited States
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Peter L Ralph
- Department of Biology and Institute of Ecology and Evolution, University of OregonEugeneUnited States
- Department of Mathematics, University of OregonEugeneUnited States
| | - Daniel R Schrider
- Department of Genetics, University of North Carolina at Chapel HillChapel HillUnited States
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Jerome Kelleher
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of OxfordOxfordUnited Kingdom
| | - Andrew D Kern
- Department of Biology and Institute of Ecology and Evolution, University of OregonEugeneUnited States
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78
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Branching out: what omics can tell us about primate evolution. Curr Opin Genet Dev 2020; 62:65-71. [DOI: 10.1016/j.gde.2020.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 12/25/2022]
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79
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Mogielnicki C, Pearl K. Hominid sexual nature. Theory Biosci 2020; 139:191-207. [PMID: 32170558 PMCID: PMC7244608 DOI: 10.1007/s12064-020-00312-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 03/03/2020] [Indexed: 11/28/2022]
Abstract
The aim of the paper is to identify psychosomatic evolutionary adaptations of hominids, which direct them at maximizing their reproductive success, and on the basis of which their various social structures are built. Selected features of the hominid last common ancestor were extracted; by reducing the influence of the social structure, they were defined as the hominid "sexual nature"; these considerations were supported by the analysis of sexual jealousy as a function of socio-environmental conditions. The "sexuality core" of a hominid female was defined as "selective polyandry"-the female selects the best males among those available; and of a hominid male as "tolerant promiscuity"-the male strives for multi-male and multi-female copulations with sexually attractive females. The extracted "sexuality cores" condemn hominids to a patriarchal social structure and thus to sexual coercion and jealousy. The source of male sexual jealousy is limited access to females. Hominid female jealousy of the male results mainly from the need for protection and support. Hominids' social structures are determined by females' sexual selectivity or opportunism and by their continuous or periodic proceptivity and estrus signaling. Evolutionary functions developed by women: out-estrus sexuality, copulation calls, multiple orgasms, allow them to obtain the best possible spermatozoid. The institution of marriage blocks the influence of sexual selection in the species Homo sapiens.
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80
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Ola M, O'Brien CE, Coughlan AY, Ma Q, Donovan PD, Wolfe KH, Butler G. Polymorphic centromere locations in the pathogenic yeast Candida parapsilosis. Genome Res 2020; 30:684-696. [PMID: 32424070 PMCID: PMC7263194 DOI: 10.1101/gr.257816.119] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/24/2020] [Indexed: 11/24/2022]
Abstract
Centromeres pose an evolutionary paradox: strongly conserved in function but rapidly changing in sequence and structure. However, in the absence of damage, centromere locations are usually conserved within a species. We report here that isolates of the pathogenic yeast species Candida parapsilosis show within-species polymorphism for the location of centromeres on two of its eight chromosomes. Its old centromeres have an inverted-repeat (IR) structure, whereas its new centromeres have no obvious structural features but are located within 30 kb of the old site. Centromeres can therefore move naturally from one chromosomal site to another, apparently spontaneously and in the absence of any significant changes in DNA sequence. Our observations are consistent with a model in which all centromeres are genetically determined, such as by the presence of short or long IRs or by the ability to form cruciforms. We also find that centromeres have been hotspots for genomic rearrangements in the C. parapsilosis clade.
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Affiliation(s)
- Mihaela Ola
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Caoimhe E O'Brien
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Aisling Y Coughlan
- School of Medicine, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Qinxi Ma
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Paul D Donovan
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kenneth H Wolfe
- School of Medicine, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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81
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Etherington GJ, Heavens D, Baker D, Lister A, McNelly R, Garcia G, Clavijo B, Macaulay I, Haerty W, Di Palma F. Sequencing smart: De novo sequencing and assembly approaches for a non-model mammal. Gigascience 2020; 9:5836134. [PMID: 32396200 PMCID: PMC7216774 DOI: 10.1093/gigascience/giaa045] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 02/28/2020] [Accepted: 04/15/2020] [Indexed: 01/05/2023] Open
Abstract
Background Whilst much sequencing effort has focused on key mammalian model organisms such as mouse and human, little is known about the relationship between genome sequencing techniques for non-model mammals and genome assembly quality. This is especially relevant to non-model mammals, where the samples to be sequenced are often degraded and of low quality. A key aspect when planning a genome project is the choice of sequencing data to generate. This decision is driven by several factors, including the biological questions being asked, the quality of DNA available, and the availability of funds. Cutting-edge sequencing technologies now make it possible to achieve highly contiguous, chromosome-level genome assemblies, but rely on high-quality high molecular weight DNA. However, funding is often insufficient for many independent research groups to use these techniques. Here we use a range of different genomic technologies generated from a roadkill European polecat (Mustela putorius) to assess various assembly techniques on this low-quality sample. We evaluated different approaches for de novo assemblies and discuss their value in relation to biological analyses. Results Generally, assemblies containing more data types achieved better scores in our ranking system. However, when accounting for misassemblies, this was not always the case for Bionano and low-coverage 10x Genomics (for scaffolding only). We also find that the extra cost associated with combining multiple data types is not necessarily associated with better genome assemblies. Conclusions The high degree of variability between each de novo assembly method (assessed from the 7 key metrics) highlights the importance of carefully devising the sequencing strategy to be able to carry out the desired analysis. Adding more data to genome assemblies does not always result in better assemblies, so it is important to understand the nuances of genomic data integration explained here, in order to obtain cost-effective value for money when sequencing genomes.
