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Federico C, Brancato D, Bruno F, Galvano D, Caruso M, Saccone S. Robertsonian Translocation between Human Chromosomes 21 and 22, Inherited across Three Generations, without Any Phenotypic Effect. Genes (Basel) 2024; 15:722. [PMID: 38927657 PMCID: PMC11202415 DOI: 10.3390/genes15060722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Chromosomal translocations can result in phenotypic effects of varying severity, depending on the position of the breakpoints and the rearrangement of genes within the interphase nucleus of the translocated chromosome regions. Balanced translocations are often asymptomatic phenotypically and are typically detected due to a decrease in fertility resulting from issues during meiosis. Robertsonian translocations are among the most common chromosomal abnormalities, often asymptomatic, and can persist in the population as a normal polymorphism. We serendipitously discovered a Robertsonian translocation between chromosome 21 and chromosome 22, which is inherited across three generations without any phenotypic effect, notably only in females. In situ hybridization with alpha-satellite DNAs revealed the presence of both centromeric sequences in the translocated chromosome. The reciprocal translocation resulted in a partial deletion of the short arm of both chromosomes 21, and 22, with the ribosomal RNA genes remaining present in the middle part of the new metacentric chromosome. The rearrangement did not cause alterations to the long arm. The spread of an asymptomatic heterozygous chromosomal polymorphism in a population can lead to mating between heterozygous individuals, potentially resulting in offspring with a homozygous chromosomal configuration for the anomaly they carry. This new karyotype may not produce phenotypic effects in the individual who presents it. The frequency of karyotypes with chromosomal rearrangements in asymptomatic heterozygous form in human populations is likely underestimated, and molecular karyotype by array Comparative Genomic Hybridization (array-CGH) analysis does not allow for the identification of this type of chromosomal anomaly, making classical cytogenetic analysis the preferred method for obtaining clear results on a karyotype carrying a balanced rearrangement.
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Affiliation(s)
- Concetta Federico
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (C.F.); (D.B.); (F.B.)
| | - Desiree Brancato
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (C.F.); (D.B.); (F.B.)
| | - Francesca Bruno
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (C.F.); (D.B.); (F.B.)
| | - Daiana Galvano
- Cytogenetic Laboratory, A.O.U. Policlinico Vittorio Emanuele, 95124 Catania, Italy; (D.G.); (M.C.)
| | - Mariella Caruso
- Cytogenetic Laboratory, A.O.U. Policlinico Vittorio Emanuele, 95124 Catania, Italy; (D.G.); (M.C.)
| | - Salvatore Saccone
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (C.F.); (D.B.); (F.B.)
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2
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Arnoult N, Cech TR. Telomerase misbehaves after a breakup. Science 2024; 383:702-703. [PMID: 38359118 DOI: 10.1126/science.adn7791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Suppressing telomerase action at broken DNA preserves genome integrity.
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Affiliation(s)
- Nausica Arnoult
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Thomas R Cech
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
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Brannan EO, Hartley GA, O’Neill RJ. Mechanisms of Rapid Karyotype Evolution in Mammals. Genes (Basel) 2023; 15:62. [PMID: 38254952 PMCID: PMC10815390 DOI: 10.3390/genes15010062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Chromosome reshuffling events are often a foundational mechanism by which speciation can occur, giving rise to highly derivative karyotypes even amongst closely related species. Yet, the features that distinguish lineages prone to such rapid chromosome evolution from those that maintain stable karyotypes across evolutionary time are still to be defined. In this review, we summarize lineages prone to rapid karyotypic evolution in the context of Simpson's rates of evolution-tachytelic, horotelic, and bradytelic-and outline the mechanisms proposed to contribute to chromosome rearrangements, their fixation, and their potential impact on speciation events. Furthermore, we discuss relevant genomic features that underpin chromosome variation, including patterns of fusions/fissions, centromere positioning, and epigenetic marks such as DNA methylation. Finally, in the era of telomere-to-telomere genomics, we discuss the value of gapless genome resources to the future of research focused on the plasticity of highly rearranged karyotypes.
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Affiliation(s)
- Emry O. Brannan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (E.O.B.); (G.A.H.)
| | - Gabrielle A. Hartley
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (E.O.B.); (G.A.H.)
| | - Rachel J. O’Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (E.O.B.); (G.A.H.)
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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Dedukh D, Maslova A, Al-Rikabi A, Padutsch N, Liehr T, Krasikova A. Karyotypes of water frogs from the Pelophylax esculentus complex: results of cross-species chromosomal painting. Chromosoma 2023; 132:329-342. [PMID: 38001396 DOI: 10.1007/s00412-023-00812-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023]
Abstract
Amphibian species have the largest genome size enriched with repetitive sequences and relatively similar karyotypes. Moreover, many amphibian species frequently hybridize causing nuclear and mitochondrial genome introgressions. In addition, hybridization in some amphibian species may lead to clonality and polyploidization. All such events were found in water frogs from the genus Pelophylax. Among the species within the genus Pelophylax, P. esculentus complex is the most widely distributed and well-studied. This complex includes two parental species, P. ridibundus and P. lessonae, and their hybrids, P. esculentus, reproducing hemiclonally. Parental species and their hybrids have similar but slightly polymorphic karyotypes, so their precise identification is still required. Here, we have developed a complete set of 13 chromosome painting probes for two parental species allowing the precise identification of all chromosomes. Applying chromosomal painting, we identified homologous chromosomes in both parental species and orthologous chromosomes in their diploid hemiclonal hybrids. Comparative painting did not reveal interchromosomal exchanges between the studied water frog species and their hybrids. Using cross-specific chromosome painting, we detected unequal distribution of the signals along chromosomes suggesting the presence of species-specific tandem repeats. Application of chromosomal paints to the karyotypes of hybrids revealed differences in the intensity of staining for P. ridibundus and P. lessonae chromosomes. Thus, both parental genomes have a divergence in unique sequences. Obtained chromosome probes may serve as a powerful tool to unravel chromosomal evolution in phylogenetically related species, identify individual chromosomes in different cell types, and investigate the elimination of chromosomes in hybrid water frogs.
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Affiliation(s)
- Dmitrij Dedukh
- Laboratory of Cell Nucleus Structure and Dynamics, Saint-Petersburg State University, Saint-Petersburg, Russia
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Antonina Maslova
- Laboratory of Cell Nucleus Structure and Dynamics, Saint-Petersburg State University, Saint-Petersburg, Russia
| | - Ahmed Al-Rikabi
- Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Jena, Germany
| | - Niklas Padutsch
- Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Jena, Germany
| | - Thomas Liehr
- Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Jena, Germany
| | - Alla Krasikova
- Laboratory of Cell Nucleus Structure and Dynamics, Saint-Petersburg State University, Saint-Petersburg, Russia.
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5
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Zhou B, He Y, Chen Y, Su B. Comparative Genomic Analysis Identifies Great-Ape-Specific Structural Variants and Their Evolutionary Relevance. Mol Biol Evol 2023; 40:msad184. [PMID: 37565562 PMCID: PMC10461412 DOI: 10.1093/molbev/msad184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/01/2023] [Accepted: 08/10/2023] [Indexed: 08/12/2023] Open
Abstract
During the origin of great apes about 14 million years ago, a series of phenotypic innovations emerged, such as the increased body size, the enlarged brain volume, the improved cognitive skill, and the diversified diet. Yet, the genomic basis of these evolutionary changes remains unclear. Utilizing the high-quality genome assemblies of great apes (including human), gibbon, and macaque, we conducted comparative genome analyses and identified 15,885 great ape-specific structural variants (GSSVs), including eight coding GSSVs resulting in the creation of novel proteins (e.g., ACAN and CMYA5). Functional annotations of the GSSV-related genes revealed the enrichment of genes involved in development and morphogenesis, especially neurogenesis and neural network formation, suggesting the potential role of GSSVs in shaping the great ape-shared traits. Further dissection of the brain-related GSSVs shows great ape-specific changes of enhancer activities and gene expression in the brain, involving a group of GSSV-regulated genes (such as NOL3) that potentially contribute to the altered brain development and function in great apes. The presented data highlight the evolutionary role of structural variants in the phenotypic innovations during the origin of the great ape lineage.
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Affiliation(s)
- Bin Zhou
- 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
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yaoxi He
- 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
| | - Yongjie Chen
- 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
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Bing Su
- 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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6
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Kuse R, Ishii K. Flexible Attachment and Detachment of Centromeres and Telomeres to and from Chromosomes. Biomolecules 2023; 13:1016. [PMID: 37371596 DOI: 10.3390/biom13061016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/15/2023] [Accepted: 06/18/2023] [Indexed: 06/29/2023] Open
Abstract
Accurate transmission of genomic information across multiple cell divisions and generations, without any losses or errors, is fundamental to all living organisms. To achieve this goal, eukaryotes devised chromosomes. Eukaryotic genomes are represented by multiple linear chromosomes in the nucleus, each carrying a centromere in the middle, a telomere at both ends, and multiple origins of replication along the chromosome arms. Although all three of these DNA elements are indispensable for chromosome function, centromeres and telomeres possess the potential to detach from the original chromosome and attach to new chromosomal positions, as evident from the events of telomere fusion, centromere inactivation, telomere healing, and neocentromere formation. These events seem to occur spontaneously in nature but have not yet been elucidated clearly, because they are relatively infrequent and sometimes detrimental. To address this issue, experimental setups have been developed using model organisms such as yeast. In this article, we review some of the key experiments that provide clues as to the extent to which these paradoxical and elusive features of chromosomally indispensable elements may become valuable in the natural context.
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Affiliation(s)
- Riku Kuse
- Laboratory of Chromosome Function and Regulation, Graduate School of Engineering, Kochi University of Technology, Kochi 782-8502, Japan
| | - Kojiro Ishii
- Laboratory of Chromosome Function and Regulation, Graduate School of Engineering, Kochi University of Technology, Kochi 782-8502, Japan
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7
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Shao Y, Zhou L, Li F, Zhao L, Zhang BL, Shao F, Chen JW, Chen CY, Bi X, Zhuang XL, Zhu HL, Hu J, Sun Z, Li X, Wang D, Rivas-González I, Wang S, Wang YM, Chen W, Li G, Lu HM, Liu Y, Kuderna LFK, Farh KKH, Fan PF, Yu L, Li M, Liu ZJ, Tiley GP, Yoder AD, Roos C, Hayakawa T, Marques-Bonet T, Rogers J, Stenson PD, Cooper DN, Schierup MH, Yao YG, Zhang YP, Wang W, Qi XG, Zhang G, Wu DD. Phylogenomic analyses provide insights into primate evolution. Science 2023; 380:913-924. [PMID: 37262173 DOI: 10.1126/science.abn6919] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/26/2023] [Indexed: 06/03/2023]
Abstract
Comparative analysis of primate genomes within a phylogenetic context is essential for understanding the evolution of human genetic architecture and primate diversity. We present such a study of 50 primate species spanning 38 genera and 14 families, including 27 genomes first reported here, with many from previously less well represented groups, the New World monkeys and the Strepsirrhini. Our analyses reveal heterogeneous rates of genomic rearrangement and gene evolution across primate lineages. Thousands of genes under positive selection in different lineages play roles in the nervous, skeletal, and digestive systems and may have contributed to primate innovations and adaptations. Our study reveals that many key genomic innovations occurred in the Simiiformes ancestral node and may have had an impact on the adaptive radiation of the Simiiformes and human evolution.
