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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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da Silva NKN, Nagamachi CY, Rodrigues LRR, O’Brien PCM, Yang F, Ferguson-Smith MA, Pieczarka JC. Chromosome painting and phylogenetic analysis suggest that the genus Lophostoma (Chiroptera, Phyllostomidae) is paraphyletic. Sci Rep 2022; 12:19514. [PMID: 36376355 PMCID: PMC9663435 DOI: 10.1038/s41598-022-21391-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/27/2022] [Indexed: 11/15/2022] Open
Abstract
The subfamily Phyllostominae (Chiroptera, Phyllostomidae) comprises 10 genera of Microchiroptera bats from the Neotropics. The taxonomy of this group is controversial due to incongruities in the phylogenetic relationships evident from different datasets. The genus Lophostoma currently includes eight species whose phylogenetic relationships have not been resolved. Integrative analyzes including morphological, molecular and chromosomal data are powerful tools to investigate the phylogenetics of organisms, particularly if obtained by chromosomal painting. In the present work we performed comparative genomic mapping of three species of Lophostoma (L. brasiliense 2n = 30, L. carrikeri 2n = 26 and L. schulzi 2n = 26), by chromosome painting using whole chromosome probes from Phyllostomus hastatus and Carollia brevicauda; this included mapping interstitial telomeric sites. The karyotype of L. schulzi (LSC) is a new cytotype. The species L. brasiliense and L. carrikeri showed interstitial telomeric sequences that probably resulted from expansions of repetitive sequences near pericentromeric regions. The addition of chromosomal painting data from other species of Phyllostominae allowed phylogeny construction by maximum parsimony, and the determination that the genera of this subfamily are monophyletic, and that the genus Lophostoma is paraphyletic. Additionally, a review of the taxonomic status of LSC is suggested to determine if this species should be reclassified as part of the genus Tonatia.
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Affiliation(s)
- Natalia Karina Nascimento da Silva
- grid.271300.70000 0001 2171 5249Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará Brazil ,grid.442052.5Departamento de Morfofuncional, Universidade do Estado do Pará, Tucuruí, Pará Brazil
| | - Cleusa Yoshiko Nagamachi
- grid.271300.70000 0001 2171 5249Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará Brazil
| | - Luis Reginaldo Ribeiro Rodrigues
- grid.448725.80000 0004 0509 0076Laboratório de Genética & Biodiversidade, Instituto de Ciências da Educação, Universidade Federal do Oeste do Pará, Santarém, Pará Brazil
| | - Patricia Caroline Mary O’Brien
- grid.5335.00000000121885934Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, UK
| | - Fengtang Yang
- grid.10306.340000 0004 0606 5382Cytogenetics Facility, Wellcome Trust Sanger Institute, Hinxton, UK ,grid.27255.370000 0004 1761 1174School of Life Sciences and Medicine, Shandong University, Jinan, China
| | - Malcolm Andrew Ferguson-Smith
- grid.5335.00000000121885934Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, UK
| | - Julio Cesar Pieczarka
- grid.271300.70000 0001 2171 5249Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará Brazil
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Steinberg ER, Bressa MJ, Mudry MD. Sex chromosome systems in Neotropical Primates: What have we learnt so far from cytogenetics and genomics? J Evol Biol 2022; 35:1589-1600. [PMID: 35731796 DOI: 10.1111/jeb.14039] [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: 01/30/2022] [Revised: 05/10/2022] [Accepted: 05/26/2022] [Indexed: 11/29/2022]
Abstract
Neotropical Primates (Platyrrhini) show great diversity in their life histories, ecology, behaviour and genetics. This diversity extends to their chromosome complements, both to autosomes and to sex chromosomes. In this contribution, we will review what is currently known about sex chromosomes in this group, both from cytogenetic and from genomic evidence. The X and Y chromosomes in Neotropical Primates, also known as New World Monkeys, have striking structural differences compared with Old World Monkeys when Catarrhini sex chromosomes are considered. The XY bivalent displays a different meiotic behaviour in prophase I, and their Y chromosome shows extensive genomic differences. Even though the most widespread sex chromosome system is the XX/XY and thus considered the ancestral one for Platyrrhini, modifications of this sexual system are observed within this group. Multiple sex chromosome systems originated from Y-autosome translocations were described in several genera (Aotus, Callimico and Alouatta). In the howler monkeys, genus Alouatta, an independent origin of the sexual systems in South American and Mesoamerican species was postulated. All the above-mentioned evidence suggests that the Y chromosome of Platyrrhini has a different evolutionary history compared with the Catarrhini Y. There is still much to understand regarding their sex chromosome systems.
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Affiliation(s)
- Eliana Ruth Steinberg
- Grupo de Investigación en Biología Evolutiva (GIBE). Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Departamento de Ecología, Genética y Evolución (EGE), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), CONICET, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - María José Bressa
- Grupo de Citogenética de Insectos. Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Departamento de Ecología, Genética y Evolución (EGE), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), CONICET, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Marta Dolores Mudry
- Grupo de Investigación en Biología Evolutiva (GIBE). Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Departamento de Ecología, Genética y Evolución (EGE), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), CONICET, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
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4
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Benathar TCM, Nagamachi CY, Rodrigues LRR, O’Brien PCM, Ferguson-Smith MA, Yang F, Pieczarka JC. Karyotype, evolution and phylogenetic reconstruction in Micronycterinae bats with implications for the ancestral karyotype of Phyllostomidae. BMC Evol Biol 2019; 19:98. [PMID: 31064342 PMCID: PMC6505122 DOI: 10.1186/s12862-019-1421-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 04/11/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The Micronycterinae form a subfamily of leaf-nosed bats (Phyllostomidae) that contains the genera Lampronycteris Sanborn, 1949, and Micronycteris Gray, 1866 (stricto sensu), and is characterized by marked karyotypic variability and discrepancies in the phylogenetic relationships suggested by the molecular versus morphological data. In the present study, we investigated the chromosomal evolution of the Micronycterinae using classical cytogenetics and multidirectional chromosome painting with whole-chromosomes probes of Phyllostomus hastatus and Carollia brevicauda. Our goal was to perform comparative chromosome mapping between the genera of this subfamily and explore the potential for using chromosomal rearrangements as phylogenetic markers. RESULTS The Micronycterinae exhibit great inter- and intraspecific karyotype diversity, with large blocks of telomere-like sequences inserted within or adjacent to constitutive heterochromatin regions. The phylogenetic results generated from our chromosomal data revealed that the Micronycterinae hold a basal position in the phylogenetic tree of the Phyllostomidae. Molecular cytogenetic data confirmed that there is a low degree of karyotype similarity between Lampronycteris and Micronycteris specimens analyzed, indicating an absence of synapomorphic associations in Micronycterinae. CONCLUSIONS We herein confirm that karyotypic variability is present in subfamily Micronycterinae. We further report intraspecific variation and describe a new cytotype in M. megalotis. The cytogenetic data show that this group typically has large blocks of interstitial telomeric sequences that do not appear to be correlated with chromosomal rearrangement events. Phylogenetic analysis using chromosome data recovered the basal position for Micronycterinae, but did not demonstrate that it is a monophyletic lineage, due to the absence of common chromosomal synapomorphy between the genera. These findings may be related to an increase in the rate of chromosomal evolution during the time period that separates Lampronycteris from Micronycteris.