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Affiliation(s)
| | - Darren Heavens
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - David Baker
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Ashleigh Lister
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Rose McNelly
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Gonzalo Garcia
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Bernardo Clavijo
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Iain Macaulay
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Wilfried Haerty
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
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82
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Heijmans CMC, de Groot NG, Bontrop RE. Comparative genetics of the major histocompatibility complex in humans and nonhuman primates. Int J Immunogenet 2020; 47:243-260. [PMID: 32358905 DOI: 10.1111/iji.12490] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/01/2020] [Accepted: 04/12/2020] [Indexed: 12/13/2022]
Abstract
The major histocompatibility complex (MHC) is one of the most gene-dense regions of the mammalian genome. Multiple genes within the human MHC (HLA) show extensive polymorphism, and currently, more than 26,000 alleles divided over 39 different genes are known. Nonhuman primate (NHP) species are grouped into great and lesser apes and Old and New World monkeys, and their MHC is studied mostly because of their important role as animal models in preclinical research or in connection with conservation biology purposes. The evolutionary equivalents of many of the HLA genes are present in NHP species, and these genes may also show abundant levels of polymorphism. This review is intended to provide a comprehensive comparison relating to the organization and polymorphism of human and NHP MHC regions.
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Affiliation(s)
- Corrine M C Heijmans
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
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83
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Ohzeki JI, Otake K, Masumoto H. Human artificial chromosome: Chromatin assembly mechanisms and CENP-B. Exp Cell Res 2020; 389:111900. [PMID: 32044309 DOI: 10.1016/j.yexcr.2020.111900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 12/12/2022]
Abstract
The centromere is a specialized chromosomal locus required for accurate chromosome segregation. Heterochromatin also assembles around centromere chromatin and forms a base that supports sister chromatid cohesion until anaphase begins. Both centromere chromatin and heterochromatin assemble on a centromeric DNA sequence, a highly repetitive sequence called alphoid DNA (α-satellite DNA) in humans. Alphoid DNA can form a de novo centromere and subsequent human artificial chromosome (HAC) when introduced into the human culture cells HT1080. HAC is maintained stably as a single chromosome independent of other human chromosomes. For de novo centromere assembly and HAC formation, the centromere protein CENP-B and its binding sites, CENP-B boxes, are required in the repeating units of alphoid DNA. CENP-B has multiple roles in de novo centromere chromatin assembly and stabilization and in heterochromatin formation upon alphoid DNA introduction into the cells. Here we review recent progress in human artificial chromosome construction and centromere/heterochromatin assembly and maintenance, focusing on the involvement of human centromere DNA and CENP-B protein.
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Affiliation(s)
- Jun-Ichirou Ohzeki
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818, Japan
| | - Koichiro Otake
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818, Japan
| | - Hiroshi Masumoto
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818, Japan.
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84
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Gambogi CW, Dawicki-McKenna JM, Logsdon GA, Black BE. The unique kind of human artificial chromosome: Bypassing the requirement for repetitive centromere DNA. Exp Cell Res 2020; 391:111978. [PMID: 32246994 DOI: 10.1016/j.yexcr.2020.111978] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 12/20/2022]
Abstract
Centromeres are essential components of all eukaryotic chromosomes, including artificial/synthetic ones built in the laboratory. In humans, centromeres are typically located on repetitive α-satellite DNA, and these sequences are the "major ingredient" in first-generation human artificial chromosomes (HACs). Repetitive centromeric sequences present a major challenge for the design of synthetic mammalian chromosomes because they are difficult to synthesize, assemble, and characterize. Additionally, in most eukaryotes, centromeres are defined epigenetically. Here, we review the role of the genetic and epigenetic contributions to establishing centromere identity, highlighting recent work to hijack the epigenetic machinery to initiate centromere identity on a new generation of HACs built without α-satellite DNA. We also discuss the opportunities and challenges in developing useful unique sequence-based HACs.