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Affiliation(s)
- Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Long Zhou
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Fang Li
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Institute of Animal Sex and Development, ZhejiangWanli University, Ningbo 315100, China
| | - Lan Zhao
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China
| | | | - Chun-Yan Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xupeng Bi
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiao-Lin Zhuang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650204, China
| | | | - Jiang Hu
- Grandomics Biosciences, Beijing 102206, China
| | - Zongyi Sun
- Grandomics Biosciences, Beijing 102206, China
| | - Xin Li
- Grandomics Biosciences, Beijing 102206, China
| | - Depeng Wang
- Grandomics Biosciences, Beijing 102206, China
| | | | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Yun-Mei Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Wu Chen
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou 510070, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Hui-Meng Lu
- School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Lukas F K Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA 92122, USA
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA 92122, USA
| | - Peng-Fei Fan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhi-Jin Liu
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - George P Tiley
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Japan Monkey Centre, Inuyama, Aichi 484-0081, Japan
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | | | - Yong-Gang Yao
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650204, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, 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 650107, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, 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 650107, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiao-Guang Qi
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, 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 650107, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650204, China
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Milioto V, Sineo L, Dumas F. Chromosome Painting in Cercopithecus petaurista (Schreber, 1774) Compared to Other Monkeys of the Cercopithecini Tribe (Catarrhini, Primates). Life (Basel) 2023; 13:life13051203. [PMID: 37240848 DOI: 10.3390/life13051203] [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: 02/21/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
The Cercopithecini tribe includes terrestrial and arboreal clades whose relationships are controversial, with a high level of chromosome rearrangements. In order to provide new insights on the tribe's phylogeny, chromosome painting, using the complete set of human syntenic probes, was performed in Cercopithecus petaurista, a representative species of the Cercopithecini tribe. The results show C. petaurista with a highly rearranged karyotype characterized by the fission of human chromosomes 1, 2, 3, 5, 6, 8, 11, and 12. These results compared with the literature data permit us to confirm the monophyly of the Cercopithecini tribe (fissions of chromosomes 5 and 6), as previously proposed by chromosomal and molecular data. Furthermore, we support the monophyly of the strictly arboreal Cercopithecus clade, previously proposed by the molecular approach, identifying chromosomal synapomorphies (fissions of chromosomes 1, 2, 3, 11, 12). We also add additional markers that can be useful for deciphering arboreal Cercopithecini phylogeny. For example, the fission of chromosome 8 is synapomorphy linking C. petaurista, C. erythrogaster, and C. nictitans among the arboreal species. Finally, a telomeric sequence probe was mapped on C. petaurista, showing only classic telomeric signals and giving no support to a previous hypothesis regarding a link between interspersed telomeric sequences in high rearranged genomes.
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Affiliation(s)
- Vanessa Milioto
- Department of Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), University of Palermo, 90100 Palermo, Italy
| | - Luca Sineo
- Department of Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), University of Palermo, 90100 Palermo, Italy
| | - Francesca Dumas
- Department of Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), University of Palermo, 90100 Palermo, Italy
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Fogel AS, Oduor PO, Nyongesa AW, Kimwele CN, Alberts SC, Archie EA, Tung J. Ecology and age, but not genetic ancestry, predict fetal loss in a wild baboon hybrid zone. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:618-632. [PMID: 38445762 DOI: 10.1002/ajpa.24686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/08/2022] [Accepted: 12/15/2022] [Indexed: 03/07/2024]
Abstract
OBJECTIVES Pregnancy failure represents a major fitness cost for any mammal, particularly those with slow life histories such as primates. Here, we quantified the risk of fetal loss in wild hybrid baboons, including genetic, ecological, and demographic sources of variance. We were particularly interested in testing the hypothesis that hybridization increases fetal loss rates. Such an effect would help explain how baboons may maintain genetic and phenotypic integrity despite interspecific gene flow. MATERIALS AND METHODS We analyzed outcomes for 1020 pregnancies observed over 46 years in a natural yellow baboon-anubis baboon hybrid zone. Fetal losses and live births were scored based on records of female reproductive state and the appearance of live neonates. We modeled the probability of fetal loss as a function of a female's genetic ancestry (the proportion of her genome estimated to be descended from anubis [vs. yellow] ancestors), age, number of previous fetal losses, dominance rank, group size, climate, and habitat quality using binomial mixed effects models. RESULTS Female genetic ancestry did not predict fetal loss. Instead, the risk of fetal loss is elevated for very young and very old females. Fetal loss is most robustly predicted by ecological factors, including poor habitat quality prior to a home range shift and extreme heat during pregnancy. DISCUSSION Our results suggest that gene flow between yellow and anubis baboons is not impeded by an increased risk of fetal loss for hybrid females. Instead, ecological conditions and female age are key determinants of this component of female reproductive success.
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Affiliation(s)
- Arielle S Fogel
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
| | - Peter O Oduor
- Department of Veterinary Anatomy and Physiology, University of Nairobi, Nairobi, Kenya
| | - Albert W Nyongesa
- Department of Veterinary Anatomy and Physiology, University of Nairobi, Nairobi, Kenya
| | - Charles N Kimwele
- Department of Veterinary Anatomy and Physiology, University of Nairobi, Nairobi, Kenya
| | - Susan C Alberts
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
- Department of Biology, Duke University, Durham, North Carolina, USA
- Duke Population Research Institute, Duke University, Durham, North Carolina, USA
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
- Department of Biology, Duke University, Durham, North Carolina, USA
- Duke Population Research Institute, Duke University, Durham, North Carolina, USA
- Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Saxony, Germany
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10
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Genomic signatures of high-altitude adaptation and chromosomal polymorphism in geladas. Nat Ecol Evol 2022; 6:630-643. [PMID: 35332281 PMCID: PMC9090980 DOI: 10.1038/s41559-022-01703-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/15/2022] [Indexed: 01/31/2023]
Abstract
Primates have adapted to numerous environments and lifestyles, but very few species are native to high elevations. Here, we investigated high-altitude adaptations in the gelada (Theropithecus gelada), a monkey endemic to the Ethiopian Plateau. We examined genome-wide variation in conjunction with measurements of hematological and morphological traits. Our new gelada reference genome is highly intact and assembled at chromosome-length levels. Unexpectedly, we identified a chromosomal polymorphism in geladas that could potentially contribute to reproductive barriers between populations. Compared to baboons at low altitude, we found that high-altitude geladas exhibit significantly expanded chest circumferences, potentially allowing for greater lung surface area for increased oxygen diffusion. We identified gelada-specific amino acid substitutions in the alpha-chain subunit of adult hemoglobin but found that gelada hemoglobin does not exhibit markedly altered oxygenation properties compared to lowland primates. We also found that geladas at high altitude do not exhibit elevated blood hemoglobin concentrations, in contrast to the normal acclimatization response to hypoxia in lowland primates. The absence of altitude-related polycythemia suggests that geladas are able to sustain adequate tissue-oxygen delivery despite environmental hypoxia. Finally, we identified numerous genes and genomic regions exhibiting accelerated rates of evolution, as well as gene families exhibiting expansions in the gelada lineage, potentially reflecting altitude-related selection. Our findings lend insight into putative mechanisms of high-altitude adaptation while suggesting promising avenues for functional hypoxia research.
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11
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Fan X, Pinthong K, de Oliveira EHC, Tanomtong A, Chen H, Weise A, Liehr T. First Comprehensive Characterization of Phayre’s Leaf-Monkey (Trachypithecus phayrei) Karyotype. Front Genet 2022; 13:841681. [PMID: 35360869 PMCID: PMC8961670 DOI: 10.3389/fgene.2022.841681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/31/2022] [Indexed: 11/24/2022] Open
Abstract
The chromosomal homologies of human (Homo sapiens—HSA) and Trachypithecus phayrei (TPH—Phayre’s leaf-monkey, family Cercopithecidae) have previously been studied by using classical chromosome staining/banding and fluorescence in situ hybridization (FISH) from the 1970s to 1990s. In this study, we carried out molecular cytogenetics applying human multicolor banding (MCB), locus-specific, and human heterochromatin-specific probes to establish the first detailed chromosomal map of TPH, which was not available until now. Accordingly, it was possible to precisely determine evolutionary-conserved breakpoints (ECBs) and the orientation of evolutionary-conserved segments compared to HSA. It could be shown that five chromosomes remained completely unchanged between these two species, and 16 chromosomes underwent only intrachromosomal changes. In addition, 50 ECBs that failed to be resolved in previous reports were exactly identified and characterized in this study. It could also be shown that 43.5% of TPH centromere positions were conserved and 56.5% were altered compared to HSA. Interestingly, 82% ECBs in TPH corresponded to human fragile sites. Overall, this study is an essential contribution to future studies and reviews on chromosomal evolution in Cercopithecidae.
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Affiliation(s)
- Xiaobo Fan
- Bioengineering School, Xuzhou University of Technology, Xuzhou, China
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Krit Pinthong
- Department of Biology Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Edivaldo H. C. de Oliveira
- Faculdade de Ciências Naturais, ICEN, Universidade Federal do Pará, Campus Universitário do Guamá, Belém, Brazil
| | - Alongklod Tanomtong
- Department of Biology Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Hongwei Chen
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Anja Weise
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
- *Correspondence: Thomas Liehr,
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12
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Kimura A, Yahashi S, Chatani F, Tanabe H. Identification of Chromosome 17 Trisomy in a Cynomolgus Monkey (Macaca fascicularis) by Multicolor FISH Techniques. Cytogenet Genome Res 2021; 161:243-248. [PMID: 34265761 DOI: 10.1159/000516337] [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: 01/28/2021] [Accepted: 04/06/2021] [Indexed: 11/19/2022] Open
Abstract
A female cynomolgus monkey (Macaca fascicularis) with facial features characteristic of Down syndrome showed abnormal behavior, unwariness toward humans, and poor concentration. The number of metaphase chromosomes in blood lymphocytes was examined and found to be 43, which indicated one extra chromosome to the normal diploid number (2n = 42). We then used Q-banding and multicolor FISH techniques to identify the extra chromosome. The results revealed an additional chromosome 17, with no other chromosomal rearrangements, such as translocations. Since no mosaicism or heterozygous variant chromosomes were observed, full trisomy 17 was assessed in this female cynomolgus monkey. Chromosome 17 corresponds to human chromosome 13, and human trisomy 13, known as Patau syndrome, results in severe clinical signs and, often, a short life span; however, this individual has reached an age of 10 years with only mild clinical signs. Although genomic differences exist between human and macaques, this individual's case could help to reveal the pathological and genetic mechanisms of Patau syndrome.