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Affiliation(s)
| | - C. Y. Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Av. Perimetral, sn. Guamá, Belém, Pará 66077 Brasil
- CNPq, Brasilia, Brazil
| | - L. R. R. Rodrigues
- Laboratório de Genética e Biodiversidade, ICED, Universidade Federal do Oeste do Pará, Belém, Brasil
| | - P. C. M. O’Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - M. A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - F. Yang
- Cytogenetics Facility, Welcome Trust Sanger Institute, Hinxton, UK
| | - J. C. Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Av. Perimetral, sn. Guamá, Belém, Pará 66077 Brasil
- CNPq, Brasilia, Brazil
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5
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Ostromohov N, Huber D, Bercovici M, Kaigala GV. Real-Time Monitoring of Fluorescence in Situ Hybridization Kinetics. Anal Chem 2018; 90:11470-11477. [DOI: 10.1021/acs.analchem.8b02630] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Nadya Ostromohov
- IBM Research—Zurich, Säumerstrasse 4, 8803 Rüschlikon, Zurich, Switzerland
- Faculty of Mechanical Engineering, Technion—Israel Institute of Technology, Haifa 3200003, Israel
| | - Deborah Huber
- IBM Research—Zurich, Säumerstrasse 4, 8803 Rüschlikon, Zurich, Switzerland
| | - Moran Bercovici
- Faculty of Mechanical Engineering, Technion—Israel Institute of Technology, Haifa 3200003, Israel
| | - Govind V. Kaigala
- IBM Research—Zurich, Säumerstrasse 4, 8803 Rüschlikon, Zurich, Switzerland
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7
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Martinez PA, Jacobina UP, Fernandes RV, Brito C, Penone C, Amado TF, Fonseca CR, Bidau CJ. A comparative study on karyotypic diversification rate in mammals. Heredity (Edinb) 2016; 118:366-373. [PMID: 27804966 DOI: 10.1038/hdy.2016.110] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 09/19/2016] [Accepted: 09/27/2016] [Indexed: 01/23/2023] Open
Abstract
Chromosomal rearrangements have a relevant role in organismic evolution. However, little is known about the mechanisms that lead different phylogenetic clades to have different chromosomal rearrangement rates. Here, we investigate the causes behind the wide karyotypic diversity exhibited by mammals. In particular, we analyzed the role of metabolic, reproductive, biogeographic and genomic characteristics on the rates of macro- and microstructural karyotypic diversification (rKD) using comparative phylogenetic methods. We found evidence that reproductive characteristics such as larger litter size per year and longevity, by allowing a higher number of meioses in absolute time, favor a higher probability of chromosomal change. Furthermore, families with large geographic distributions but containing species with restricted geographic ranges showed a greater probability of fixation of macrostructural chromosomal changes in different geographic areas. Finally, rKD does not evolve by Brownian motion because the mutation rate depends on the concerted evolution of repetitive sequences. The decisive factors of rKD evolution will be natural selection, genetic drift and meiotic drive that will eventually allow or not the fixation of the rearrangements. Our results indicate that mammalian karyotypic diversity is influenced by historical and adaptive mechanisms where reproductive and genomic factors modulate the rate of chromosomal change.
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Affiliation(s)
- P A Martinez
- PIBi Lab-Laboratorio de Pesquisas Integrativas em Biodiversidade, Pós-Graduação em Ecologia e Conservação, Universidade Federal de Sergipe, São Cristovão, Brazil
| | | | - R V Fernandes
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - C Brito
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - C Penone
- Institute of Plant Science, University of Bern, Bern, Switzerland
| | - T F Amado
- BioMa-Biodiversity and Macroecology Lab, Department of Biology and Geology, Physics and Inorganic Chemistry, Rey Juan Carlos University, Mostoles, Spain
| | - C R Fonseca
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - C J Bidau
- Paraná y Los Claveles, Garupá, Argentina
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8
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Giannuzzi G, Pazienza M, Huddleston J, Antonacci F, Malig M, Vives L, Eichler EE, Ventura M. Hominoid fission of chromosome 14/15 and the role of segmental duplications. Genome Res 2013; 23:1763-73. [PMID: 24077392 PMCID: PMC3814877 DOI: 10.1101/gr.156240.113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ape chromosomes homologous to human chromosomes 14 and 15 were generated by a fission event of an ancestral submetacentric chromosome, where the two chromosomes were joined head-to-tail. The hominoid ancestral chromosome most closely resembles the macaque chromosome 7. In this work, we provide insights into the evolution of human chromosomes 14 and 15, performing a comparative study between macaque boundary region 14/15 and the orthologous human regions. We construct a 1.6-Mb contig of macaque BAC clones in the region orthologous to the ancestral hominoid fission site and use it to define the structural changes that occurred on human 14q pericentromeric and 15q subtelomeric regions. We characterize the novel euchromatin–heterochromatin transition region (∼20 Mb) acquired during the neocentromere establishment on chromosome 14, and find it was mainly derived through pericentromeric duplications from ancestral hominoid chromosomes homologous to human 2q14–qter and 10. Further, we show a relationship between evolutionary hotspots and low-copy repeat loci for chromosome 15, revealing a possible role of segmental duplications not only in mediating but also in “stitching” together rearrangement breakpoints.
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Affiliation(s)
- Giuliana Giannuzzi
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
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Fluorescence in situ hybridization on electrophoresed cells to detect sequence specific DNA damage. Methods Mol Biol 2013; 1054:219-35. [PMID: 23913296 DOI: 10.1007/978-1-62703-565-1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Fluorescence in situ hybridization (FISH) to label fragments of DNA with probes which can specifically locate a genomic region of interest, combined with the single cell electrophoresis (Comet) assay, also termed Comet-FISH, allows the quantification of DNA damage and repair at a specific genomic locus. While the Comet assay alone quantifies only the overall DNA damage of an individual cell, subsequent FISH on the electrophoresed single cell genome enables the coincidental localization of fluorescently labelled sequences (i.e., probes) to the respective damaged or undamaged genes or specific genomic regions of interest. In that way sequence specific DNA damage, global genomic and transcription coupled repair or the three dimensional ultrastructure of cells from any tissue can be comparatively investigated. This protocol provides a detailed description of the principles and basic methodology of a standard Comet-FISH experiment to study interphase cells of any tissue. Also important variations of the protocol (e.g., neutral conditions to detect double strand breaks) as well as the production of fluorochrome-labelled DNA probes via random priming are described.
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Graphodatsky A, Ferguson-Smith MA, Stanyon R. A short introduction to cytogenetic studies in mammals with reference to the present volume. Cytogenet Genome Res 2012; 137:83-96. [PMID: 22846392 DOI: 10.1159/000341502] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Genome diversity has long been studied from the comparative cytogenetic perspective. Early workers documented differences between species in diploid chromosome number and fundamental number. Banding methods allowed more detailed descriptions of between-species rearrangements and classes of differentially staining chromosome material. The infusion of molecular methods into cytogenetics provided a third revolution, which is still not exhausted. Chromosome painting has provided a global view of the translocation history of mammalian genome evolution, well summarized in the contributions to this special volume. More recently, FISH of cloned DNA has provided details on defining breakpoint and intrachromosomal marker order, which have helped to document inversions and centromere repositioning. The most recent trend in comparative molecular cytogenetics is to integrate sequencing information in order to formulate and test reconstructions of ancestral genomes and phylogenomic hypotheses derived from comparative cytogenetics. The integration of comparative cytogenetics and sequencing promises to provide an understanding of what drives chromosome rearrangements and genome evolution in general. We believe that the contributions in this volume, in no small way, point the way to the next phase in cytogenetic studies.
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Affiliation(s)
- A Graphodatsky
- Institute of Molecular and Cellular Biology, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
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Nie W. Molecular cytogenetic studies in strepsirrhine primates, Dermoptera and Scandentia. Cytogenet Genome Res 2012; 137:246-58. [PMID: 22614467 DOI: 10.1159/000338727] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Since the first chromosome painting study between human and strepsirrhine primates was performed in 1996, nearly 30 species in Strepsirrhini, Dermoptera and Scandentia have been analyzed by cross-species chromosome painting. Here, the contribution of chromosome painting data to our understanding of primate genome organization, chromosome evolution and the karyotype phylogenetic relationships within strepsirrhine primates, Dermoptera and Scandentia is reviewed. Twenty-six to 43 homologous chromosome segments have been revealed in different species with human chromosome-specific paint probes. Various landmark rearrangements characteristic for each different lineage have been identified, as cytogenetic signatures that potentially unite certain lineages within strepsirrhine primates, Dermoptera and Scandentia.
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Affiliation(s)
- W Nie
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China.