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Affiliation(s)
- Craig W Gambogi
- Department of Biochemistry and Biophysics, Graduate Program in Biochemistry and Molecular Biophysics, Penn Center for Genome Integrity, and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jennine M Dawicki-McKenna
- Department of Biochemistry and Biophysics, Graduate Program in Biochemistry and Molecular Biophysics, Penn Center for Genome Integrity, and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Ben E Black
- Department of Biochemistry and Biophysics, Graduate Program in Biochemistry and Molecular Biophysics, Penn Center for Genome Integrity, and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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85
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Hu JY, Hao ZQ, Frantz L, Wu SF, Chen W, Jiang YF, Wu H, Kuang WM, Li H, Zhang YP, Yu L. Genomic consequences of population decline in critically endangered pangolins and their demographic histories. Natl Sci Rev 2020; 7:798-814. [PMID: 34692098 PMCID: PMC8288997 DOI: 10.1093/nsr/nwaa031] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 01/29/2020] [Accepted: 02/19/2020] [Indexed: 12/14/2022] Open
Abstract
Pangolins are among the most critically endangered animals due to heavy poaching and worldwide trafficking. However, their demographic histories and the genomic consequences of their recent population declines remain unknown. We generated high-quality de novo reference genomes for critically endangered Malayan (Manis javanica, MJ) and Chinese (M. pentadactyla, MP) pangolins and re-sequencing population genomic data from 74 MJs and 23 MPs. We recovered the population identities of illegally traded pangolins and previously unrecognized genetic populations that should be protected as evolutionarily distinct conservation units. Demographic reconstruction suggested environmental changes have resulted in a population size fluctuation of pangolins. Additionally, recent population size declines due to human activities have resulted in an increase in inbreeding and genetic load. Deleterious mutations were enriched in genes related to cancer/diseases and cholesterol homeostasis, which may have increased their susceptibility to diseases and decreased their survival potential to adapt to environmental changes and high-cholesterol diets. This comprehensive study provides not only high-quality pangolin reference genomes, but also valuable information concerning the driving factors of long-term population size fluctuations and the genomic impact of recent population size declines due to human activities, which is essential for pangolin conservation management and global action planning.
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Affiliation(s)
- Jing-Yang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Zi-Qian Hao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Laurent Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
- The Palaeogenomics and Bio-Archaeology Research Network, Department of Archaeology, University of Oxford, Oxford OX1 3TG, UK
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Wu Chen
- Guangzhou Zoo, Guangzhou 510070, China
| | - Yun-Fang Jiang
- Lushui Management and Conservation Branch of Gaoligong Mountain National Nature Reserve, Nujiang 673100, China
| | - Hong Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Wei-Min Kuang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Haipeng Li
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Ya-Ping Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
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86
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Mandáková T, Hloušková P, Koch MA, Lysak MA. Genome Evolution in Arabideae Was Marked by Frequent Centromere Repositioning. THE PLANT CELL 2020; 32:650-665. [PMID: 31919297 PMCID: PMC7054033 DOI: 10.1105/tpc.19.00557] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 12/02/2019] [Accepted: 01/09/2020] [Indexed: 05/04/2023]
Abstract
Centromere position may change despite conserved chromosomal collinearity. Centromere repositioning and evolutionary new centromeres (ENCs) were frequently encountered during vertebrate genome evolution but only rarely observed in plants. The largest crucifer tribe, Arabideae (∼550 species; Brassicaceae, the mustard family), diversified into several well-defined subclades in the virtual absence of chromosome number variation. Bacterial artificial chromosome-based comparative chromosome painting uncovered a constancy of genome structures among 10 analyzed genomes representing seven Arabideae subclades classified as four genera: Arabis, Aubrieta, Draba, and Pseudoturritis Interestingly, the intra-tribal diversification was marked by a high frequency of ENCs on five of the eight homoeologous chromosomes in the crown-group genera, but not in the most ancestral Pseudoturritis genome. From the 32 documented ENCs, at least 26 originated independently, including 4 ENCs recurrently formed at the same position in not closely related species. While chromosomal localization of ENCs does not reflect the phylogenetic position of the Arabideae subclades, centromere seeding was usually confined to long chromosome arms, transforming acrocentric chromosomes to (sub)metacentric chromosomes. Centromere repositioning is proposed as the key mechanism differentiating overall conserved homoeologous chromosomes across the crown-group Arabideae subclades. The evolutionary significance of centromere repositioning is discussed in the context of possible adaptive effects on recombination and epigenetic regulation of gene expression.