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Affiliation(s)
- Aoi Kimura
- Drug Safety Research Laboratories, Shin Nippon Biomedical Laboratories, Ltd., Kagoshima, Japan
| | - Satowa Yahashi
- Drug Safety Research Laboratories, Shin Nippon Biomedical Laboratories, Ltd., Kagoshima, Japan
| | - Fumio Chatani
- Drug Safety Research Laboratories, Shin Nippon Biomedical Laboratories, Ltd., Kagoshima, Japan
| | - Hideyuki Tanabe
- Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, The Graduate University for Advanced Studies, SOKENDAI, Hayama, Japan
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13
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Ahmad SF, Singchat W, Jehangir M, Suntronpong A, Panthum T, Malaivijitnond S, Srikulnath K. Dark Matter of Primate Genomes: Satellite DNA Repeats and Their Evolutionary Dynamics. Cells 2020; 9:E2714. [PMID: 33352976 PMCID: PMC7767330 DOI: 10.3390/cells9122714] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
A substantial portion of the primate genome is composed of non-coding regions, so-called "dark matter", which includes an abundance of tandemly repeated sequences called satellite DNA. Collectively known as the satellitome, this genomic component offers exciting evolutionary insights into aspects of primate genome biology that raise new questions and challenge existing paradigms. A complete human reference genome was recently reported with telomere-to-telomere human X chromosome assembly that resolved hundreds of dark regions, encompassing a 3.1 Mb centromeric satellite array that had not been identified previously. With the recent exponential increase in the availability of primate genomes, and the development of modern genomic and bioinformatics tools, extensive growth in our knowledge concerning the structure, function, and evolution of satellite elements is expected. The current state of knowledge on this topic is summarized, highlighting various types of primate-specific satellite repeats to compare their proportions across diverse lineages. Inter- and intraspecific variation of satellite repeats in the primate genome are reviewed. The functional significance of these sequences is discussed by describing how the transcriptional activity of satellite repeats can affect gene expression during different cellular processes. Sex-linked satellites are outlined, together with their respective genomic organization. Mechanisms are proposed whereby satellite repeats might have emerged as novel sequences during different evolutionary phases. Finally, the main challenges that hinder the detection of satellite DNA are outlined and an overview of the latest methodologies to address technological limitations is presented.
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Affiliation(s)
- Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Maryam Jehangir
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo 18618-689, Brazil
| | - Aorarat Suntronpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Suchinda Malaivijitnond
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi 18110, Thailand;
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi 18110, Thailand;
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
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14
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Abstract
The study of chromosome evolution is undergoing a resurgence of interest owing to advances in DNA sequencing technology that facilitate the production of chromosome-scale whole-genome assemblies de novo. This review focuses on the history, methods, discoveries, and current challenges facing the field, with an emphasis on vertebrate genomes. A detailed examination of the literature on the biology of chromosome rearrangements is presented, specifically the relationship between chromosome rearrangements and phenotypic evolution, adaptation, and speciation. A critical review of the methods for identifying, characterizing, and visualizing chromosome rearrangements and computationally reconstructing ancestral karyotypes is presented. We conclude by looking to the future, identifying the enormous technical and scientific challenges presented by the accumulation of hundreds and eventually thousands of chromosome-scale assemblies.
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Affiliation(s)
- Joana Damas
- The Genome Center, University of California, Davis, California 95616, USA; , ,
| | - Marco Corbo
- The Genome Center, University of California, Davis, California 95616, USA; , ,
| | - Harris A Lewin
- The Genome Center, University of California, Davis, California 95616, USA; , , .,Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616, USA
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15
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Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution. Genome Res 2020; 30:1680-1693. [PMID: 33093070 PMCID: PMC7605249 DOI: 10.1101/gr.265322.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/02/2020] [Indexed: 12/14/2022]
Abstract
Rhesus macaque is an Old World monkey that shared a common ancestor with human ∼25 Myr ago and is an important animal model for human disease studies. A deep understanding of its genetics is therefore required for both biomedical and evolutionary studies. Among structural variants, inversions represent a driving force in speciation and play an important role in disease predisposition. Here we generated a genome-wide map of inversions between human and macaque, combining single-cell strand sequencing with cytogenetics. We identified 375 total inversions between 859 bp and 92 Mbp, increasing by eightfold the number of previously reported inversions. Among these, 19 inversions flanked by segmental duplications overlap with recurrent copy number variants associated with neurocognitive disorders. Evolutionary analyses show that in 17 out of 19 cases, the Hominidae orientation of these disease-associated regions is always derived. This suggests that duplicated sequences likely played a fundamental role in generating inversions in humans and great apes, creating architectures that nowadays predispose these regions to disease-associated genetic instability. Finally, we identified 861 genes mapping at 156 inversions breakpoints, with some showing evidence of differential expression in human and macaque cell lines, thus highlighting candidates that might have contributed to the evolution of species-specific features. This study depicts the most accurate fine-scale map of inversions between human and macaque using a two-pronged integrative approach, such as single-cell strand sequencing and cytogenetics, and represents a valuable resource toward understanding of the biology and evolution of primate species.
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16
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Guin K, Chen Y, Mishra R, Muzaki SRBM, Thimmappa BC, O'Brien CE, Butler G, Sanyal A, Sanyal K. Spatial inter-centromeric interactions facilitated the emergence of evolutionary new centromeres. eLife 2020; 9:e58556. [PMID: 32469306 PMCID: PMC7292649 DOI: 10.7554/elife.58556] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022] Open
Abstract
Centromeres of Candida albicans form on unique and different DNA sequences but a closely related species, Candida tropicalis, possesses homogenized inverted repeat (HIR)-associated centromeres. To investigate the mechanism of centromere type transition, we improved the fragmented genome assembly and constructed a chromosome-level genome assembly of C. tropicalis by employing PacBio sequencing, chromosome conformation capture sequencing (3C-seq), chromoblot, and genetic analysis of engineered aneuploid strains. Further, we analyzed the 3D genome organization using 3C-seq data, which revealed spatial proximity among the centromeres as well as telomeres of seven chromosomes in C. tropicalis. Intriguingly, we observed evidence of inter-centromeric translocations in the common ancestor of C. albicans and C. tropicalis. Identification of putative centromeres in closely related Candida sojae, Candida viswanathii and Candida parapsilosis indicates loss of ancestral HIR-associated centromeres and establishment of evolutionary new centromeres (ENCs) in C. albicans. We propose that spatial proximity of the homologous centromere DNA sequences facilitated karyotype rearrangements and centromere type transitions in human pathogenic yeasts of the CUG-Ser1 clade.
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Affiliation(s)
- Krishnendu Guin
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
| | - Yao Chen
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
| | - Radha Mishra
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
| | | | - Bhagya C Thimmappa
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
| | - Caoimhe E O'Brien
- School Of Biomolecular & Biomed Science, Conway Institute of Biomolecular and Biomedical Research, University College DublinDublinIreland
| | - Geraldine Butler
- School Of Biomolecular & Biomed Science, Conway Institute of Biomolecular and Biomedical Research, University College DublinDublinIreland
| | - Amartya Sanyal
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
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17
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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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18
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Valeri MP, Dias GB, Moreira CN, Yonenaga-Yassuda Y, Stanyon R, Kuhn GCES, Svartman M. Characterization of Satellite DNAs in Squirrel Monkeys genus Saimiri (Cebidae, Platyrrhini). Sci Rep 2020; 10:7783. [PMID: 32385398 PMCID: PMC7210261 DOI: 10.1038/s41598-020-64620-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/15/2020] [Indexed: 02/01/2023] Open
Abstract
The genus Saimiri is a decades-long taxonomic and phylogenetic puzzle to which cytogenetics has contributed crucial data. All Saimiri species apparently have a diploid number of 2n = 44 but vary in the number of chromosome arms. Repetitive sequences such as satellite DNAs are potentially informative cytogenetic markers because they display high evolutionary rates. Our goal is to increase the pertinent karyological data by more fully characterizing satellite DNA sequences in the Saimiri genus. We were able to identify two abundant satellite DNAs, alpha (~340 bp) and CapA (~1,500 bp), from short-read clustering of sequencing datasets from S. boliviensis. The alpha sequences comprise about 1% and the CapA 2.2% of the S. boliviensis genome. We also mapped both satellite DNAs in S. boliviensis, S. sciureus, S. vanzolinii, and S. ustus. The alpha has high interspecific repeat homogeneity and was mapped to the centromeres of all analyzed species. CapA is associated with non-pericentromeric heterochromatin and its distribution varies among Saimiri species. We conclude that CapA genomic distribution and its pervasiveness across Platyrrhini makes it an attractive cytogenetic marker for Saimiri and other New World monkeys.
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Affiliation(s)
- Mirela Pelizaro Valeri
- Laboratório de Citogenômica Evolutiva, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Guilherme Borges Dias
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Camila Nascimento Moreira
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Yatiyo Yonenaga-Yassuda
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Roscoe Stanyon
- Department of Biology, University of Florence, Florence, Italy
| | - Gustavo Campos E Silva Kuhn
- Laboratório de Citogenômica Evolutiva, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marta Svartman
- Laboratório de Citogenômica Evolutiva, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
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19
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Evolution of the Human Chromosome 13 Synteny: Evolutionary Rearrangements, Plasticity, Human Disease Genes and Cancer Breakpoints. Genes (Basel) 2020; 11:genes11040383. [PMID: 32244767 PMCID: PMC7230465 DOI: 10.3390/genes11040383] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/27/2020] [Accepted: 03/27/2020] [Indexed: 01/29/2023] Open
Abstract
The history of each human chromosome can be studied through comparative cytogenetic approaches in mammals which permit the identification of human chromosomal homologies and rearrangements between species. Comparative banding, chromosome painting, Bacterial Artificial Chromosome (BAC) mapping and genome data permit researchers to formulate hypotheses about ancestral chromosome forms. Human chromosome 13 has been previously shown to be conserved as a single syntenic element in the Ancestral Primate Karyotype; in this context, in order to study and verify the conservation of primate chromosomes homologous to human chromosome 13, we mapped a selected set of BAC probes in three platyrrhine species, characterised by a high level of rearrangements, using fluorescence in situ hybridisation (FISH). Our mapping data on Saguinus oedipus, Callithrix argentata and Alouatta belzebul provide insight into synteny of human chromosome 13 evolution in a comparative perspective among primate species, showing rearrangements across taxa. Furthermore, in a wider perspective, we have revised previous cytogenomic literature data on chromosome 13 evolution in eutherian mammals, showing a complex origin of the eutherian mammal ancestral karyotype which has still not been completely clarified. Moreover, we analysed biomedical aspects (the OMIM and Mitelman databases) regarding human chromosome 13, showing that this autosome is characterised by a certain level of plasticity that has been implicated in many human cancers and diseases.