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Farré M, Bosch M, López-Giráldez F, Ponsà M, Ruiz-Herrera A. Assessing the role of tandem repeats in shaping the genomic architecture of great apes. PLoS One 2011; 6:e27239. [PMID: 22076140 PMCID: PMC3208591 DOI: 10.1371/journal.pone.0027239] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 10/12/2011] [Indexed: 11/18/2022] Open
Abstract
Background Ancestral reconstructions of mammalian genomes have revealed that evolutionary breakpoint regions are clustered in regions that are more prone to break and reorganize. What is still unclear to evolutionary biologists is whether these regions are physically unstable due solely to sequence composition and/or genome organization, or do they represent genomic areas where the selection against breakpoints is minimal. Methodology and Principal Findings Here we present a comprehensive study of the distribution of tandem repeats in great apes. We analyzed the distribution of tandem repeats in relation to the localization of evolutionary breakpoint regions in the human, chimpanzee, orangutan and macaque genomes. We observed an accumulation of tandem repeats in the genomic regions implicated in chromosomal reorganizations. In the case of the human genome our analyses revealed that evolutionary breakpoint regions contained more base pairs implicated in tandem repeats compared to synteny blocks, being the AAAT motif the most frequently involved in evolutionary regions. We found that those AAAT repeats located in evolutionary regions were preferentially associated with Alu elements. Significance Our observations provide evidence for the role of tandem repeats in shaping mammalian genome architecture. We hypothesize that an accumulation of specific tandem repeats in evolutionary regions can promote genome instability by altering the state of the chromatin conformation or by promoting the insertion of transposable elements.
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Affiliation(s)
- Marta Farré
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | | | - Francesc López-Giráldez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Montserrat Ponsà
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- * E-mail:
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13
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Richards LR, Rambau RV, Lamb JM, Taylor PJ, Yang F, Schoeman MC, Goodman SM. Cross-species chromosome painting in bats from Madagascar: the contribution of Myzopodidae to revealing ancestral syntenies in Chiroptera. Chromosome Res 2010; 18:635-53. [PMID: 20596765 DOI: 10.1007/s10577-010-9139-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Revised: 05/24/2010] [Accepted: 05/31/2010] [Indexed: 11/25/2022]
Abstract
The chiropteran fauna of Madagascar comprises eight of the 19 recognized families of bats, including the endemic Myzopodidae. While recent systematic studies of Malagasy bats have contributed to our understanding of the morphological and genetic diversity of the island's fauna, little is known about their cytosystematics. Here we investigate karyotypic relationships among four species, representing four families of Chiroptera endemic to the Malagasy region using cross-species chromosome painting with painting probes of Myotis myotis: Myzopodidae (Myzopoda aurita, 2n = 26), Molossidae (Mormopterus jugularis, 2n = 48), Miniopteridae (Miniopterus griveaudi, 2n = 46), and Vespertilionidae (Myotis goudoti, 2n = 44). This study represents the first time a member of the family Myzopodidae has been investigated using chromosome painting. Painting probes of M. myotis were used to delimit 29, 24, 23, and 22 homologous chromosomal segments in the genomes of M. aurita, M. jugularis, M. griveaudi, and M. goudoti, respectively. Comparison of GTG-banded homologous chromosomes/chromosomal segments among the four species revealed the genome of M. aurita has been structured through 14 fusions of chromosomes and chromosomal segments of M. myotis chromosomes leading to a karyotype consisting solely of bi-armed chromosomes. In addition, chromosome painting revealed a novel X-autosome translocation in M. aurita. Comparison of our results with published chromosome maps provided further evidence for karyotypic conservatism within the genera Mormopterus, Miniopterus, and Myotis. Mapping of chromosomal rearrangements onto a molecular consensus phylogeny revealed ancestral syntenies shared between Myzopoda and other bat species of the infraorders Pteropodiformes and Vespertilioniformes. Our study provides further evidence for the involvement of Robertsonian (Rb) translocations and fusions/fissions in chromosomal evolution within Chiroptera.
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Affiliation(s)
- Leigh R Richards
- School of Biological and Conservation Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.
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14
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Bugno-Poniewierska M, Pawlina K, Dardzińska A, Zabek T, Słota E, Klukowka-Rötzler J. FISH mapping of six genes responsible for development of the nervous and skeletal systems on donkey (Equus asinus) chromosomes. Hereditas 2010; 147:132-5. [PMID: 20626768 DOI: 10.1111/j.1601-5223.2010.02178.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The results obtained in the present study made it possible to place selected markers responsible for development of the nervous and skeletal systems on the physical map of the donkey genome. Fluorescence in situ hybridization (FISH) was used to localize genes such as GDF5 (15q13), FRZB (4q23.1), TWIST (1q31), PAX6 (20q25), SALL1 (24q15) and SHH (1q35) on donkey chromosomes. The identification of their localization confirmed previously proposed homologies using ZOO-FISH technique, except for FRZB and SALL1 genes. This suggests that they were affected by rearrangements that changed their localization compared to horse, and in the case of the SALL1 gene also compared to human.
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Affiliation(s)
- Monika Bugno-Poniewierska
- Department of Immuno and Cytogenetics, National Research Institute of Animal Production, Balice, Poland.
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15
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Evolution of chromosome 6 of Solanum species revealed by comparative fluorescence in situ hybridization mapping. Chromosoma 2010; 119:435-42. [PMID: 20352244 DOI: 10.1007/s00412-010-0269-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 02/15/2010] [Accepted: 02/23/2010] [Indexed: 01/30/2023]
Abstract
Comparative genetic linkage mapping using a common set of DNA markers in related species is an important methodology in plant genome research. Here, we demonstrate a comparative fluorescence in situ hybridization (FISH) mapping strategy in plants. A set of 13 bacterial artificial chromosome clones spanning the entire length of potato chromosome 6 was used for pachytene chromosome-based FISH mapping in seven distantly related Solanum species including potato, tomato, and eggplant. We discovered one paracentric inversion and one pericentric inversion within specific lineages of these species. The comparative FISH mapping data revealed the ancestral structure of this chromosome. We demonstrate that comparative FISH mapping is an efficient and powerful methodology to study chromosomal evolution among plant species diverged for up to 12 million years.
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16
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Karyotypic relationships in Asiatic asses (kulan and kiang) as defined using horse chromosome arm-specific and region-specific probes. Chromosome Res 2009; 17:783-90. [PMID: 19731053 DOI: 10.1007/s10577-009-9069-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Accepted: 07/23/2009] [Indexed: 01/02/2023]
Abstract
Cross-species chromosome painting has been applied to most of the species making up the numerically small family Equidae. However, comparative mapping data were still lacking in Asiatic asses kulan (Equus hemionus kulan) and kiang (E. kiang). The set of horse arm-specific probes generated by laser microdissection was hybridized onto kulan (E. hemionus kulan) and kiang (E. kiang) chromosomes in order to establish a genome-wide chromosomal correspondence between these Asiatic asses and the horse. Moreover, region-specific probes were generated to determine fusion configuration and orientation of conserved syntenic blocks. The kulan karyotype (2n = 54) was ascertained to be almost identical to the previously investigated karyotype of onager E. h. onager (2n = 56). The only difference is in fusion/fission of chromosomes homologous to horse 2q/3q, which are involved in chromosome number polymorphism in many Equidae species. E. kiang karyotype differs from the karyotype of E. hemionus by two additional fusions 8q/15 and 7/25. Chromosomes equivalent to 2q and 3q are not fused in kiang individuals with 2n = 52. Several discrepancies in centromere positions among kulan, kiang and horse chromosomes have been described. Most of the chromosome fusions in Asiatic asses are of centromere-centromere type. Comparative chromosome painting in kiang completed the efforts to establish chromosomal homologies in all representatives of the family Equidae. Application of region-specific probes allows refinement comparative maps of Asiatic asses.
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17
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Alekseyev MA, Pevzner PA. Breakpoint graphs and ancestral genome reconstructions. Genes Dev 2009; 19:943-57. [PMID: 19218533 PMCID: PMC2675983 DOI: 10.1101/gr.082784.108] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Accepted: 01/22/2009] [Indexed: 11/24/2022]
Abstract
Recently completed whole-genome sequencing projects marked the transition from gene-based phylogenetic studies to phylogenomics analysis of entire genomes. We developed an algorithm MGRA for reconstructing ancestral genomes and used it to study the rearrangement history of seven mammalian genomes: human, chimpanzee, macaque, mouse, rat, dog, and opossum. MGRA relies on the notion of the multiple breakpoint graphs to overcome some limitations of the existing approaches to ancestral genome reconstructions. MGRA also generates the rearrangement-based characters guiding the phylogenetic tree reconstruction when the phylogeny is unknown.