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Affiliation(s)
- Terezie Mandáková
- Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Petra Hloušková
- Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Marcus A Koch
- Centre for Organismal Studies (COS) Heidelberg, Biodiversity and Plant Systematics/Botanical Garden and Herbarium (HEID), Heidelberg University, Heidelberg, Germany
| | - Martin A Lysak
- Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
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87
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Murillo-Pineda M, Jansen LET. Genetics, epigenetics and back again: Lessons learned from neocentromeres. Exp Cell Res 2020; 389:111909. [PMID: 32068000 DOI: 10.1016/j.yexcr.2020.111909] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/04/2020] [Accepted: 02/10/2020] [Indexed: 12/12/2022]
Abstract
The duplication and segregation of the genome during cell division is crucial to maintain cell identity, development of organisms and tissue maintenance. Centromeres are at the basis of accurate chromosome segregation as they define the site of assembly of the kinetochore, a large complex of proteins that attaches to spindle microtubules driving chromosome movement during cell division. Here we summarize nearly 40 years of research focussed on centromere specification and the role of local cis elements in creating a stable centromere. Initial discoveries in budding yeast in the 1980s opened up the field and revealed essential DNA sequence elements that define centromere position and function. Further work in humans discovered a centromeric DNA sequence-specific binding protein and centromeric α-satellite DNA was found to have the capacity to seed centromeres de novo. Despite the early indication of genetic elements as drivers of centromere specification, the discovery in the nineties of neocentromeres that form on unrelated DNA sequences, shifted the focus to epigenetic mechanisms. While specific sequence elements appeared non-essential, the histone H3 variant CENP-A was identified as a crucial component in centromere specification. Neocentromeres, occurring naturally or induced experimentally, have become an insightful tool to understand the mechanisms for centromere specification and will be the focus of this review. They have helped to define the strong epigenetic chromatin-based component underlying centromere inheritance but also provide new opportunities to understand the enigmatic, yet crucial role that DNA sequence elements play in centromere function and inheritance.
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Affiliation(s)
| | - Lars E T Jansen
- Department of Biochemistry, University of Oxford, OX1 3QU, United Kingdom.
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88
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Centromere chromatin structure - Lessons from neocentromeres. Exp Cell Res 2020; 389:111899. [PMID: 32044308 DOI: 10.1016/j.yexcr.2020.111899] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/01/2020] [Accepted: 02/07/2020] [Indexed: 11/22/2022]
Abstract
Centromeres are highly specialized genomic loci that function during mitosis to maintain genome stability. Formed primarily on repetitive α-satellite DNA sequence characterisation of native centromeric chromatin structure has remained challenging. Fortuitously, neocentromeres are formed on a unique DNA sequence and represent an excellent model to interrogate centromeric chromatin structure. This review uncovers the specific findings from independent neocentromere studies that have advanced our understanding of canonical centromere chromatin structure.
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89
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Hori T, Fukagawa T. Artificial generation of centromeres and kinetochores to understand their structure and function. Exp Cell Res 2020; 389:111898. [PMID: 32035949 DOI: 10.1016/j.yexcr.2020.111898] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/18/2020] [Accepted: 02/05/2020] [Indexed: 01/19/2023]
Abstract
The centromere is an essential genomic region that provides the surface to form the kinetochore, which binds to the spindle microtubes to mediate chromosome segregation during mitosis and meiosis. Centromeres of most organisms possess highly repetitive sequences, making it difficult to study these loci. However, an unusual centromere called a "neocentromere," which does not contain repetitive sequences, was discovered in a patient and can be generated experimentally. Recent advances in genome biology techniques allow us to analyze centromeric chromatin using neocentromeres. In addition to neocentromeres, artificial kinetochores have been generated on non-centromeric loci, using protein tethering systems. These are powerful tools to understand the mechanism of the centromere specification and kinetochore assembly. In this review, we introduce recent studies utilizing the neocentromeres and artificial kinetochores and discuss current problems in centromere biology.
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Affiliation(s)
- Tetsuya Hori
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Tatsuo Fukagawa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan.