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20
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Harris RA, Raveendran M, Worley KC, Rogers J. Unusual sequence characteristics of human chromosome 19 are conserved across 11 nonhuman primates. BMC Evol Biol 2020; 20:33. [PMID: 32106815 PMCID: PMC7045612 DOI: 10.1186/s12862-020-1595-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/11/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Human chromosome 19 has many unique characteristics including gene density more than double the genome-wide average and 20 large tandemly clustered gene families. It also has the highest GC content of any chromosome, especially outside gene clusters. The high GC content and concomitant high content of hypermutable CpG sites raises the possibility chromosome 19 exhibits higher levels of nucleotide diversity both within and between species, and may possess greater variation in DNA methylation that regulates gene expression. RESULTS We examined GC and CpG content of chromosome 19 orthologs across representatives of the primate order. In all 12 primate species with suitable genome assemblies, chromosome 19 orthologs have the highest GC content of any chromosome. CpG dinucleotides and CpG islands are also more prevalent in chromosome 19 orthologs than other chromosomes. GC and CpG content are generally higher outside the gene clusters. Intra-species variation based on SNPs in human common dbSNP, rhesus, crab eating macaque, baboon and marmoset datasets is most prevalent on chromosome 19 and its orthologs. Inter-species comparisons based on phyloP conservation show accelerated nucleotide evolution for chromosome 19 promoter flanking and enhancer regions. These same regulatory regions show the highest CpG density of any chromosome suggesting they possess considerable methylome regulatory potential. CONCLUSIONS The pattern of high GC and CpG content in chromosome 19 orthologs, particularly outside gene clusters, is present from human to mouse lemur representing 74 million years of primate evolution. Much CpG variation exists both within and between primate species with a portion of this variation occurring in regulatory regions.
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Affiliation(s)
- R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA.
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA
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21
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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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22
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Xin H, Zhang T, Wu Y, Zhang W, Zhang P, Xi M, Jiang J. An extraordinarily stable karyotype of the woody Populus species revealed by chromosome painting. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:253-264. [PMID: 31529535 DOI: 10.1111/tpj.14536] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/25/2019] [Accepted: 09/02/2019] [Indexed: 05/22/2023]
Abstract
The karyotype represents the basic genetic make-up of a eukaryotic species. Comparative cytogenetic analysis of related species based on individually identified chromosomes has been conducted in only a few plant groups and not yet in woody plants. We have developed a complete set of 19 chromosome painting probes based on the reference genome of the model woody plant Populus trichocarpa. Using sequential fluorescence in situ hybridization we were able to identify all poplar chromosomes in the same metaphase cells, which led to the development of poplar karyotypes based on individually identified chromosomes. We demonstrate that five Populus species, belonging to five different sections within Populus, have maintained a remarkably conserved karyotype. No inter-chromosomal structural rearrangements were observed on any of the 19 chromosomes among the five species. Thus, the chromosomal synteny in Populus has been remarkably maintained after nearly 14 million years of divergence. We propose that the karyotypes of woody species are more stable than those of herbaceous plants since it may take a longer period of time for woody plants to fix chromosome number or structural variants in natural populations.
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Affiliation(s)
- Haoyang Xin
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037, China
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Centre for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Yufeng Wu
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenli Zhang
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Pingdong Zhang
- National Engineering Laboratory for Tree Breeding, College of Bioscience and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Mengli Xi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037, China
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA
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23
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Hirai H, Go Y, Hirai Y, Rakotoarisoa G, Pamungkas J, Baicharoen S, Jahan I, Sajuthi D, Tosi AJ. Considerable Synteny and Sequence Similarity of Primate Chromosomal Region VIIq31. Cytogenet Genome Res 2019; 158:88-97. [PMID: 31220833 DOI: 10.1159/000500796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2009] [Indexed: 11/19/2022] Open
Abstract
Human chromosome 7 has been the focus of many behavioral, genetic, and medical studies because it carries genes related to cancer and neurodevelopment. We examined the evolution of the chromosome 7 homologs, and the 7q31 region in particular, using chromosome painting analyses and 3 paint probes derived from (i) the whole of chimpanzee chromosome VII (wcVII), (ii) human 7q31 (h7q31), and (iii) the chimpanzee homolog VIIq31 (cVIIq31). The wcVII probe was used instead of the whole human chromosome 7 because the chimpanzee contains additional C-bands and revealed large areas of synteny conservation as well as fragmentation across 20 primate species. Analyses focusing specifically on the 7q31 homolog and vicinity revealed considerable conservation across lineages with 2 exceptions. First, the probes verified an insertion of repetitive sequence at VIIq22 in chimpanzees and bonobos and also detected the sequence in most subtelomeres of the African apes. Second, a paracentric inversion with a breakpoint in the cVIIq31 block was found in the common marmoset, confirming earlier studies. Subsequent in silico comparative genome analysis of 17 primate species revealed that VIIq31.1 is more significantly conserved at the sequence level than other regions of chromosome VII, which indicates that its components are likely responsible for critical shared traits across the order, including conditions necessary for proper human development and wellbeing.
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24
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Stanyon R, Giusti D, Araújo NP, Bigoni F, Svartman M. Chromosome painting of the red-handed tamarin (Saguinus midas) compared to other Callitrichinae monkeys. Genome 2018; 61:771-776. [PMID: 30222938 DOI: 10.1139/gen-2018-0119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Here we present, for the first time, the complete chromosome painting map of Saguinus midas, the red-handed tamarin. Chromosome banding and painting with human chromosome-specific probes were used to compare the karyotype of this species with those of four other Neotropical primates of the subfamily Callitrichinae: Leontopithecus rosalia, Callithrix geoffroyi, C. penicillata, and Mico argentatus. The chromosome painting map of S. midas was identical to that of L. rosalia and other previously studied tamarin species (genera Saguinus and Leontopithecus). The three marmoset species studied (genera Callithrix and Mico) differed in the painting pattern of four human probes (chromosomes 1, 2, 10, and 16). These paints identified the presence or absence of chromosome associations HSA 1/10 and 2/16 in these taxa. By integrating our data with those from the literature, we were able to propose an ancestral Callitrichinae karyotype. The genera Saguinus and Leontopithecus (tamarins) conserve the ancestral Callitrichinae karyotype, while Mico and Callithrix (marmosets) show more derived karyotypes due to chromosome translocations and fissions that occurred during the evolution of these taxa.
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Affiliation(s)
- Roscoe Stanyon
- a Department of Biology, University of Florence, Via del Proconsolo 12, 50122 Firenze, Italy
| | - Dorotea Giusti
- a Department of Biology, University of Florence, Via del Proconsolo 12, 50122 Firenze, Italy
| | - Naiara Pereira Araújo
- b Department of General Biology, Federal University of Minas Gerais, Avenida Antônio Carlos, 6627, Pampulha, CEP 31270-901, Belo Horizonte, MG, Brazil
| | - Francesca Bigoni
- c Museum of Natural History, Anthropology Section, University of Florence, Via del Proconsolo 12, 50122 Firenze, Italy
| | - Marta Svartman
- b Department of General Biology, Federal University of Minas Gerais, Avenida Antônio Carlos, 6627, Pampulha, CEP 31270-901, Belo Horizonte, MG, Brazil
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25
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Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S, Meyerson OS, Underwood JG, Nelson BJ, Chaisson MJP, Dougherty ML, Munson KM, Hastie AR, Diekhans M, Hormozdiari F, Lorusso N, Hoekzema K, Qiu R, Clark K, Raja A, Welch AE, Sorensen M, Baker C, Fulton RS, Armstrong J, Graves-Lindsay TA, Denli AM, Hoppe ER, Hsieh P, Hill CM, Pang AWC, Lee J, Lam ET, Dutcher SK, Gage FH, Warren WC, Shendure J, Haussler D, Schneider VA, Cao H, Ventura M, Wilson RK, Paten B, Pollen A, Eichler EE. High-resolution comparative analysis of great ape genomes. Science 2018; 360:eaar6343. [PMID: 29880660 PMCID: PMC6178954 DOI: 10.1126/science.aar6343] [Citation(s) in RCA: 237] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 04/02/2018] [Indexed: 12/22/2022]
Abstract
Genetic studies of human evolution require high-quality contiguous ape genome assemblies that are not guided by the human reference. We coupled long-read sequence assembly and full-length complementary DNA sequencing with a multiplatform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies. By comparing these with two long-read de novo human genome assemblies and a gorilla genome assembly, we characterized lineage-specific and shared great ape genetic variation ranging from single- to mega-base pair-sized variants. We identified ~17,000 fixed human-specific structural variants identifying genic and putative regulatory changes that have emerged in humans since divergence from nonhuman apes. Interestingly, these variants are enriched near genes that are down-regulated in human compared to chimpanzee cerebral organoids, particularly in cells analogous to radial glial neural progenitors.