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Affiliation(s)
- Max A. Alekseyev
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, California 92093-0404, USA
| | - Pavel A. Pevzner
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, California 92093-0404, USA
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18
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Abstract
Chromosome sorting by flow cytometry is the principle source of chromosome-specific DNA not only for chromosome painting, but also for many other types of genomic analysis such as library construction, discovery and isolation of genes, chromosome specific direct DNA selection, and array painting. Chromosome sorting coupled with chromosome painting is a rapid method for global phylogenomic comparisons. These two techniques have made notable contributions to our knowledge of the evolution of the mammalian genome. The flow sorting of multiple species allows reciprocal painting and permits the delineation of subchromosomal homology and the definition of chromosomal breakpoints. Chromosomes are valuable phylogenetic makers because rearrangements that become fixed at the species level are considered rare events and apparently tightly bound to the speciation process. This chapter covers the preparation of a single chromosome suspension from cell cultures, bivariate chromosome flow sorting, preparation of chromosome paints by degenerate oligonucleotide primed-PCR and the fluorescence in-situ hybridization and detection of whole chromosome specific probes.
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19
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Abstract
There is increasing interest in the use of the free-living nematode Caenorhabditis elegans as a tool for parasitic nematode research and there are now a number of compelling examples of its successful application. C. elegans has the potential to become a standard tool for molecular helminthology researchers, just as yeast is routinely used by molecular biologists to study vertebrate biology. However, in order to exploit C. elegans in a meaningful manner, we need a detailed understanding of the extent to which different aspects of C. elegans biology have been conserved with particular groups of parasitic nematodes. This review first considers the current state of knowledge regarding the conservation of genome organisation across the nematode phylum and then discusses some recent evolutionary development studies in free-living nematodes. The aim is to provide some important concepts that are relevant to the extrapolation of information from C. elegans to parasitic nematodes and also to the interpretation of experiments that use C. elegans as a surrogate expression system. In general, examples have been specifically chosen because they highlight the importance of careful experimentation and interpretation of data. Consequently, the focus is on the differences that have been found between nematode species rather than the similarities. Finally, there is a detailed discussion of the current status of C. elegans as a heterologous expression system to study parasite gene function and regulation using successful examples from the literature.
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Affiliation(s)
- J S Gilleard
- Department of Veterinary Parasitology, Institute of Comparative Medicine, Faculty of Veterinary Medicine, University of Glasgow, Glasgow, UK.
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20
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Abstract
The evolution of karyotypes has been the subject of intensive study since the middle of the 20th century. This was motivated by the observation that the karyotypes of related species showed remarkable conservation. The recent emergence of whole-genome sequencing projects gives the opportunity to complement the cytogenetic approaches by addressing the conservation of karyotypes using chromosome sequence comparison. In this short review we present a description of recent advances in computational biology methods dedicated to the study of chromosome evolution and more specifically ancestral karyotype reconstruction in an attempt to provide an integrated overview of both cytogenetic and computational approaches.
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21
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Griffin DK, Robertson LB, Tempest HG, Vignal A, Fillon V, Crooijmans RPMA, Groenen MAM, Deryusheva S, Gaginskaya E, Carré W, Waddington D, Talbot R, Völker M, Masabanda JS, Burt DW. Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution. BMC Genomics 2008; 9:168. [PMID: 18410676 PMCID: PMC2375447 DOI: 10.1186/1471-2164-9-168] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Accepted: 04/14/2008] [Indexed: 11/25/2022] Open
Abstract
Background Comparative genomics is a powerful means of establishing inter-specific relationships between gene function/location and allows insight into genomic rearrangements, conservation and evolutionary phylogeny. The availability of the complete sequence of the chicken genome has initiated the development of detailed genomic information in other birds including turkey, an agriculturally important species where mapping has hitherto focused on linkage with limited physical information. No molecular study has yet examined conservation of avian microchromosomes, nor differences in copy number variants (CNVs) between birds. Results We present a detailed comparative cytogenetic map between chicken and turkey based on reciprocal chromosome painting and mapping of 338 chicken BACs to turkey metaphases. Two inter-chromosomal changes (both involving centromeres) and three pericentric inversions have been identified between chicken and turkey; and array CGH identified 16 inter-specific CNVs. Conclusion This is the first study to combine the modalities of zoo-FISH and array CGH between different avian species. The first insight into the conservation of microchromosomes, the first comparative cytogenetic map of any bird and the first appraisal of CNVs between birds is provided. Results suggest that avian genomes have remained relatively stable during evolution compared to mammalian equivalents.
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Affiliation(s)
- Darren K Griffin
- Department of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK.
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22
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23
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Rocchi M, Archidiacono N, Stanyon R. Ancestral genomes reconstruction: An integrated, multi-disciplinary approach is needed. Genome Res 2006; 16:1441-4. [PMID: 17053088 DOI: 10.1101/gr.5687906] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Mariano Rocchi
- Department of Genetics and Microbiology, University of Bari, Bari 70126, Italy.
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24
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Jiang J, Gill BS. Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome 2006; 49:1057-68. [PMID: 17110986 DOI: 10.1139/g06-076] [Citation(s) in RCA: 187] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fluorescence in situ hybridization (FISH), which allows direct mapping of DNA sequences on chromosomes, has become the most important technique in plant molecular cytogenetics research. Repetitive DNA sequence can generate unique FISH patterns on individual chromosomes for karyotyping and phylogenetic analysis. FISH on meiotic pachytene chromosomes coupled with digital imaging systems has become an efficient method to develop physical maps in plant species. FISH on extended DNA fibers provides a high-resolution mapping approach to analyze large DNA molecules and to characterize large genomic loci. FISH-based physical mapping provides a valuable complementary approach in genome sequencing and map-based cloning research. We expect that FISH will continue to play an important role in relating DNA sequence information to chromosome biology. FISH coupled with immunoassays will be increasingly used to study features of chromatin at the cytological level that control expression and regulation of genes.
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Affiliation(s)
- Jiming Jiang
- Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA.
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25
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Holmquist GP, Ashley T. Chromosome organization and chromatin modification: influence on genome function and evolution. Cytogenet Genome Res 2006; 114:96-125. [PMID: 16825762 DOI: 10.1159/000093326] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Accepted: 12/15/2005] [Indexed: 11/19/2022] Open
Abstract
Histone modifications of nucleosomes distinguish euchromatic from heterochromatic chromatin states, distinguish gene regulation in eukaryotes from that of prokaryotes, and appear to allow eukaryotes to focus recombination events on regions of highest gene concentrations. Four additional epigenetic mechanisms that regulate commitment of cell lineages to their differentiated states are involved in the inheritance of differentiated states, e.g., DNA methylation, RNA interference, gene repositioning between interphase compartments, and gene replication time. The number of additional mechanisms used increases with the taxon's somatic complexity. The ability of siRNA transcribed from one locus to target, in trans, RNAi-associated nucleation of heterochromatin in distal, but complementary, loci seems central to orchestration of chromatin states along chromosomes. Most genes are inactive when heterochromatic. However, genes within beta-heterochromatin actually require the heterochromatic state for their activity, a property that uniquely positions such genes as sources of siRNA to target heterochromatinization of both the source locus and distal loci. Vertebrate chromosomes are organized into permanent structures that, during S-phase, regulate simultaneous firing of replicon clusters. The late replicating clusters, seen as G-bands during metaphase and as meiotic chromomeres during meiosis, epitomize an ontological utilization of all five self-reinforcing epigenetic mechanisms to regulate the reversible chromatin state called facultative (conditional) heterochromatin. Alternating euchromatin/heterochromatin domains separated by band boundaries, and interphase repositioning of G-band genes during ontological commitment can impose constraints on both meiotic interactions and mammalian karyotype evolution.
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Affiliation(s)
- G P Holmquist
- Biology Department, City of Hope Medical Center, Duarte, CA, USA.