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90
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Talbert PB, Henikoff S. What makes a centromere? Exp Cell Res 2020; 389:111895. [PMID: 32035948 DOI: 10.1016/j.yexcr.2020.111895] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/18/2020] [Accepted: 02/05/2020] [Indexed: 12/26/2022]
Abstract
Centromeres are the eukaryotic chromosomal sites at which the kinetochore forms and attaches to spindle microtubules to orchestrate chromosomal segregation in mitosis and meiosis. Although centromeres are essential for cell division, their sequences are not conserved and evolve rapidly. Centromeres vary dramatically in size and organization. Here we categorize their diversity and explore the evolutionary forces shaping them. Nearly all centromeres favor AT-rich DNA that is gene-free and transcribed at a very low level. Repair of frequent centromere-proximal breaks probably contributes to their rapid sequence evolution. Point centromeres are only ~125 bp and are specified by common protein-binding motifs, whereas short regional centromeres are 1-5 kb, typically have unique sequences, and may have pericentromeric repeats adapted to facilitate centromere clustering. Transposon-rich centromeres are often ~100-300 kb and are favored by RNAi machinery that silences transposons, by suppression of meiotic crossovers at centromeres, and by the ability of some transposons to target centromeres. Megabase-length satellite centromeres arise in plants and animals with asymmetric female meiosis that creates centromere competition, and favors satellite monomers one or two nucleosomes in length that position and stabilize centromeric nucleosomes. Holocentromeres encompass the length of a chromosome and may differ dramatically between mitosis and meiosis. We propose a model in which low level transcription of centromeres facilitates the formation of non-B DNA that specifies centromeres and promotes loading of centromeric nucleosomes.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.
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91
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Durvasula A, Sankararaman S. Recovering signals of ghost archaic introgression in African populations. SCIENCE ADVANCES 2020; 6:eaax5097. [PMID: 32095519 PMCID: PMC7015685 DOI: 10.1126/sciadv.aax5097] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 12/03/2019] [Indexed: 05/18/2023]
Abstract
While introgression from Neanderthals and Denisovans has been documented in modern humans outside Africa, the contribution of archaic hominins to the genetic variation of present-day Africans remains poorly understood. We provide complementary lines of evidence for archaic introgression into four West African populations. Our analyses of site frequency spectra indicate that these populations derive 2 to 19% of their genetic ancestry from an archaic population that diverged before the split of Neanderthals and modern humans. Using a method that can identify segments of archaic ancestry without the need for reference archaic genomes, we built genome-wide maps of archaic ancestry in the Yoruba and the Mende populations. Analyses of these maps reveal segments of archaic ancestry at high frequency in these populations that represent potential targets of adaptive introgression. Our results reveal the substantial contribution of archaic ancestry in shaping the gene pool of present-day West African populations.
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Affiliation(s)
- Arun Durvasula
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sriram Sankararaman
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
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92
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Tolomeo D, Capozzi O, Chiatante G, Sineo L, Ishida T, Archidiacono N, Rocchi M, Stanyon R. Eight million years of maintained heterozygosity in chromosome homologs of cercopithecine monkeys. Chromosoma 2020; 129:57-67. [PMID: 31925526 DOI: 10.1007/s00412-020-00731-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/13/2019] [Accepted: 01/02/2020] [Indexed: 10/25/2022]
Abstract
In the Cercopithecini ancestor two chromosomes, homologous to human chromosomes 20 and 21, fused to form the Cercopithecini specific 20/21 association. In some individuals from the genus Cercopithecus, this association was shown to be polymorphic for the position of the centromere, suggesting centromere repositioning events. We set out to test this hypothesis by defining the evolutionary history of the 20/21 association in four Cercopithecini species from three different genera. The marker order of the various 20/21 associations was established using molecular cytogenetic techniques, including an array of more than 100 BACs. We discovered that five different forms of the 20/21 association were present in the four studied Cercopithecini species. Remarkably, in the two Cercopithecus species, we found individuals in which one homolog conserved the ancestral condition, but the other homolog was highly rearranged. The phylogenetic analysis showed that the heterozygosity in these two species originated about 8 million years ago and was maintained for this entire arc of time, surviving multiple speciation events. Our report is a remarkable extension of Dobzhansky's pioneering observation in Drosophila concerning the maintenance of chromosomal heterozygosity due to selective advantage. Dobzhansky's hypothesis recently received strong support in a series of detailed reports on the fruit fly genome. Our findings are first extension to primates, indeed to Old World monkeys phylogenetically close to humans of an analogous situation. Our results have important implications for hypotheses on how chromosome rearrangements, selection, and speciation are related.
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Affiliation(s)
- Doron Tolomeo
- Department of Biology, University of Florence, Florence, Italy
| | | | | | - Luca Sineo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Palermo, Italy
| | - Takafumi Ishida
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | | | | | - Roscoe Stanyon
- Department of Biology, University of Florence, Florence, Italy.