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Affiliation(s)
- Zev N Kronenberg
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ian T Fiddes
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Gordon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Shwetha Murali
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Stuart Cantsilieris
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Olivia S Meyerson
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jason G Underwood
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Pacific Biosciences (PacBio) of California, Inc., Menlo Park, CA 94025, USA
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Mark J P Chaisson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Computational Biology and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
| | - Max L Dougherty
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Fereydoun Hormozdiari
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA 95817, USA
| | - Nicola Lorusso
- Department of Biology, University of Bari, Aldo Moro, Bari 70121, Italy
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ruolan Qiu
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Karen Clark
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Archana Raja
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - AnneMarie E Welch
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Melanie Sorensen
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Robert S Fulton
- Departments of Medicine and Genetics, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Joel Armstrong
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tina A Graves-Lindsay
- Departments of Medicine and Genetics, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Ahmet M Denli
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Emma R Hoppe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - PingHsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Christopher M Hill
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | - Joyce Lee
- Bionano Genomics, San Diego, CA 92121, USA
| | | | - Susan K Dutcher
- Departments of Medicine and Genetics, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Fred H Gage
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Wesley C Warren
- Departments of Medicine and Genetics, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - David Haussler
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Valerie A Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Han Cao
- Bionano Genomics, San Diego, CA 92121, USA
| | - Mario Ventura
- Department of Biology, University of Bari, Aldo Moro, Bari 70121, Italy
| | - Richard K Wilson
- Departments of Medicine and Genetics, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alex Pollen
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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26
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Catacchio CR, Maggiolini FAM, D'Addabbo P, Bitonto M, Capozzi O, Lepore Signorile M, Miroballo M, Archidiacono N, Eichler EE, Ventura M, Antonacci F. Inversion variants in human and primate genomes. Genome Res 2018; 28:910-920. [PMID: 29776991 PMCID: PMC5991517 DOI: 10.1101/gr.234831.118] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/26/2018] [Indexed: 02/06/2023]
Abstract
For many years, inversions have been proposed to be a direct driving force in speciation since they suppress recombination when heterozygous. Inversions are the most common large-scale differences among humans and great apes. Nevertheless, they represent large events easily distinguishable by classical cytogenetics, whose resolution, however, is limited. Here, we performed a genome-wide comparison between human, great ape, and macaque genomes using the net alignments for the most recent releases of genome assemblies. We identified a total of 156 putative inversions, between 103 kb and 91 Mb, corresponding to 136 human loci. Combining literature, sequence, and experimental analyses, we analyzed 109 of these loci and found 67 regions inverted in one or multiple primates, including 28 newly identified inversions. These events overlap with 81 human genes at their breakpoints, and seven correspond to sites of recurrent rearrangements associated with human disease. This work doubles the number of validated primate inversions larger than 100 kb, beyond what was previously documented. We identified 74 sites of errors, where the sequence has been assembled in the wrong orientation, in the reference genomes analyzed. Our data serve two purposes: First, we generated a map of evolutionary inversions in these genomes representing a resource for interrogating differences among these species at a functional level; second, we provide a list of misassembled regions in these primate genomes, involving over 300 Mb of DNA and 1978 human genes. Accurately annotating these regions in the genome references has immediate applications for evolutionary and biomedical studies on primates.
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Affiliation(s)
| | | | - Pietro D'Addabbo
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
| | - Miriana Bitonto
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
| | - Oronzo Capozzi
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
| | | | - Mattia Miroballo
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
| | | | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| | - Mario Ventura
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
| | - Francesca Antonacci
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
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27
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Robicheau BM, Susko E, Harrigan AM, Snyder M. Ribosomal RNA Genes Contribute to the Formation of Pseudogenes and Junk DNA in the Human Genome. Genome Biol Evol 2018; 9:380-397. [PMID: 28204512 PMCID: PMC5381670 DOI: 10.1093/gbe/evw307] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2016] [Indexed: 12/20/2022] Open
Abstract
Approximately 35% of the human genome can be identified as sequence devoid of a selected-effect function, and not derived from transposable elements or repeated sequences. We provide evidence supporting a known origin for a fraction of this sequence. We show that: 1) highly degraded, but near full length, ribosomal DNA (rDNA) units, including both 45S and Intergenic Spacer (IGS), can be found at multiple sites in the human genome on chromosomes without rDNA arrays, 2) that these rDNA sequences have a propensity for being centromere proximal, and 3) that sequence at all human functional rDNA array ends is divergent from canonical rDNA to the point that it is pseudogenic. We also show that small sequence strings of rDNA (from 45S + IGS) can be found distributed throughout the genome and are identifiable as an “rDNA-like signal”, representing 0.26% of the q-arm of HSA21 and ∼2% of the total sequence of other regions tested. The size of sequence strings found in the rDNA-like signal intergrade into the size of sequence strings that make up the full-length degrading rDNA units found scattered throughout the genome. We conclude that the displaced and degrading rDNA sequences are likely of a similar origin but represent different stages in their evolution towards random sequence. Collectively, our data suggests that over vast evolutionary time, rDNA arrays contribute to the production of junk DNA. The concept that the production of rDNA pseudogenes is a by-product of concerted evolution represents a previously under-appreciated process; we demonstrate here its importance.
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Affiliation(s)
- Brent M Robicheau
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
| | - Edward Susko
- Center for Comparative Genomics and Evolutionary Bioinformatics, Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Amye M Harrigan
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
| | - Marlene Snyder
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
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28
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Capozzi O, Stanyon R, Archidiacono N, Ishida T, Romanenko SA, Rocchi M. Rapid emergence of independent "chromosomal lineages" in silvered-leaf monkey triggered by Y/autosome translocation. Sci Rep 2018; 8:3250. [PMID: 29459623 PMCID: PMC5818525 DOI: 10.1038/s41598-018-21509-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 02/06/2018] [Indexed: 12/17/2022] Open
Abstract
Sex/autosome translocations are rare events. The only known example in catarrhines is in the silvered-leaf monkey. Here the Y chromosome was reciprocally translocated with chromosome 1. The rearrangement produced an X1X2Y1Y2 sex chromosome system. At least three chromosomal variants of the intact chromosome 1 are known to exist. We characterized in high resolution the translocation products (Y1 and Y2) and the polymorphic forms of the intact chromosome 1 with a panel of more than 150 human BAC clones. We showed that the translocation products were extremely rearranged, in contrast to the high level of marker order conservation of the other silvered-leaf monkey chromosomes. Surprisingly, each translocation product appeared to form independent "chromosome lineages"; each having a myriad of distinct rearrangements. We reconstructed the evolutionary history of the translocation products by comparing the homologous chromosomes of two other colobine species: the African mantled guereza and the Indian langur. The results showed a massive reuse of breakpoints: only 12, out of the 40 breaks occurred in domains never reused in other rearrangements, while, strikingly, some domains were used up to four times. Such frequent breakpoint reuse if proved to be a general phenomenon has profound implications for mechanisms of chromosome evolution.
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Affiliation(s)
| | - Roscoe Stanyon
- Department of Biology, University of Florence, 50122, Florence, Italy.
| | | | - Takafumi Ishida
- Department of Biological Sciences, Human Biology & Genetics, Graduate School of Science, University of Tokyo, 113-0033, Tokyo, Japan
| | - Svetlana A Romanenko
- Institute of Molecular and Cellular Biology SB RAS, 630090, Novosibirsk, Russia
- Novosibirsk State University, 630090, Novosibirsk, Russia
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29
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Lo Bianco S, Masters JC, Sineo L. The evolution of the Cercopithecini: a (post)modern synthesis. Evol Anthropol 2017; 26:336-349. [PMID: 29265656 DOI: 10.1002/evan.21567] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2017] [Indexed: 11/11/2022]
Abstract
The Cercopithecini, or African guenon monkeys, are one of the most diverse clades of living primates and comprise the most species-rich clade of Catarrhini. Species identity is announced by flamboyant coloration of the facial and genital regions and, more cryptically, by vigorous chromosomal rearrangements among taxa. Beneath the skin, however, these animals are skeletally conservative and show low levels of genetic sequence divergence consonant with recent divergence between congeneric species. The guenons clearly demonstrate that morphological, cytogenetic, and reproductive differentiation proceed at different rates during speciation. We review diverse kinds of data in an effort to understand this conundrum.
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Affiliation(s)
- Stefania Lo Bianco
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Via Archirafi 18, 90123, Palermo, Italy
| | - Judith C Masters
- African Primate Initiative for Ecology and Speciation (APIES), University of Fort Hare, and Africa Earth Observatory Network (AEON), Earth Stewardship Science Research Institute, Nelson Mandela University, 6031, Port Elizabeth, South Africa
| | - Luca Sineo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Via Archirafi 18, 90123, Palermo, Italy
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30
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Schrago CG, Mello B, Pereira AG, Furtado C, Seuánez HN. Impact of long-term chromosomal shuffling on the multispecies coalescent analysis of two anthropoid primate lineages. Ecol Evol 2017; 8:1206-1216. [PMID: 29375791 PMCID: PMC5773316 DOI: 10.1002/ece3.3736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/21/2017] [Accepted: 11/27/2017] [Indexed: 01/03/2023] Open
Abstract
Multispecies coalescent (MSC) theory assumes that gene trees inferred from individual loci are independent trials of the MSC process. As genes might be physically close in syntenic associations spanning along chromosome regions, these assumptions might be flawed in evolutionary lineages with substantial karyotypic shuffling. Neotropical primates (NP) represent an ideal case for assessing the performance of MSC methods in such scenarios because chromosome diploid number varies significantly in this lineage. To this end, we investigated the effect of sequence length on the theoretical expectations of MSC model, as well as the results of coalescent‐based tree inference methods. This was carried out by comparing NP with hominids, a lineage in which chromosome macrostructure has been stable for at least 15 million years. We found that departure from the MSC model in Neotropical primates decreased with smaller sequence fragments, where sites sharing the same evolutionary history were more frequently found than in longer fragments. This scenario probably resulted from extensive karyotypic rearrangement occurring during the radiation of NP, contrary to the comparatively stable chromosome evolution in hominids.
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Affiliation(s)
- Carlos G Schrago
- Department of Genetics Federal University of Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Beatriz Mello
- Department of Genetics Federal University of Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Anieli G Pereira
- Department of Genetics Federal University of Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Carolina Furtado
- Division of Genetics National Cancer Institute Rio de Janeiro Brazil
| | - Hector N Seuánez
- Department of Genetics Federal University of Rio de Janeiro Rio de Janeiro RJ Brazil.,Division of Genetics National Cancer Institute Rio de Janeiro Brazil
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31
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Chiatante G, Giannuzzi G, Calabrese FM, Eichler EE, Ventura M. Centromere Destiny in Dicentric Chromosomes: New Insights from the Evolution of Human Chromosome 2 Ancestral Centromeric Region. Mol Biol Evol 2017; 34:1669-1681. [PMID: 28333343 DOI: 10.1093/molbev/msx108] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Dicentric chromosomes are products of genomic rearrangements that place two centromeres on the same chromosome. Due to the presence of two primary constrictions, they are inherently unstable and overcome their instability by epigenetically inactivating and/or deleting one of the two centromeres, thus resulting in functionally monocentric chromosomes that segregate normally during cell division. Our understanding to date of dicentric chromosome formation, behavior and fate has been largely inferred from observational studies in plants and humans as well as artificially produced de novo dicentrics in yeast and in human cells. We investigate the most recent product of a chromosome fusion event fixed in the human lineage, human chromosome 2, whose stability was acquired by the suppression of one centromere, resulting in a unique difference in chromosome number between humans (46 chromosomes) and our most closely related ape relatives (48 chromosomes). Using molecular cytogenetics, sequencing, and comparative sequence data, we deeply characterize the relicts of the chromosome 2q ancestral centromere and its flanking regions, gaining insight into the ancestral organization that can be easily broadened to all acrocentric chromosome centromeres. Moreover, our analyses offered the opportunity to trace the evolutionary history of rDNA and satellite III sequences among great apes, thus suggesting a new hypothesis for the preferential inactivation of some human centromeres, including IIq. Our results suggest two possible centromere inactivation models to explain the evolutionarily stabilization of human chromosome 2 over the last 5-6 million years. Our results strongly favor centromere excision through a one-step process.