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26
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Paulis M, Bensi M, Moralli D, De Carli L, Raimondi E. A set of duplicons on human chromosome 9 is involved in the origin of a supernumerary marker chromosome. Genomics 2006; 87:747-57. [PMID: 16597496 DOI: 10.1016/j.ygeno.2006.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2005] [Revised: 02/21/2006] [Accepted: 02/27/2006] [Indexed: 01/25/2023]
Abstract
Human chromosome 9 is involved in a number of recurrent structural rearrangements; moreover, its pericentromeric region exhibits a remarkable evolutionary plasticity. In this study we present the molecular characterization of a constitutional rearrangement, involving the 9p21.1q13 region, which led to the formation of a supernumerary marker chromosome (SMC). We defined the sequence of the breakpoints and identified a new set of duplicons on human chromosome 9, named LCR9s (chromosome 9 low-copy repeats). Two of these duplicons were shown to be involved in a somatic exchange leading to the formation of the SMC. High-resolution FISH coupled to database search demonstrated that a total number of 35 LCR9 paralogs are present in the human genome. These newly described chromosome 9 duplicons have features that may be crucial in driving structural chromosome rearrangements in germinal and somatic cells.
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Affiliation(s)
- Marianna Paulis
- Dipartimento di Genetica e Microbiologia A. Buzzati Traverso, Università di Pavia, Via Ferrata 1, 27100 Pavia, Italy
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27
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Nanda I, Karl E, Volobouev V, Griffin DK, Schartl M, Schmid M. Extensive gross genomic rearrangements between chicken and Old World vultures (Falconiformes: Accipitridae). Cytogenet Genome Res 2006; 112:286-95. [PMID: 16484785 DOI: 10.1159/000089883] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2005] [Accepted: 08/10/2005] [Indexed: 11/19/2022] Open
Abstract
The karyotypes of most birds consist of a small number of macrochromosomes and numerous microchromosomes. Intriguingly, most accipitrids which include hawks, eagles, kites, and Old World vultures (Falconiformes) show a sharp contrast to this basic avian karyotype. They exhibit strikingly few microchromosomes and appear to have been drastically restructured during evolution. Chromosome paints specific to the chicken (GGA) macrochromosomes 1-10 were hybridized to metaphase spreads of three species of Old World vultures (Gyps rueppelli, Gyps fulvus, Gypaetus barbatus). Paints of GGA chromosomes 6-10 hybridize only to single chromosomes or large chromosome segments, illustrating the existence of high chromosome homology. In contrast, paints of the large macrochromosomes 1-5 show split hybridization signals on the chromosomes of the accipitrids, disclosing excessive chromosome rearrangements which is in clear contrast to the high degree of chromosome conservation substantiated from comparative chromosome painting in other birds. Furthermore, the GGA chromosome paint hybridization patterns reveal remarkable interchromosomal conservation among the two species of the genus Gyps.
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Affiliation(s)
- I Nanda
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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28
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Dobigny G, Yang F, O'Brien PCM, Volobouev V, Kovács A, Pieczarka JC, Ferguson-Smith MA, Robinson TJ. Low rate of genomic repatterning in Xenarthra inferred from chromosome painting data. Chromosome Res 2005; 13:651-63. [PMID: 16235115 DOI: 10.1007/s10577-005-1002-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2005] [Accepted: 07/18/2005] [Indexed: 10/25/2022]
Abstract
Comparative cytogenetic studies on Xenarthra, one of the most basal mammalian clades in the Placentalia, are virtually absent, being restricted largely to descriptions of conventional karyotypes and diploid numbers. We present a molecular cytogenetic comparison of chromosomes from the two-toed (Choloepus didactylus, 2n = 65) and three-toed sloth species (Bradypus tridactylus, 2n = 52), an anteater (Tamandua tetradactyla, 2n = 54) which, together with some data on the six-banded armadillo (Euphractus sexcinctus, 2n = 58), collectively represent all the major xenarthran lineages. Our results, based on interspecific chromosome painting using flow-sorted two-toed sloth chromosomes as painting probes, show the sloth species to be karyotypically closely related but markedly different from the anteater. We also test the synteny disruptions and segmental associations identified within Pilosa (anteaters and sloths) against the chromosomes of the six-banded armadillo as outgroup taxon. We could thus polarize the 35 non-ambiguously identified chromosomal changes characterizing the evolution of the anteater and sloth genomes and map these to a published sequence-based phylogeny for the group. These data suggest a low rate of genomic repatterning when placed in the context of divergence estimates based on molecular and fossil data. Finally, our results provide a glimpse of a likely ancestral karyotype for the extant Xenarthra, a pivotal group for understanding eutherian genome evolution.
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Affiliation(s)
- G Dobigny
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
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29
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Dumas F, Bigoni F, Stone G, Sineo L, Stanyon R. Mapping genomic rearrangements in titi monkeys by chromosome flow sorting and multidirectional in-situ hybridization. Chromosome Res 2005; 13:85-96. [PMID: 15791414 DOI: 10.1007/s10577-005-7063-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2004] [Revised: 11/22/2004] [Accepted: 11/22/2004] [Indexed: 11/24/2022]
Abstract
We developed chromosome painting probes for Callicebus pallescens from flow-sorted chromosomes and used multidirectional chromosome painting to investigate the genomic rearrangements in C. cupreus and C. pallescens. Multidirectional painting provides information about chromosomal homologies at the subchromosomal level and rearrangement break points, allowing chromosomes to be used as cladistic markers. Chromosome paints of C. pallescens were hybridized to human metaphases and 43 signals were detected. Then, both human and C. pallescens probes were hybridized to the chromosomes of another titi monkey, C. cupreus. The human chromosome paints detected 45 segments in the haploid karyotype of C. cupreus. We found that all the syntenic associations proposed for the ancestral platyrrhine karyotype are present in C. cupreus and in C. pallescens. The rearrangements differentiating C. pallescens from C. cupreus re one inversion, one fission and three fusions (two tandem and one Robertsonian)that occurred on the C. cupreus lineage. Our results support the hypothesis that karyological evolution in titi monkeys has resulted in reduction in diploid number and that species with higher diploid numbers (with less derived, more ancestral karyotypes)are localized in the centre of the geographic range of the genera, while more derived species appear to occupy the periphery.
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Affiliation(s)
- F Dumas
- Dipartimento di Biologia animale (DBA) Università degli Studi di Palermo, via Archirafi 18 Palermo, Italy
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30
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Nieves M, Ascunce MS, Rahn MI, Mudry MD. Phylogenetic relationships among some Ateles species: the use of chromosomic and molecular characters. Primates 2005; 46:155-64. [PMID: 15657638 DOI: 10.1007/s10329-004-0120-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2003] [Accepted: 09/23/2004] [Indexed: 10/25/2022]
Abstract
As with most platyrrhines, the systematics of Ateles is under discussion. In order to help clarify its systematic, we employed chromosomic and molecular characters to analyze the phylogenetic relationship among some species of the genus Ateles. Chromosomic studies were conducted on 14 atelid specimens: eight Ateles from A. paniscus, A. chamek, A. belzebuth and A. geoffroyi, and six Alouatta caraya. Ateles paniscus showed 2N=32, whereas A. chamek, A. belzebuth and A. geoffroyi presented 2N=34, XX/XY (with a submetacentric X and a variable Y) corroborated by male meiosis. Nucleotide sequence variation at the mitochondrial cytochrome c oxidase subunit II gene (COII) was analyzed in ten New World monkey specimens. Parsimony trees showed consistent phylogenetic relationships using both chromosomic forms and mitochondrial COII gene sequences as characters. Particularly, chromosomic phylogenies showed A. hybridus as a divergent taxon from the remaining group, whereas A. chamek, A. belzebuth and A. marginatus form an unresolved clade with A. geoffroyi as sister group.
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Affiliation(s)
- Mariela Nieves
- Grupo de Investigación en Biología Evolutiva, Dept. de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina.