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93
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Glinsky GV. A Catalogue of 59,732 Human-Specific Regulatory Sequences Reveals Unique-to-Human Regulatory Patterns Associated with Virus-Interacting Proteins, Pluripotency, and Brain Development. DNA Cell Biol 2019; 39:126-143. [PMID: 31730374 DOI: 10.1089/dna.2019.4988] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Extensive searches for genomic regions harboring various types of candidate human-specific regulatory sequences (HSRS) identified thousands' HSRS using high-resolution next-generation sequencing technologies and methodologically diverse comparative analyses of human and nonhuman primates' (NHPs) reference genomes. In this study, a comprehensive catalogue of 59,732 genomic loci harboring candidate HSRS has been assembled to facilitate the systematic analyses of genomic sequences that were either inherited from extinct common ancestors (ECAs) or created de novo in human genomes. These analyses identified thousands of candidate HSRS and HSRS-harboring loci that appear inherited from ECAs, yet absent in genomes of our closest evolutionary relatives, chimpanzee and bonobo, presumably due to the incomplete lineage sorting and/or species-specific loss or regulatory DNA. This pattern is particularly prominent for HSRS-harboring loci that have been putatively associated with human-specific gene expression changes in cerebral organoid models. A prominent majority of regions harboring human-specific mutations associated with human-specific expression changes during brain development is highly conserved in chimpanzee, bonobo, and gorilla genomes. Among NHPs, dominant fractions of HSRS-harboring loci associated with human-specific gene expression in both excitatory neurons (347 loci; 67%) and radial glia (683 loci; 72%) are highly conserved in the gorilla genome. Analysis of 4433 genes encoding virus-interacting proteins (VIPs) revealed that 95.9% of human VIPs are components of human-specific regulatory networks that appear to operate in distinct types of human cells from preimplantation embryos to adult dorsolateral prefrontal cortex. These analyses demonstrate that modern humans captured unique genome-wide combinations of regulatory sequences, divergent subsets of which are highly conserved in distinct species of six NHP separated by 30 million years of evolution. Concurrently, this unique-to-human mosaic of genomic regulatory patterns inherited from ECAs was supplemented with 12,486 created de novo HSRS. Genes encoding VIPs appear to represent a principal genomic target during evolution of human-specific regulatory networks, which contribute to fitness of Homo sapiens and affect a functionally diverse spectrum of biological and cellular processes controlled by VIP-containing liquid-liquid phase-separated condensates.
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Affiliation(s)
- Gennadi V Glinsky
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California
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94
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Tang W, Liang P. Comparative Genomics Analysis Reveals High Levels of Differential Retrotransposition among Primates from the Hominidae and the Cercopithecidae Families. Genome Biol Evol 2019; 11:3309-3325. [PMID: 31651947 PMCID: PMC6934888 DOI: 10.1093/gbe/evz234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2019] [Indexed: 12/11/2022] Open
Abstract
Mobile elements (MEs), making ∼50% of primate genomes, are known to be responsible for generating inter- and intra-species genomic variations and play important roles in genome evolution and gene function. Using a bioinformatics comparative genomics approach, we performed analyses of species-specific MEs (SS-MEs) in eight primate genomes from the families of Hominidae and Cercopithecidae, focusing on retrotransposons. We identified a total of 230,855 SS-MEs, with which we performed normalization based on evolutionary distances, and we also analyzed the most recent SS-MEs in these genomes. Comparative analysis of SS-MEs reveals striking differences in ME transposition among these primate genomes. Interesting highlights of our results include: 1) the baboon genome has the highest number of SS-MEs with a strong bias for SINEs, while the crab-eating macaque genome has a sustained extremely low transposition for all ME classes, suggesting the existence of a genome-wide mechanism suppressing ME transposition; 2) while SS-SINEs represent the dominant class in general, the orangutan genome stands out by having SS-LINEs as the dominant class; 3) the human genome stands out among the eight genomes by having the largest number of recent highly active ME subfamilies, suggesting a greater impact of ME transposition on its recent evolution; and 4) at least 33% of the SS-MEs locate to genic regions, including protein coding regions, presenting significant potentials for impacting gene function. Our study, as the first of its kind, demonstrates that mobile elements evolve quite differently among these primates, suggesting differential ME transposition as an important mechanism in primate evolution.
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Affiliation(s)
| | - Ping Liang
- Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada
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95
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Muñiz Moreno MDM, Brault V, Birling MC, Pavlovic G, Herault Y. Modeling Down syndrome in animals from the early stage to the 4.0 models and next. PROGRESS IN BRAIN RESEARCH 2019; 251:91-143. [PMID: 32057313 DOI: 10.1016/bs.pbr.2019.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The genotype-phenotype relationship and the physiopathology of Down Syndrome (DS) have been explored in the last 20 years with more and more relevant mouse models. From the early age of transgenesis to the new CRISPR/CAS9-derived chromosomal engineering and the transchromosomic technologies, mouse models have been key to identify homologous genes or entire regions homologous to the human chromosome 21 that are necessary or sufficient to induce DS features, to investigate the complexity of the genetic interactions that are involved in DS and to explore therapeutic strategies. In this review we report the new developments made, how genomic data and new genetic tools have deeply changed our way of making models, extended our panel of animal models, and increased our understanding of the neurobiology of the disease. But even if we have made an incredible progress which promises to make DS a curable condition, we are facing new research challenges to nurture our knowledge of DS pathophysiology as a neurodevelopmental disorder with many comorbidities during ageing.