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Affiliation(s)
- Giorgia Chiatante
- Department of Biology, University of Bari "Aldo Moro", Bari, Italy.,Department of Biology, Anthropology Laboratories University of Florence, Florence, Italy
| | - Giuliana Giannuzzi
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | | | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA
| | - Mario Ventura
- Department of Biology, University of Bari "Aldo Moro", Bari, Italy
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Genomic properties of chromosomal bands are linked to evolutionary rearrangements and new centromere formation in primates. Chromosome Res 2017; 25:261-276. [PMID: 28717965 DOI: 10.1007/s10577-017-9560-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 06/28/2017] [Accepted: 07/03/2017] [Indexed: 10/19/2022]
Abstract
Chromosomal rearrangements in humans are largely related to pathological conditions, and phenotypic effects are also linked to alterations in the expression profile following nuclear relocation of genes between functionally different compartments, generally occupying the periphery or the inner part of the cell nuclei. On the other hand, during evolution, chromosomal rearrangements may occur apparently without damaging phenotypic effects and are visible in currently phylogenetically related species. To increase our insight into chromosomal reorganisation in the cell nucleus, we analysed 18 chromosomal regions endowed with different genomic properties in cell lines derived from eight primate species covering the entire evolutionary tree. We show that homologous loci, in spite of their evolutionary relocation along the chromosomes, generally remain localised to the same functional compartment of the cell nuclei. We conclude that evolutionarily successful chromosomal rearrangements are those that leave the nuclear position of the regions involved unchanged. On the contrary, in pathological situations, the effect typically observed is on gene structure alteration or gene nuclear reposition. Moreover, our data indicate that new centromere formation could potentially occur everywhere in the chromosomes, but only those emerging in very GC-poor/gene-poor regions, generally located in the nuclear periphery, have a high probability of being retained through evolution. This suggests that, in the cell nucleus of related species, evolutionary chromosomal reshufflings or new centromere formation does not alter the functionality of the regions involved or the interactions between different loci, thus preserving the expression pattern of orthologous genes.
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Abstract
Whole-genome assemblies of 19 placental mammals and two outgroup species were used to reconstruct the order and orientation of syntenic fragments in chromosomes of the eutherian ancestor and six other descendant ancestors leading to human. For ancestral chromosome reconstructions, we developed an algorithm (DESCHRAMBLER) that probabilistically determines the adjacencies of syntenic fragments using chromosome-scale and fragmented genome assemblies. The reconstructed chromosomes of the eutherian, boreoeutherian, and euarchontoglires ancestor each included >80% of the entire length of the human genome, whereas reconstructed chromosomes of the most recent common ancestor of simians, catarrhini, great apes, and humans and chimpanzees included >90% of human genome sequence. These high-coverage reconstructions permitted reliable identification of chromosomal rearrangements over ∼105 My of eutherian evolution. Orangutan was found to have eight chromosomes that were completely conserved in homologous sequence order and orientation with the eutherian ancestor, the largest number for any species. Ruminant artiodactyls had the highest frequency of intrachromosomal rearrangements, and interchromosomal rearrangements dominated in murid rodents. A total of 162 chromosomal breakpoints in evolution of the eutherian ancestral genome to the human genome were identified; however, the rate of rearrangements was significantly lower (0.80/My) during the first ∼60 My of eutherian evolution, then increased to greater than 2.0/My along the five primate lineages studied. Our results significantly expand knowledge of eutherian genome evolution and will facilitate greater understanding of the role of chromosome rearrangements in adaptation, speciation, and the etiology of inherited and spontaneously occurring diseases.
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Dumas F, Mazzoleni S. Neotropical primate evolution and phylogenetic reconstruction using chromosomal data. EUROPEAN ZOOLOGICAL JOURNAL 2017. [DOI: 10.1080/11250003.2016.1260655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- F. Dumas
- Department of “Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche”, University of Palermo, Italy
| | - S. Mazzoleni
- Department of “Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche”, University of Palermo, Italy
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
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Giulotto E, Raimondi E, Sullivan KF. The Unique DNA Sequences Underlying Equine Centromeres. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2017; 56:337-354. [PMID: 28840244 DOI: 10.1007/978-3-319-58592-5_14] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Centromeres are highly distinctive genetic loci whose function is specified largely by epigenetic mechanisms. Understanding the role of DNA sequences in centromere function has been a daunting task due to the highly repetitive nature of centromeres in animal chromosomes. The discovery of a centromere devoid of satellite DNA in the domestic horse consolidated observations on the epigenetic nature of centromere identity, showing that entirely natural chromosomes could function without satellite DNA cues. Horses belong to the genus Equus which exhibits a very high degree of evolutionary plasticity in centromere position and DNA sequence composition. Examination of horses has revealed that the position of the satellite-free centromere is variable among individuals. Analysis of centromere location and composition in other Equus species, including domestic donkey and zebras, confirms that the satellite-less configuration of centromeres is common in this group which has undergone particularly rapid karyotype evolution. These features have established the equids as a new mammalian system in which to investigate the molecular organization, dynamics and evolutionary behaviour of centromeres.
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Affiliation(s)
- Elena Giulotto
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Elena Raimondi
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy
| | - Kevin F Sullivan
- National University of Ireland Galway, University Road, Galway, Ireland
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Clusters of alpha satellite on human chromosome 21 are dispersed far onto the short arm and lack ancient layers. Chromosome Res 2016; 24:421-36. [PMID: 27430641 DOI: 10.1007/s10577-016-9530-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/03/2016] [Indexed: 10/21/2022]
Abstract
Human alpha satellite (AS) sequence domains that currently function as centromeres are typically flanked by layers of evolutionarily older AS that presumably represent the remnants of earlier primate centromeres. Studies on several human chromosomes reveal that these older AS arrays are arranged in an age gradient, with the oldest arrays farthest from the functional centromere and arrays progressively closer to the centromere being progressively younger. The organization of AS on human chromosome 21 (HC21) has not been well-characterized. We have used newly available HC21 sequence data and an HC21p YAC map to determine the size, organization, and location of the AS arrays, and compared them to AS arrays found on other chromosomes. We find that the majority of the HC21 AS sequences are present on the p-arm of the chromosome and are organized into at least five distinct isolated clusters which are distributed over a larger distance from the functional centromere than that typically seen for AS on other chromosomes. Using both phylogenetic and L1 element age estimations, we found that all of the HC21 AS clusters outside the functional centromere are of a similar relatively recent evolutionary origin. HC21 contains none of the ancient AS layers associated with early primate evolution which is present on other chromosomes, possibly due to the fact that the p-arm of HC21 and the other acrocentric chromosomes underwent substantial reorganization about 20 million years ago.
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Gariou-Papalexiou A, Giardini MC, Augustinos AA, Drosopoulou E, Lanzavecchia SB, Cladera JL, Caceres C, Bourtzis K, Mavragani-Tsipidou P, Zacharopoulou A. Cytogenetic Analysis of the South American Fruit Fly Anastrepha fraterculus (Diptera:Tephritidae) Species Complex: Construction of Detailed Photographic Polytene Chromosome Maps of the Argentinian Af. sp.1 Member. PLoS One 2016; 11:e0157192. [PMID: 27362546 PMCID: PMC4928812 DOI: 10.1371/journal.pone.0157192] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 05/25/2016] [Indexed: 01/28/2023] Open
Abstract
Genetic and cytogenetic studies constitute a significant basis for understanding the biology of insect pests and the design and the construction of genetic tools for biological control strategies. Anastrepha fraterculus is an important pest of the Tephritidae family. It is distributed from southern Texas through eastern Mexico, Central America and South America causing significant crop damage and economic losses. Currently it is considered as a species complex; until now seven members have been described based on multidisciplinary approaches. Here we report the cytogenetic analysis of an Argentinian population characterized as Af. sp.1 member of the Anastrepha fraterculus species complex. The mitotic karyotype and the first detailed photographic maps of the salivary gland polytene chromosomes are presented. The mitotic metaphase complement consists of six (6) pairs of chromosomes, including one pair of heteromorphic sex chromosomes, with the male being the heterogametic sex. The analysis of the salivary gland polytene complement shows a total number of five long chromosomes that correspond to the five autosomes of the mitotic karyotype and a heterochromatic network corresponding to the sex chromosomes. Comparison of the polytene chromosome maps between this species and Anastrepha ludens shows significant similarity. The polytene maps presented here are suitable for cytogenetic studies that could shed light on the species limits within this species complex and support the development of genetic tools for sterile insect technique (SIT) applications.
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Affiliation(s)
| | - María Cecilia Giardini
- Instituto de Genética EA Favret, Instituto Nacional Tecnología Agropecuaria, Hurlingham, Provincia de Buenos Aires, Argentina
| | - Antonios A. Augustinos
- Biology Department, University of Patras, Patras, Greece
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, Vienna, Austria
| | - Elena Drosopoulou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Silvia B. Lanzavecchia
- Instituto de Genética EA Favret, Instituto Nacional Tecnología Agropecuaria, Hurlingham, Provincia de Buenos Aires, Argentina
| | - Jorge L. Cladera
- Instituto de Genética EA Favret, Instituto Nacional Tecnología Agropecuaria, Hurlingham, Provincia de Buenos Aires, Argentina
| | - Carlos Caceres
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, Vienna, Austria
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, Vienna, Austria
| | - Penelope Mavragani-Tsipidou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Gordon D, Huddleston J, Chaisson MJP, Hill CM, Kronenberg ZN, Munson KM, Malig M, Raja A, Fiddes I, Hillier LW, Dunn C, Baker C, Armstrong J, Diekhans M, Paten B, Shendure J, Wilson RK, Haussler D, Chin CS, Eichler EE. Long-read sequence assembly of the gorilla genome. Science 2016; 352:aae0344. [PMID: 27034376 PMCID: PMC4920363 DOI: 10.1126/science.aae0344] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/26/2016] [Indexed: 12/24/2022]
Abstract
Accurate sequence and assembly of genomes is a critical first step for studies of genetic variation. We generated a high-quality assembly of the gorilla genome using single-molecule, real-time sequence technology and a string graph de novo assembly algorithm. The new assembly improves contiguity by two to three orders of magnitude with respect to previously released assemblies, recovering 87% of missing reference exons and incomplete gene models. Although regions of large, high-identity segmental duplications remain largely unresolved, this comprehensive assembly provides new biological insight into genetic diversity, structural variation, gene loss, and representation of repeat structures within the gorilla genome. The approach provides a path forward for the routine assembly of mammalian genomes at a level approaching that of the current quality of the human genome.