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31
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Abstract
Chromosomal data have been underutilized in phylogenetic investigations despite the obvious potential that cytogenetic studies have to reveal both structural and functional homologies among taxa. In large part this is associated with difficulties in scoring conventional and molecular cytogenetic information for phylogenetic analysis. The manner in which chromosomal data have been used by most authors in the past was often conceptionally flawed in terms of the methods and principles underpinning modern cladistics. We present herein a review of the different methods employed, examine their relative strengths, and then outline a simple approach that considers the chromosomal change as the character, and its presence or absence the character state. We test this using one simulated and several empirical data sets. Features that are unique to cytogenetic investigations, including B-chromosomes, heterochromatic additions/deletions, and the location and number of nucleolar organizer regions (NORs), as well as the weighting of chromosomal characters, are critically discussed with regard to their suitability for phylogenetic reconstruction. We conclude that each of these classes of data have inherent problems that limit their usefulness in phylogenetic analyses and in most of these instances, inclusion should be subject to rigorous appraisal that addresses the criterion of unequivocal homology.
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Affiliation(s)
- Gauthier Dobigny
- Museum National d'Histoire Naturelle, Laboratoire Origine, Structure et Evolution de la Biodiversité, 55, rue Buffon, F75005 Paris, France.
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32
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Stanyon R, Bigoni F, Slaby T, Muller S, Stone G, Bonvicino CR, Neusser M, Seuánez HN. Multi-directional chromosome painting maps homologies between species belonging to three genera of New World monkeys and humans. Chromosoma 2004; 113:305-15. [PMID: 15616867 DOI: 10.1007/s00412-004-0320-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2004] [Revised: 09/17/2004] [Accepted: 09/27/2004] [Indexed: 10/26/2022]
Abstract
We mapped chromosomal homologies in two species of Chiropotes (Pitheciini, Saki Monkeys) and one species of Aotus (Aotinae, Owl Monkey) by multi-directional chromosome painting. Human chromosome probes were hybridized to Chiropotes utahicki, C. israelita and Aotus nancymae metaphases. Wooly Monkey chromosome paints were also hybridized to Owl Monkey metaphases. We established Owl Monkey chromosome paint probes by flow sorting and reciprocally hybridized them to human chromosomes. The karyotypes of the Bearded Saki Monkeys studied here are close to the hypothesized ancestral platyrrhine karytoype, while that of the Owl Monkey appears to be highly derived. The A. nancymae karyotype is highly shuffled and only three human syntenic groups were found conserved coexisting with 17 derived human homologous associations. A minimum of 14 fissions and 13 fusions would be required to derive the A. nancymae karyotype from that of the ancestral New World primate karyotype. An inversion between homologs to segments of human 10 and 16 suggests a link between Callicebus and Chiropotes, while the syntenic association of 10/11 found in Aotus and Callicebus suggests a link between these two genera. Future molecular cytogenetic work will be needed to determine whether these rearrangements represent synapomorphic chromosomal traits.
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Affiliation(s)
- R Stanyon
- Comparative Molecular Cytogenetics Core, BRL, National Cancer Institute-Frederick, Frederick, MD, USA.
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33
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Weise A, Starke H, Mrasek K, Claussen U, Liehr T. New insights into the evolution of chromosome 1. Cytogenet Genome Res 2004; 108:217-22. [PMID: 15545733 DOI: 10.1159/000080819] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2003] [Accepted: 11/07/2003] [Indexed: 11/19/2022] Open
Abstract
A complex low-repetitive human DNA probe (BAC RP11-35B4) together with two microdissection-derived region-specific probes of the multicolor banding (MCB) probe-set for chromosome 1 were used to re-analyze the evolution of human chromosome 1 in comparison to four ape species. BAC RP11-35B4 derives from 1q21 and contains 143 kb of non-repetitive DNA; however, it produces three specific FISH signals in 1q21, 1p12 and 1p36.1 of Homo sapiens (HSA). Human chromosome 1 was studied in comparison to its homologues in Hylobates lar (HLA), Pongo pygmaeus (PPY), Gorilla gorilla (GGO) and Pan troglodytes (PTR). A duplication of sequences homologous to human 1p36.1 could be detected in PPY plus an additional signal on PPY 16q. The region homologous to HSA 1p36.1 is also duplicated in HLA, and split onto chromosomes 7q and 9p; the region homologous to HSA 1q21/1p12 is present as one region on 5q. Additionally, the breakpoint of a small pericentric inversion in the evolution of human chromosome 1 compared to other great ape species could be refined. In summary, the results obtained here are in concordance with previous reports; however, there is evidence for a deletion of regions homologous to human 1p34.2-->p34.1 during evolution in the Pongidae branch after separation of PPY.
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Affiliation(s)
- A Weise
- Institut für Humangenetik und Anthropologie, Jena, Germany
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34
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Affiliation(s)
- L Scott Cram
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.
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35
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Lee-Jones L, Ramsahoye B, Booth M, Thompson P, Whittaker J, Hoy T. Characterization of psu dic(6;5)(p21.3;q13) with reverse chromosome painting in a patient with secondary myelodysplastic syndrome following treatment for multiple myeloma. ACTA ACUST UNITED AC 2004; 148:49-54. [PMID: 14697641 DOI: 10.1016/s0165-4608(03)00218-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We report a case of a psu dic(6;5)(p21.3;q13) in a patient with secondary myelodysplastic syndrome (sMDS) following treatment for multiple myeloma. The abnormal chromosome was isolated by flow karyotyping and initially identified by reverse chromosome painting. The findings were then confirmed by forward painting. The value of flow karyotyping as a diagnostic technique in hematologic malignancies is discussed.
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Affiliation(s)
- Lisa Lee-Jones
- Tumour Molecular Genetics Group, Institute of Medical Genetics, University of Wales College of Medicine, Heath Park, Cardiff CF14 4XN, Wales, UK.
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Grützner F, Deakin J, Rens W, El-Mogharbel N, Marshall Graves JA. The monotreme genome: a patchwork of reptile, mammal and unique features? Comp Biochem Physiol A Mol Integr Physiol 2003; 136:867-81. [PMID: 14667850 DOI: 10.1016/j.cbpb.2003.09.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The first specimen of platypus (Ornithorhynchus anatinus) that reached Britain in the late 18th century was regarded a scientific hoax. Over decades the anatomical characteristics of these unique mammals, such as egg laying and the existence of mammary glands, were hotly debated before they were accepted. Within the last 40 years, more and more details of monotreme physiology, histology, reproduction and genetics have been revealed. Some show similarities with birds or reptiles, some with therian mammals, but many are very specific to monotremes. The genome is no exception to monotreme uniqueness. An early opinion was that the karyotype, composed of a few large chromosomes and many small ones, resembled bird and reptile macro- and micro-chromosomes. However, the platypus genome also features characteristics that are not present in other mammals, such as a complex translocation system. The sex chromosome system is still not resolved. Nothing is known about dosage compensation and, unlike in therian mammals, there seems to be no genomic imprinting. In this article we will recount the mysteries of the monotreme genome and describe how we are using recently developed technology to identify chromosomes in mitosis, meiosis and sperm, to map genes to chromosomes, to unravel the sex chromosome system and the translocation chain and investigate X inactivation and genomic imprinting in monotremes.
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Affiliation(s)
- Frank Grützner
- Research School of Biological Sciences, Australian National University, G.P.O. Box 475, Canberra, Australian Capital Territory 2601, Australia.
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37
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Martins RR, Ramos HI, Llerena Jr. JC, Almeida JC. Investigação clínica e genética em meninas com baixa estatura idiopática. ACTA ACUST UNITED AC 2003. [DOI: 10.1590/s0004-27302003000600010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Em 10 meninas com diagnóstico de baixa estatura idiopática (BEI), realizamos avaliação citogenética após revisão clínica. Dois cariótipos foram anormais: mos 45,X/46,XX; mos 45,X/46,X,der(Xp)/46,X,r(X), e para sua elucidação foram aplicadas técnicas de citogenética molecular e análise de microssatélites, incluindo SHOX CA repeat. Os resultados confirmaram a origem dos cromossomos anômalos e a identificação da haploinsuficiência do gene SHOX. Nos oito casos com cariótipo normal, a pesquisa de mosaicismos crípticos pela técnica FISH através da sonda centromérica (DXZ1) em células de mucosa oral (nuc ish) evidenciou a presença de dois mosaicos verdadeiros (DXZ1x2/DXZ1x1). A revisão clínica da paciente com anomalia estrutural de X e das 2 meninas com mosaicismo detectados pelo nuc ish, mostrou a presença de 3 ou mais sinais clínicos observados na síndrome de Turner (ST). Estes resultados reafirmam a importância da análise citogenética em meninas com diagnóstico de BEI e sinais clínicos da ST. Os resultados do estudo molecular para o gene SHOX confirmam sua relação com estigmas da ST. Sendo normal o cariótipo, a pesquisa de mosaicismos crípticos em outros tecidos deve ser considerada. O diagnóstico mais preciso poderá modificar a conduta terapêutica, como indicação do GH nessas meninas.