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Affiliation(s)
- Maria Del Mar Muñiz Moreno
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Véronique Brault
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Marie-Christine Birling
- Université de Strasbourg, CNRS, INSERM, PHENOMIN Institut Clinique de la Souris, Illkirch, France
| | - Guillaume Pavlovic
- Université de Strasbourg, CNRS, INSERM, PHENOMIN Institut Clinique de la Souris, Illkirch, France
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Université de Strasbourg, CNRS, INSERM, PHENOMIN Institut Clinique de la Souris, Illkirch, France.
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96
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Centromere repositioning causes inversion of meiosis and generates a reproductive barrier. Proc Natl Acad Sci U S A 2019; 116:21580-21591. [PMID: 31597736 PMCID: PMC6815110 DOI: 10.1073/pnas.1911745116] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Mutations in inner kinetochore components induce centromere repositioning without alteration in the centromeric DNA sequence, revealing a feedback mechanism underlying the high epigenetic stability of the centromere. This also provides a desirable experimental system to explore the functional significance of centromere positioning in meiosis. We discovered that in a heterozygotic meiosis, a repositioned centromere generates a reproductive barrier, suggesting a functional role of evolutionary new centromeres in speciation; furthermore, in a homozygotic meiosis, chromosomes carrying repositioned centromeres frequently undergo the 2 stages of meiotic segregation in an inverted order, demonstrating high flexibility in the meiotic process. The chromosomal position of each centromere is determined epigenetically and is highly stable, whereas incremental cases have supported the occurrence of centromere repositioning on an evolutionary time scale (evolutionary new centromeres, ENCs), which is thought to be important in speciation. The mechanisms underlying the high stability of centromeres and its functional significance largely remain an enigma. Here, in the fission yeast Schizosaccharomyces pombe, we identify a feedback mechanism: The kinetochore, whose assembly is guided by the centromere, in turn, enforces centromere stability. Upon going through meiosis, specific inner kinetochore mutations induce centromere repositioning—inactivation of the original centromere and formation of a new centromere elsewhere—in 1 of the 3 chromosomes at random. Repositioned centromeres reside asymmetrically in the pericentromeric regions and cells carrying them are competent in mitosis and homozygotic meiosis. However, when cells carrying a repositioned centromere are crossed with those carrying the original centromere, the progeny suffer severe lethality due to defects in meiotic chromosome segregation. Thus, repositioned centromeres constitute a reproductive barrier that could initiate genetic divergence between 2 populations with mismatched centromeres, documenting a functional role of ENCs in speciation. Surprisingly, homozygotic repositioned centromeres tend to undergo meiosis in an inverted order—that is, sister chromatids segregate first, and homologous chromosomes separate second—whereas the original centromeres on other chromosomes in the same cell undergo meiosis in the canonical order, revealing hidden flexibility in the perceived rigid process of meiosis.
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97
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Edsall LE, Berrio A, Majoros WH, Swain-Lenz D, Morrow S, Shibata Y, Safi A, Wray GA, Crawford GE, Allen AS. Evaluating Chromatin Accessibility Differences Across Multiple Primate Species Using a Joint Modeling Approach. Genome Biol Evol 2019; 11:3035-3053. [PMID: 31599933 PMCID: PMC6821351 DOI: 10.1093/gbe/evz218] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/13/2022] Open
Abstract
Changes in transcriptional regulation are thought to be a major contributor to the evolution of phenotypic traits, but the contribution of changes in chromatin accessibility to the evolution of gene expression remains almost entirely unknown. To address this important gap in knowledge, we developed a new method to identify DNase I Hypersensitive (DHS) sites with differential chromatin accessibility between species using a joint modeling approach. Our method overcomes several limitations inherent to conventional threshold-based pairwise comparisons that become increasingly apparent as the number of species analyzed rises. Our approach employs a single quantitative test which is more sensitive than existing pairwise methods. To illustrate, we applied our joint approach to DHS sites in fibroblast cells from five primates (human, chimpanzee, gorilla, orangutan, and rhesus macaque). We identified 89,744 DHS sites, of which 41% are identified as differential between species using the joint model compared with 33% using the conventional pairwise approach. The joint model provides a principled approach to distinguishing single from multiple chromatin accessibility changes among species. We found that nondifferential DHS sites are enriched for nucleotide conservation. Differential DHS sites with decreased chromatin accessibility relative to rhesus macaque occur more commonly near transcription start sites (TSS), while those with increased chromatin accessibility occur more commonly distal to TSS. Further, differential DHS sites near TSS are less cell type-specific than more distal regulatory elements. Taken together, these results point to distinct classes of DHS sites, each with distinct characteristics of selection, genomic location, and cell type specificity.