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Affiliation(s)
- David Gordon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - John Huddleston
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Mark J P Chaisson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Christopher M Hill
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Zev N Kronenberg
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Maika Malig
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Archana Raja
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Ian Fiddes
- Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, CA 95064, USA
| | - LaDeana W Hillier
- McDonnell Genome Institute, Department of Medicine, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | | | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Joel Armstrong
- Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, CA 95064, USA
| | - Mark Diekhans
- Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, CA 95064, USA
| | - Benedict Paten
- Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, CA 95064, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Richard K Wilson
- McDonnell Genome Institute, Department of Medicine, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - David Haussler
- Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, CA 95064, USA
| | - Chen-Shan Chin
- Pacific Biosciences of California, Menlo Park, CA 94025, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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Dumas F, Cuttaia H, Sineo L. Chromosomal distribution of interstitial telomeric sequences in nine neotropical primates (Platyrrhini): possible implications in evolution and phylogeny. J ZOOL SYST EVOL RES 2016. [DOI: 10.1111/jzs.12131] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francesca Dumas
- Dipartimento di Scienze e Tecnologie Biologiche; Chimiche e Farmaceutiche; Università degli Studi Palermo; Palermo Italy
| | - Helenia Cuttaia
- Azienda ospedaliera Ospedali Riuniti Villa Sofia - Cervello; Laboratorio di Citogenetica Medica; Palermo Italy
| | - Luca Sineo
- Dipartimento di Scienze e Tecnologie Biologiche; Chimiche e Farmaceutiche; Università degli Studi Palermo; Palermo Italy
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41
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The 14/15 association as a paradigmatic example of tracing karyotype evolution in New World monkeys. Chromosoma 2015; 125:747-56. [DOI: 10.1007/s00412-015-0565-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/24/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
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Fan X, Supiwong W, Weise A, Mrasek K, Kosyakova N, Tanomtong A, Pinthong K, Trifonov VA, Cioffi MDB, Grothmann P, Liehr T, Oliveira EH. Comprehensive characterization of evolutionary conserved breakpoints in four New World Monkey karyotypes compared to Chlorocebus aethiops and Homo sapiens. Heliyon 2015; 1:e00042. [PMID: 27441227 PMCID: PMC4945616 DOI: 10.1016/j.heliyon.2015.e00042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/20/2015] [Accepted: 10/23/2015] [Indexed: 11/21/2022] Open
Abstract
Comparative cytogenetic analysis in New World Monkeys (NWMs) using human multicolor banding (MCB) probe sets were not previously done. Here we report on an MCB based FISH-banding study complemented with selected locus-specific and heterochromatin specific probes in four NWMs and one Old World Monkey (OWM) species, i.e. in Alouatta caraya (ACA), Callithrix jacchus (CJA), Cebus apella (CAP), Saimiri sciureus (SSC), and Chlorocebus aethiops (CAE), respectively. 107 individual evolutionary conserved breakpoints (ECBs) among those species were identified and compared with those of other species in previous reports. Especially for chromosomal regions being syntenic to human chromosomes 6, 8, 9, 10, 11, 12 and 16 previously cryptic rearrangements could be observed. 50.4% (54/107) NWM-ECBs were colocalized with those of OWMs, 62.6% (62/99) NWM-ECBs were related with those of Hylobates lar (HLA) and 66.3% (71/107) NWM-ECBs corresponded with those known from other mammalians. Furthermore, human fragile sites were aligned with the ECBs found in the five studied species and interestingly 66.3% ECBs colocalized with those fragile sites (FS). Overall, this study presents detailed chromosomal maps of one OWM and four NWM species. This data will be helpful to further investigation on chromosome evolution in NWM and hominoids in general and is prerequisite for correct interpretation of future sequencing based genomic studies in those species.
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Key Words
- ACA, Alouatta caraya
- Atelidae
- BACs, bacterial artificial chromosomes
- CAE, Chlorocebus aethiops
- CAP, Cebus apella
- CJA, Callithrix jacchus
- Cebidae
- EC, evolutionary conserved
- ECBs, evolutionary conserved breakpoints
- Evolutionary conserved breakpoints
- Evolutionary genetics
- FISH, fluorescence in situ hybridization
- FS, fragile site
- Fragile sites
- Genetics
- HCM, heterochromatin mix
- HLA, Hylobates lar
- HSA, Homo sapiens
- HSBs, homologous syntenic blocks
- MCB, multicolor banding
- Multicolor banding
- NGS, Next-generation sequencing
- NOR, nucleolus organizer region
- NWMs, New World Monkeys
- New World Monkeys
- OWMs, Old World Monkeys
- Old World Monkeys
- SSC, Saimiri sciureus
- subCTM, sub-centromere/subtelomere-specific multicolor (FISH)
- wcp, whole human chromosome painting
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Affiliation(s)
- Xiaobo Fan
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Weerayuth Supiwong
- Department of Biology Faculty of Science, KhonKaen University, 123 Moo 16 Mittapap Rd., Muang District, KhonKaen 40002, Thailand
| | - Anja Weise
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Kristin Mrasek
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Nadezda Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Alongkoad Tanomtong
- Department of Biology Faculty of Science, KhonKaen University, 123 Moo 16 Mittapap Rd., Muang District, KhonKaen 40002, Thailand
| | - Krit Pinthong
- Department of Biology Faculty of Science, KhonKaen University, 123 Moo 16 Mittapap Rd., Muang District, KhonKaen 40002, Thailand
| | | | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Pierre Grothmann
- Serengeti-Park Hodenhagen GmbH, Am Safaripark 1, 29693, Hodenhagen, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Edivaldo H.C.de Oliveira
- Faculdade de Ciências Naturais, ICEN, Universidade Federal do Pará, Campus Universitário do Guamá, 66075-110 Belém-PA, Brazil
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Catacchio CR, Ragone R, Chiatante G, Ventura M. Organization and evolution of Gorilla centromeric DNA from old strategies to new approaches. Sci Rep 2015; 5:14189. [PMID: 26387916 PMCID: PMC4585704 DOI: 10.1038/srep14189] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/18/2015] [Indexed: 11/09/2022] Open
Abstract
The centromere/kinetochore interaction is responsible for the pairing and segregation of replicated chromosomes in eukaryotes. Centromere DNA is portrayed as scarcely conserved, repetitive in nature, quickly evolving and protein-binding competent. Among primates, the major class of centromeric DNA is the pancentromeric α-satellite, made of arrays of 171 bp monomers, repeated in a head-to-tail pattern. α-satellite sequences can either form tandem heterogeneous monomeric arrays or assemble in higher-order repeats (HORs). Gorilla centromere DNA has barely been characterized, and data are mainly based on hybridizations of human alphoid sequences. We isolated and finely characterized gorilla α-satellite sequences and revealed relevant structure and chromosomal distribution similarities with other great apes as well as gorilla-specific features, such as the uniquely octameric structure of the suprachromosomal family-2 (SF2). We demonstrated for the first time the orthologous localization of alphoid suprachromosomal families-1 and −2 (SF1 and SF2) between human and gorilla in contrast to chimpanzee centromeres. Finally, the discovery of a new 189 bp monomer type in gorilla centromeres unravels clues to the role of the centromere protein B, paving the way to solve the significance of the centromere DNA’s essential repetitive nature in association with its function and the peculiar evolution of the α-satellite sequence.
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Affiliation(s)
- C R Catacchio
- University of Bari Aldo Moro, Department of Biology, Via Orabona 4, Bari, 70125, Italy
| | - R Ragone
- University of Bari Aldo Moro, Department of Biology, Via Orabona 4, Bari, 70125, Italy
| | - G Chiatante
- University of Bari Aldo Moro, Department of Biology, Via Orabona 4, Bari, 70125, Italy
| | - M Ventura
- University of Bari Aldo Moro, Department of Biology, Via Orabona 4, Bari, 70125, Italy
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Badenhorst D, Hillier LW, Literman R, Montiel EE, Radhakrishnan S, Shen Y, Minx P, Janes DE, Warren WC, Edwards SV, Valenzuela N. Physical Mapping and Refinement of the Painted Turtle Genome (Chrysemys picta) Inform Amniote Genome Evolution and Challenge Turtle-Bird Chromosomal Conservation. Genome Biol Evol 2015; 7:2038-50. [PMID: 26108489 PMCID: PMC4524486 DOI: 10.1093/gbe/evv119] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2015] [Indexed: 01/04/2023] Open
Abstract
Comparative genomics continues illuminating amniote genome evolution, but for many lineages our understanding remains incomplete. Here, we refine the assembly (CPI 3.0.3 NCBI AHGY00000000.2) and develop a cytogenetic map of the painted turtle (Chrysemys picta-CPI) genome, the first in turtles and in vertebrates with temperature-dependent sex determination. A comparison of turtle genomes with those of chicken, selected nonavian reptiles, and human revealed shared and novel genomic features, such as numerous chromosomal rearrangements. The largest conserved syntenic blocks between birds and turtles exist in four macrochromosomes, whereas rearrangements were evident in these and other chromosomes, disproving that turtles and birds retain fully conserved macrochromosomes for greater than 300 Myr. C-banding revealed large heterochromatic blocks in the centromeric region of only few chromosomes. The nucleolar-organizing region (NOR) mapped to a single CPI microchromosome, whereas in some turtles and lizards the NOR maps to nonhomologous sex-chromosomes, thus revealing independent translocations of the NOR in various reptilian lineages. There was no evidence for recent chromosomal fusions as interstitial telomeric-DNA was absent. Some repeat elements (CR1-like, Gypsy) were enriched in the centromeres of five chromosomes, whereas others were widespread in the CPI genome. Bacterial artificial chromosome (BAC) clones were hybridized to 18 of the 25 CPI chromosomes and anchored to a G-banded ideogram. Several CPI sex-determining genes mapped to five chromosomes, and homology was detected between yet other CPI autosomes and the globally nonhomologous sex chromosomes of chicken, other turtles, and squamates, underscoring the independent evolution of vertebrate sex-determining mechanisms.