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Affiliation(s)
- Rosa R.S. Martins
- Instituto Estadual de Diabetes e Endocrinologia; Universidade Federal do Rio de Janeiro
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38
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GARCÍA F, GARCIA M, MORA L, ALARCÓN L, EGOZCUE J, PONSÀ M. Qualitative analysis of constitutive heterochromatin and primate evolution. Biol J Linn Soc Lond 2003. [DOI: 10.1046/j.1095-8312.2003.00223.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
The compilation of a dense gene map and eventually a whole genome sequence (WGS) of the domestic cat holds considerable value for human genome annotation, for veterinary medicine, and for insight into the evolution of genome organization among mammals. Human association and veterinary studies of the cat, its domestic breeds, and its charismatic wild relatives of the family Felidae have rendered the species a powerful model for human hereditary diseases, for infectious disease agents, for adaptive evolutionary divergence, for conservation genetics, and for forensic applications. Here we review the advantages, rationale, and present strategy of a feline genome project, and we describe the disease models, comparative genomics, and biological applications posed by the full resolution of the cat's genome.
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Affiliation(s)
- Stephen J O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, Maryland 21702-1201, USA.
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40
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Matsui SI, Faitar SL, Rossi MR, Cowell JK. Application of spectral karyotyping to the analysis of the human chromosome complement of interspecies somatic cell hybrids. CANCER GENETICS AND CYTOGENETICS 2003; 142:30-5. [PMID: 12660030 DOI: 10.1016/s0165-4608(02)00730-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Mouse-human somatic cell hybrids have been extensively used in the molecular genetic dissection of human disease-related chromosome rearrangements because of their ability to selectively and randomly eliminate human chromosomes. This technology allows the isolation of structural chromosome abnormalities, which then allows determination of the precise molecular address of chromosome breakpoints associated with deletions and translocations, down to the nucleotides involved. The main confounding problem with the analysis of somatic cell hybrids is determining the exact chromosome complement unequivocally and quickly. Spectral karyotyping can identify each of the individual human chromosomes in a normal metaphase spread, as well as structural chromosome rearrangements-although, because of potential cross-hybridization between the human probe and mouse DNA sequences during the hybridization reaction, it has not been determined whether the same analysis will selectively identify human chromosomes on a mouse background. We show (to our knowledge, for the first time) that, under modified conditions of chromosomal in situ suppression hybridization, the standard spectral karyotyping probe does not cross-react with mouse chromosomes and can be used to identify subtle structurally rearranged chromosomes in hybrid cells. This analysis allows for the rapid and unequivocal identification of the human chromosome complement in these hybrids, as well as structural chromosome rearrangements that occur between mouse and human chromosomes that might otherwise confound the analysis.
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Affiliation(s)
- Sei-ichi Matsui
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
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41
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de Pontbriand A, Wang XP, Cavaloc Y, Mattei MG, Galibert F. Synteny comparison between apes and human using fine-mapping of the genome. Genomics 2002; 80:395-401. [PMID: 12376093 DOI: 10.1006/geno.2002.6847] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Comparing the genomes of the great apes and human should provide novel information concerning the origins of humankind. Relative to the great apes, the human karyotype has one fewer chromosome pair, as human chromosome 2 derived from the telomeric fusion of two ancestral primate chromosomes. To identify the genomic rearrangements that accompanied human speciation, we initiated a comparative study between human, chimpanzee, and gorilla. Using the HAPPY mapping method, an acellular adaptation of the radiation hybrid method, we mapped a few hundred markers on the human, chimpanzee, and gorilla genomes. This allowed us to identify several chromosome rearrangements, in particular a pericentric inversion and a translocation. We precisely localized the synteny breakpoint that led to the formation of human chromosome 2. This breakpoint was confirmed by FISH mapping.
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Abstract
Human cytogenetics was born in 1956 with the fundamental, but empowering, discovery that normal human cells contain 46 chromosomes. Since then, this field and our understanding of the link between chromosomal defects and disease have grown in spurts that have been fuelled by advances in cytogenetic technology. As a mature enterprise, cytogenetics now informs human genomics, disease and cancer genetics, chromosome evolution and the relationship of nuclear structure to function.
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Affiliation(s)
- Barbara J Trask
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
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Bedford JS, Dewey WC. Radiation Research Society. 1952-2002. Historical and current highlights in radiation biology: has anything important been learned by irradiating cells? Radiat Res 2002; 158:251-91. [PMID: 12175305 DOI: 10.1667/0033-7587(2002)158[0251:hachir]2.0.co;2] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Around 30 years ago, a very prominent molecular biologist confidently proclaimed that nothing of fundamental importance has ever been learned by irradiating cells! The poor man obviously did not know about discoveries such as DNA repair, mutagenesis, connections between mutagenesis and carcinogenesis, genomic instability, transposable genetic elements, cell cycle checkpoints, or lines of evidence historically linking the genetic material with nucleic acids, or origins of the subject of oxidative stress in organisms, to name a few things of fundamental importance learned by irradiating cells that were well known even at that time. Early radiation studies were, quite naturally, phenomenological. They led to the realization that radiations could cause pronounced biological effects. This was followed by an accelerating expansion of investigations of the nature of these radiobiological phenomena, the beginnings of studies aimed toward better understanding the underlying mechanisms, and a better appreciation of the far-reaching implications for biology, and for society in general. Areas of principal importance included acute tissue and tumor responses for applications in medicine, whole-body radiation effects in plants and animals, radiation genetics and cytogenetics, mutagenesis, carcinogenesis, cellular radiation responses including cell reproductive death, cell cycle effects and checkpoint responses, underlying molecular targets leading to biological effects, DNA repair, and the genetic control of radiosensitivity. This review summarizes some of the highlights in these areas, and points to numerous examples where indeed, many things of considerable fundamental importance have been learned by irradiating cells.
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Affiliation(s)
- Joel S Bedford
- Department of Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523-1673, USA.
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Raudsepp T, Chowdhary BP. Correspondence of human chromosomes 9, 12, 15, 16, 19 and 20 with donkey chromosomes refines homology between horse and donkey karyotypes. Chromosome Res 2002; 9:623-9. [PMID: 11778685 DOI: 10.1023/a:1012948122600] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Whole chromosome paints for human (HSA) chromosomes 9, 12, 15 and 20 and arm-specific paints for HSA16p, 19p and 19q were applied on donkey metaphase spreads. All probes, except HSA19p, gave distinct hybridization signals on donkey chromosomes/chromosomal segments. The results show direct segmental homology between human and donkey genomes, and enable refinement of correspondence between donkey and horse karyotypes. Of specific interest is the identification of hitherto unknown correspondence between four equine acrocentric chromosomes (ECA22, 23, 25 and 28) and the donkey chromosomes. Overall, the findings mark the beginning of an ordered study of comparative organization of genomes/karyotypes of the equids, that can shed light on karyotype evolution and ancestral chromosomal condition in the Perissodactyls.