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Affiliation(s)
- Lee E Edsall
- Center for Genomic and Computational Biology, Duke University
- Division of Medical Genetics, Department of Pediatrics, Duke University
- University Program in Genetics and Genomics, Duke University
| | | | | | | | | | - Yoichiro Shibata
- Center for Genomic and Computational Biology, Duke University
- Division of Medical Genetics, Department of Pediatrics, Duke University
| | - Alexias Safi
- Center for Genomic and Computational Biology, Duke University
- Division of Medical Genetics, Department of Pediatrics, Duke University
| | - Gregory A Wray
- Center for Genomic and Computational Biology, Duke University
- Department of Biology, Duke University
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University
- Division of Medical Genetics, Department of Pediatrics, Duke University
| | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University
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98
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Fast-Evolving Human-Specific Neural Enhancers Are Associated with Aging-Related Diseases. Cell Syst 2019; 6:604-611.e4. [PMID: 29792826 DOI: 10.1016/j.cels.2018.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 01/25/2018] [Accepted: 04/05/2018] [Indexed: 01/22/2023]
Abstract
The antagonistic pleiotropy theory hypothesizes that evolutionary adaptations maximizing the fitness in early age increase disease burden after reproduction. This theory remains largely untested at the molecular level. Here, we analyzed enhancer evolution in primates to investigate the relationships between aging-related diseases and enhancers acquired after the human-chimpanzee divergence. We report a 5-fold increased evolutionary rate of enhancers that are activated in neural tissues, leading to fixation of ∼100 human-specific enhancers potentially under adaptation. These enhancers show prognostic expression levels and correlations with driver genes in cancer, and their nearby genes are enriched in known loci associated with aging-related diseases. Using CRISPR/Cas9, we further functionally validated an enhancer on chr8p23.1 as activator counteracting REST, a master regulator known to be a transcriptional suppressor of Alzheimer disease. Our results suggest an evolutionary origin of aging-related diseases: the side effects of human-specific, neural-tissue expressed enhancers. Thus, adaptive molecular changes in human macroevolution may introduce vulnerabilities to disease development in modern populations.
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100
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Sharma AB, Dimitrov S, Hamiche A, Van Dyck E. Centromeric and ectopic assembly of CENP-A chromatin in health and cancer: old marks and new tracks. Nucleic Acids Res 2019; 47:1051-1069. [PMID: 30590707 PMCID: PMC6379705 DOI: 10.1093/nar/gky1298] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/13/2018] [Accepted: 12/18/2018] [Indexed: 12/20/2022] Open
Abstract
The histone H3 variant CENP-A confers epigenetic identity to the centromere and plays crucial roles in the assembly and function of the kinetochore, thus ensuring proper segregation of our chromosomes. CENP-A containing nucleosomes exhibit unique structural specificities and lack the complex profile of gene expression-associated histone posttranslational modifications found in canonical histone H3 and the H3.3 variant. CENP-A mislocalization into noncentromeric regions resulting from its overexpression leads to chromosomal segregation aberrations and genome instability. Overexpression of CENP-A is a feature of many cancers and is associated with malignant progression and poor outcome. The recent years have seen impressive progress in our understanding of the mechanisms that orchestrate CENP-A deposition at native centromeres and ectopic loci. They have witnessed the description of novel, heterotypic CENP-A/H3.3 nucleosome particles and the exploration of the phenotypes associated with the deregulation of CENP-A and its chaperones in tumor cells. Here, we review the structural specificities of CENP-A nucleosomes, the epigenetic features that characterize the centrochromatin and the mechanisms and factors that orchestrate CENP-A deposition at centromeres. We then review our knowledge of CENP-A ectopic distribution, highlighting experimental strategies that have enabled key discoveries. Finally, we discuss the implications of deregulated CENP-A in cancer.
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Affiliation(s)
- Abhishek Bharadwaj Sharma
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (LIH), 84 Val Fleuri, L-1526 Luxembourg, Luxembourg
| | - Stefan Dimitrov
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé-Allée des Alpes, 38700 La Tronche, France.,Izmir Biomedicine and Genome Center, İzmir, Turkey
| | - Ali Hamiche
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS, INSERM, 67404 Illkirch Cedex, France
| | - Eric Van Dyck
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (LIH), 84 Val Fleuri, L-1526 Luxembourg, Luxembourg
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