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Affiliation(s)
- Daleen Badenhorst
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
| | | | - Robert Literman
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
| | | | | | - Yingjia Shen
- The Genome Institute at Washington University, St Louis
| | - Patrick Minx
- The Genome Institute at Washington University, St Louis
| | - Daniel E Janes
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University Department of Organismic and Evolutionary Biology, Harvard University
| | | | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
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Weise A, Kosyakova N, Voigt M, Aust N, Mrasek K, Löhmer S, Rubtsov N, Karamysheva TV, Trifonov VA, Hardekopf D, Jančušková T, Pekova S, Wilhelm K, Liehr T, Fan X. Comprehensive Analyses of White-Handed Gibbon Chromosomes Enables Access to 92 Evolutionary Conserved Breakpoints Compared to the Human Genome. Cytogenet Genome Res 2015; 145:42-9. [PMID: 25926034 DOI: 10.1159/000381764] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2015] [Indexed: 11/19/2022] Open
Abstract
Gibbon species (Hylobatidae) impress with an unusually high number of numerical and structural chromosomal changes within the family itself as well as compared to other Hominoidea including humans. In former studies applying molecular cytogenetic methods, 86 evolutionary conserved breakpoints (ECBs) were reported in the white-handed gibbon (Hylobates lar, HLA) with respect to the human genome. To analyze those ECBs in more detail and also to achieve a better understanding of the fast karyotype evolution in Hylobatidae, molecular data for these regions are indispensably necessary. In the present study, we obtained whole chromosome-specific probes by microdissection of all 21 HLA autosomes and prepared them for aCGH. Locus-specific DNA probes were also used for further molecular cytogenetic characterization of selected regions. Thus, we could map 6 yet unreported ECBs in HLA with respect to the human genome. Additionally, in 26 of the 86 previously reported ECBs, the present approach enabled a more precise breakpoint mapping. Interestingly, a preferred localization of ECBs within segmental duplications, copy number variant regions, and fragile sites was observed.
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Affiliation(s)
- Anja Weise
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
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Ullastres A, Farré M, Capilla L, Ruiz-Herrera A. Unraveling the effect of genomic structural changes in the rhesus macaque - implications for the adaptive role of inversions. BMC Genomics 2014; 15:530. [PMID: 24969235 PMCID: PMC4082625 DOI: 10.1186/1471-2164-15-530] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 06/19/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND By reshuffling genomes, structural genomic reorganizations provide genetic variation on which natural selection can work. Understanding the mechanisms underlying this process has been a long-standing question in evolutionary biology. In this context, our purpose in this study is to characterize the genomic regions involved in structural rearrangements between human and macaque genomes and determine their influence on meiotic recombination as a way to explore the adaptive role of genome shuffling in mammalian evolution. RESULTS We first constructed a highly refined map of the structural rearrangements and evolutionary breakpoint regions in the human and rhesus macaque genomes based on orthologous genes and whole-genome sequence alignments. Using two different algorithms, we refined the genomic position of known rearrangements previously reported by cytogenetic approaches and described new putative micro-rearrangements (inversions and indels) in both genomes. A detailed analysis of the rhesus macaque genome showed that evolutionary breakpoints are in gene-rich regions, being enriched in GO terms related to immune system. We also identified defense-response genes within a chromosome inversion fixed in the macaque lineage, underlying the relevance of structural genomic changes in evolutionary and/or adaptation processes. Moreover, by combining in silico and experimental approaches, we studied the recombination pattern of specific chromosomes that have suffered rearrangements between human and macaque lineages. CONCLUSIONS Our data suggest that adaptive alleles - in this case, genes involved in the immune response - might have been favored by genome rearrangements in the macaque lineage.
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Affiliation(s)
| | | | | | - Aurora Ruiz-Herrera
- Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain.
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Steinberg ER, Nieves M, Fantini L, Mudry MD. Primates karyological diagnosis and management programs applications. J Med Primatol 2014; 43:455-67. [DOI: 10.1111/jmp.12131] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Eliana R. Steinberg
- Grupo de Investigación en Biología Evolutiva (GIBE); Departamento de Ecología, Genética y Evolución; Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires; IEGEBA (CONICET-UBA); Ciudad Universitaria; Buenos Aires Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Buenos Aires Argentina
| | - Mariela Nieves
- Grupo de Investigación en Biología Evolutiva (GIBE); Departamento de Ecología, Genética y Evolución; Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires; IEGEBA (CONICET-UBA); Ciudad Universitaria; Buenos Aires Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Buenos Aires Argentina
| | - Lucía Fantini
- Grupo de Investigación en Biología Evolutiva (GIBE); Departamento de Ecología, Genética y Evolución; Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires; IEGEBA (CONICET-UBA); Ciudad Universitaria; Buenos Aires Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Buenos Aires Argentina
| | - Marta D. Mudry
- Grupo de Investigación en Biología Evolutiva (GIBE); Departamento de Ecología, Genética y Evolución; Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires; IEGEBA (CONICET-UBA); Ciudad Universitaria; Buenos Aires Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Buenos Aires Argentina
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Steinberg ER, Nieves M, Mudry MD. Multiple sex chromosome systems in howler monkeys (Platyrrhini, Alouatta). COMPARATIVE CYTOGENETICS 2014; 8:43-69. [PMID: 24744833 PMCID: PMC3978242 DOI: 10.3897/compcytogen.v8i1.6716] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 01/25/2014] [Indexed: 05/24/2023]
Abstract
In light of the multiple sex chromosome systems observed in howler monkeys (Alouatta Lacépède, 1799) a combined cladistic analysis using chromosomal and molecular characters was applied to discuss the possible origin of these systems. Mesoamerican and South American howlers were karyologically compared. FISH analysis using the chromosome painting probes for the #3 and #15 human chromosomes was applied to corroborate the homeology of the sexual systems. We found that the HSA3/15 syntenic association, present in the sex chromosome systems of South American Howlers, is not present in those of Mesoamerican ones. The autosomes involved in the translocation that formed the sexual systems in the Mesoamerican and South American species are different, thus suggesting an independent origin. Parsimony analysis resolved the phylogenetic relationships among howler species, demonstrating utility of the combined approach. A hypothesis for the origin of the multiple sex chromosome systems for the genus is proposed.
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Affiliation(s)
- Eliana Ruth Steinberg
- Grupo de Investigación en Biología Evolutiva (GIBE) - Departamento de Ecología, Genética y Evolución - Facultad de Ciencias Exactas y Naturales - Universidad de Buenos Aires - IEGEBA (CONICET-UBA) - Ciudad Universitaria - Pab. II -4° piso - Labs 43-46 - (C1428EGA) - Buenos Aires - Argentina
| | - Mariela Nieves
- Grupo de Investigación en Biología Evolutiva (GIBE) - Departamento de Ecología, Genética y Evolución - Facultad de Ciencias Exactas y Naturales - Universidad de Buenos Aires - IEGEBA (CONICET-UBA) - Ciudad Universitaria - Pab. II -4° piso - Labs 43-46 - (C1428EGA) - Buenos Aires - Argentina
| | - Marta Dolores Mudry
- Grupo de Investigación en Biología Evolutiva (GIBE) - Departamento de Ecología, Genética y Evolución - Facultad de Ciencias Exactas y Naturales - Universidad de Buenos Aires - IEGEBA (CONICET-UBA) - Ciudad Universitaria - Pab. II -4° piso - Labs 43-46 - (C1428EGA) - Buenos Aires - Argentina
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Xiaobo F, Pinthong K, Mkrtchyan H, Siripiyasing P, Kosyakova N, Supiwong W, Tanomtong A, Chaveerach A, Liehr T, de Bello Cioffi M, Weise A. First detailed reconstruction of the karyotype of Trachypithecus cristatus (Mammalia: Cercopithecidae). Mol Cytogenet 2013; 6:58. [PMID: 24341374 PMCID: PMC3914712 DOI: 10.1186/1755-8166-6-58] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 11/21/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The chromosomal homologies of human (Homo sapiens = HSA) and silvered leaf monkey (Trachypithecus cristatus = TCR) have been previously studied by classical chromosome staining and by fluorescence in situ hybridization (FISH) applying chromosome-specific DNA probes of all human chromosomes in the 1980s and 1990s, respectively. RESULTS However, as the resolution of these techniques is limited we used multicolor banding (MCB) at an ~250-band level, and other selected human DNA probes to establish a detailed chromosomal map of TCR. Therefore it was possible to precisely determine evolutionary conserved breakpoints, orientation of segments and distribution of specific regions in TCR compared to HSA. Overall, 69 evolutionary conserved breakpoints including chromosomal segments, which failed to be resolved in previous reports, were exactly identified and characterized. CONCLUSIONS This work also represents the first molecular cytogenetic one characterizing a multiple sex chromosome system with a male karyotype 44,XY1Y2. The obtained results are compared to other available data for old world monkeys and drawbacks in hominoid evolution are discussed.
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Affiliation(s)
- Fan Xiaobo
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, Jena D-07743, Germany
| | - Krit Pinthong
- Faculty of Science and Technology, Surindra Rajabhat University, 186 Moo 1, Surin, Maung District 32000, Thailand
| | - Hasmik Mkrtchyan
- Center of Medical Genetics and Primary Health Care, Abovyan Str 34/3, 001, Yerevan, Armenia
| | - Pornnarong Siripiyasing
- Faculty of Science and Technology, Rajabhat Maha Sarakham University, 80 Nakonsawan Rd, Maha Sarakham, Talad, Maung District 44000, Thailand
| | - Nadezda Kosyakova
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, Jena D-07743, Germany
| | - Weerayuth Supiwong
- Department of Biology, Faculty of Science, Khon Kaen University, 123 Moo 16 Mittapap Rd., Khon Kaen, Muang District 40002, Thailand
| | - Alongkoad Tanomtong
- Department of Biology, Faculty of Science, Khon Kaen University, 123 Moo 16 Mittapap Rd., Khon Kaen, Muang District 40002, Thailand
| | - Arunrat Chaveerach
- Department of Biology, Faculty of Science, Khon Kaen University, 123 Moo 16 Mittapap Rd., Khon Kaen, Muang District 40002, Thailand
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, Jena D-07743, Germany
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Anja Weise
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, Jena D-07743, Germany
- Institut für Humangenetik, Postfach, Jena D-07740, Germany
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