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MESH Headings
- Animals
- Chromosome Painting
- Chromosomes
- Chromosomes, Human
- Chromosomes, Human, Pair 12
- Chromosomes, Human, Pair 15
- Chromosomes, Human, Pair 16
- Chromosomes, Human, Pair 19
- Chromosomes, Human, Pair 20
- Chromosomes, Human, Pair 9
- Equidae/genetics
- Genome, Human
- Horses/genetics
- Humans
- Karyotyping
- Nucleic Acid Hybridization
- Physical Chromosome Mapping
- Sequence Homology, Nucleic Acid
- Species Specificity
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Affiliation(s)
- T Raudsepp
- Department of Veterinary Anatomy and Public Health, College of Veterinary Medicine, Texas A and M University, College Station 77843, USA
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Stanyon R, Koehler U, Consigliere S. Chromosome painting reveals that galagos have highly derived karyotypes. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2002; 117:319-26. [PMID: 11920367 DOI: 10.1002/ajpa.10047] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The differences in chromosome number between Otolemur crassicaudatus (2n = 62) and Galago moholi (2n = 38) are dramatic. However, the total number of signals given by hybridizing human chromosome paints to galago metaphases is similar: 42 in O. crassicaudatus and 38 G. moholi. Many human chromosome homologs are found fragmented in each species, and numerous translocations have resulted in chromosomal syntenies or hybridization associations which differ from those found in humans. Only 7 human autosomes showed conserved synteny in O. crassicaudatus, and 9 in G. moholi. Both galago species have numerous associations or syntenies not found in humans: O. crassicaudatus has 11, and G. moholi has 21. The phylogenetic line leading to the last common ancestor of the two galago species accumulated 6 synapomorphic fissions and 5 synapomorphic fusions. Since the divergence of the two galago species, 10 Robertsonian translocations have further transformed the G. moholi karyotype, and 2 fissions have been incorporated into the O. crassicaudatus karyotype. Comparison with other primates, tree shrews, and other mammals shows that both galagos have karyotypes which are a mixture of derived and conserved chromosomes, and neither has a karyotype close to that of the proposed ancestor of all primates. Am J Phys Anthropol 117:319-326, 2002. Published 2002 Wiley-Liss, Inc.
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Affiliation(s)
- Roscoe Stanyon
- Genetics Branch, Comparative Molecular Cytogenetics Section, Center for Cancer Research, National Cancer Institute-Frederick, Building 560, Room 11-74A, Frederick, MD 21702, USA.
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46
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Cavagna P, Stone G, Stanyon R. Black rat ( Rattus rattus) genomic variability characterized by chromosome painting. Mamm Genome 2002; 13:157-63. [PMID: 11919687 DOI: 10.1007/bf02684021] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2001] [Accepted: 12/03/2001] [Indexed: 10/22/2022]
Abstract
Black rats are of outstanding interest in parasitology and infective disease analysis. We used chromosome paints from both the mouse ( Mus musculus) and the Norway rat ( Rattus norvegicus) to characterize the genome of two Black rat subspecies from Italy. Both subspecies have two large metacentrics (n. 1, 4) not present in the Norway rat (2n = 42). Rattus rattus rattus has a diploid number of 2n = 38, while Rattus rattus frugivorous has two small metacentric "supernumerary" or B chromosomes for a diploid number of 2n = 38 + 2B. The 21 mouse paints gave 38 signals on the R. r. rattus karyotype and 39 signals in the R. r. frugivorous karyotype. The two metacentrics, not present in R. norvegicus, were hybridized by mouse 16/1/17 and mouse 4/10/15. These chromosomes are homologous to: RRA1 = RNO 5/7, and RRA4 = RNO 9/11 and not "4/7" and "11/12" as previously reported. Furthermore, the synteny of Chr 13 of the R. r. frugivorous with R. norvegicus Chr 16 and mouse Chrs 8/14 is not complete, because there is a small pericentromeric insertion of RNO Chr 18 (mouse Chr 18). If we consider only the two metacentrics, RRA1 and RRA4, the principal differences between R. norvegicus and R. rattus, then we can propose the derived synteny of 124 genes in the black rat. A comparison of the Z index between rats and mice shows an acceleration of genomic evolution among genus, species, and subspecies. The chromosomal differences between R. r. rattus x R. r. frugivorous suggest that they may be classified as different species because hybrids would produce 50% unbalanced gametes.
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Affiliation(s)
- Pietro Cavagna
- Department of Experimental Biology, University of Genoa, Viale Benedetto XV, 16132 Genoa, Italy
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47
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Rens W, O'Brien PC, Yang F, Solanky N, Perelman P, Graphodatsky AS, Ferguson MW, Svartman M, De Leo AA, Graves JA, Ferguson-Smith MA. Karyotype relationships between distantly related marsupials from South America and Australia. Chromosome Res 2002; 9:301-8. [PMID: 11419794 DOI: 10.1023/a:1016646629889] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Reciprocal chromosome painting and G-banding were used to compare the karyotypes of three Australian marsupials (Sminthopsis crassicaudata, Macropus eugenii, Trichosurus vulpecula) and one South American marsupial (Monodelphis domestica). The results revealed only a limited number of rearrangements between these species and that the four karyotypes can be described as different combinations of fifteen conserved segments. Five chromosomes are totally conserved between M. domestica (pairs 1, 2, 5, 8 and the X) and the presumed 2n = 14 Australian ancestral karyotype, while M. domestica pairs 3 and 6 and 4 and 7 would have been involved in fusion/fission rearrangements. Chromosome comparisons are presented in a chromosome homology map. Although the species studied diverged 70 million years ago, the karyotype of Monodelphis domestica is highly conserved in relation to those of Australian marsupials.
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Affiliation(s)
- W Rens
- Centre for Veterinary Science, Department of Clinical Veterinary Medicine, University of Cambridge, UK.
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48
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Yamasaki Y, Helou K, Watanabe TK, Sjöling A, Suzuki M, Okuno S, Ono T, Takagi T, Nakamura Y, Stahl F, Tanigami A. Mouse chromosome 19 and distal rat chromosome 1: a chromosome segment conserved in evolution. Hereditas 2001; 134:23-34. [PMID: 11525062 DOI: 10.1111/j.1601-5223.2001.00023.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Through a combination of radiation hybrid mapping and studies by FISH and zoo-FISH we have made a comparative investigation of the distal portion of rat chromosome 1 (RNO1) and the entire mouse chromosome 19 (MMU19). It was found that homologous segments of RNO1 and MMU19 are similar in banding morphology and in length as determined by several different methods, and that the gene order of the 46 genes studied appears to be conserved across the homologous segments in the two species. High-resolution zoo-FISH techniques showed that MMU19 probes highlight only a continuous segment on RNO1 (1q43-qter), with no detectable signals on other rat chromosomes. We conclude that these data suggest the evolutionary conservation of a chromosomal segment from a common rodent ancestor. This segment now constitutes the entire MMU19 and a large segment distally on RNO1q in the mouse and rat, respectively.
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Affiliation(s)
- Y Yamasaki
- Otsuka GEN Research Institute, Otsuka Pharmaceutical Co., Ltd., 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan.
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49
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Affiliation(s)
- Johannes Wienberg
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom and Human Genetics and Anthropology at the Institute of Anthropology and Human Genetics, München, Germany
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50
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Stanyon R, Consigliere S, Bigoni F, Ferguson-Smith M, O'Brien PC, Wienberg J. Reciprocal chromosome painting between a New World primate, the woolly monkey, and humans. Chromosome Res 2001; 9:97-106. [PMID: 11321373 DOI: 10.1023/a:1009274802086] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We employed fluorescence-activated chromosome sorting (FACS) to construct chromosome paint sets for the woolly monkey (Lagothrix lagotricha) and then FISH to reciprocally paint human and woolly monkey metaphases. Reciprocal chromosome painting between humans and the woolly monkey allowed us to assign subchromosomal homologies between these species. The reciprocal painting data between humans and the woolly monkey also allow a better interpretation of the chromosomal difference between humans and platyrrhines, and refine hypotheses about the genomic rearrangements that gave origin to the genome of New World monkeys. Paints of woolly monkey chromosomes were used to paint human metaphases and forty-five clear signals were detected. Paints specific to each human chromosome were used to paint woolly monkey metaphases. The 23 human paints gave 39 clear signals on the woolly monkey karyotype. The woolly monkey chromosomes painted by human paints produced 7 associations of segments homologous to human chromosomes or human chromosome segments: 2/16, 3/21, 4/15, 5/7, 8/18, 10/16 and 14/15. A derived translocation between segments homologous to human chromosomes 4 and 15 is a synapomorphic marker linking all Atelines. These species may also be linked by fragmentation of homologs to human 1, 4, and 15.
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Affiliation(s)
- R Stanyon
- Basic Research Laboratory, Molecular Cytogenetic Section, National Cancer Institute-Frederick, MD, 21702, USA.
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