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de Moraes RLR, de Menezes Cavalcante Sassi F, Vidal JAD, Goes CAG, dos Santos RZ, Stornioli JHF, Porto-Foresti F, Liehr T, Utsunomia R, de Bello Cioffi M. Chromosomal Rearrangements and Satellite DNAs: Extensive Chromosome Reshuffling and the Evolution of Neo-Sex Chromosomes in the Genus Pyrrhulina (Teleostei; Characiformes). Int J Mol Sci 2023; 24:13654. [PMID: 37686460 PMCID: PMC10563077 DOI: 10.3390/ijms241713654] [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: 08/23/2023] [Revised: 08/31/2023] [Accepted: 09/02/2023] [Indexed: 09/10/2023] Open
Abstract
Chromosomal rearrangements play a significant role in the evolution of fish genomes, being important forces in the rise of multiple sex chromosomes and in speciation events. Repetitive DNAs constitute a major component of the genome and are frequently found in heterochromatic regions, where satellite DNA sequences (satDNAs) usually represent their main components. In this work, we investigated the association of satDNAs with chromosome-shuffling events, as well as their potential relevance in both sex and karyotype evolution, using the well-known Pyrrhulina fish model. Pyrrhulina species have a conserved karyotype dominated by acrocentric chromosomes present in all examined species up to date. However, two species, namely P. marilynae and P. semifasciata, stand out for exhibiting unique traits that distinguish them from others in this group. The first shows a reduced diploid number (with 2n = 32), while the latter has a well-differentiated multiple X1X2Y sex chromosome system. In addition to isolating and characterizing the full collection of satDNAs (satellitomes) of both species, we also in situ mapped these sequences in the chromosomes of both species. Moreover, the satDNAs that displayed signals on the sex chromosomes of P. semifasciata were also mapped in some phylogenetically related species to estimate their potential accumulation on proto-sex chromosomes. Thus, a large collection of satDNAs for both species, with several classes being shared between them, was characterized for the first time. In addition, the possible involvement of these satellites in the karyotype evolution of P. marilynae and P. semifasciata, especially sex-chromosome formation and karyotype reduction in P. marilynae, could be shown.
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Affiliation(s)
- Renata Luiza Rosa de Moraes
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil; (R.L.R.d.M.); (F.d.M.C.S.); (J.A.D.V.)
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany
| | - Francisco de Menezes Cavalcante Sassi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil; (R.L.R.d.M.); (F.d.M.C.S.); (J.A.D.V.)
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany
| | - Jhon Alex Dziechciarz Vidal
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil; (R.L.R.d.M.); (F.d.M.C.S.); (J.A.D.V.)
| | - Caio Augusto Gomes Goes
- Faculdade de Ciências, UNESP, Bauru 17033-36, SP, Brazil; (C.A.G.G.); (R.Z.d.S.); (F.P.-F.); (R.U.)
| | - Rodrigo Zeni dos Santos
- Faculdade de Ciências, UNESP, Bauru 17033-36, SP, Brazil; (C.A.G.G.); (R.Z.d.S.); (F.P.-F.); (R.U.)
| | - José Henrique Forte Stornioli
- Institute of Biological Sciences and Health, Universidade Federal Rural do Rio de Janeiro, Seropédica 23890-000, RJ, Brazil;
| | - Fábio Porto-Foresti
- Faculdade de Ciências, UNESP, Bauru 17033-36, SP, Brazil; (C.A.G.G.); (R.Z.d.S.); (F.P.-F.); (R.U.)
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany
| | - Ricardo Utsunomia
- Faculdade de Ciências, UNESP, Bauru 17033-36, SP, Brazil; (C.A.G.G.); (R.Z.d.S.); (F.P.-F.); (R.U.)
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil; (R.L.R.d.M.); (F.d.M.C.S.); (J.A.D.V.)
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany
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Glugoski L, Nogaroto V, Deon GA, Azambuja M, Moreira-Filho O, Vicari MR. Enriched tandemly repeats in chromosomal fusion points of Rineloricaria latirostris (Boulenger, 1900) (Siluriformes: Loricariidae). Genome 2022; 65:479-489. [PMID: 35939838 DOI: 10.1139/gen-2022-0043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cytogenetic data showed the enrichment of repetitive DNAs in chromosomal rearrangement points between closely related species in armored catfishes. Still, few studies integrated cytogenetic and genomic data aiming to identify their prone-to-break DNA sites. Here, we aimed to obtain the repetitive fraction in Rineloricaria latirostris to recognize the microsatellite and homopolymers flanking the regions previously described as chromosomal fusion points. The results indicated that repetitive DNAs in R. latirostris are predominantly DNA transposons, and considering the microsatellite and homopolymers, A/T-rich expansions were the most abundant. The in situ localization demonstrated the A/T-rich repetitive sequences are scattered on the chromosomes, while A/G-rich microsatellites units were accumulated in some regions. The DNA transposon hAT, the 5S rDNA, and 45S rDNA (previously identified in Robertsonian fusion points in R. latirostris) are clusterized with some microsatellites, especially (CA)n, (GA)n, and poly-A, which also are enriched in regions of chromosomal fusions. Our findings demonstrated that repetitive sequences such as rDNAs, hAT transposon, and microsatellite units flank probable evolutionary breakpoint regions in R. latirostris. However, due to the sequence unit homologies in different chromosomal sites, these repeat DNAs only may have facilitated chromosome fusion events in R. latirostris rather than work as a double-strand breakpoint site.
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Affiliation(s)
- Larissa Glugoski
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Sao Carlos, São Paulo, Brazil;
| | - Viviane Nogaroto
- Universidade Estadual de Ponta Grossa, Departamento de Biologia Estrutural, Molecular e Genética, Ponta Grossa, Paraná, Brazil;
| | - Geize Aparecida Deon
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Sao Carlos, São Paulo, Brazil;
| | - Matheus Azambuja
- Universidade Federal do Paraná, Departamento de Genética, Curitiba, PR, Brazil;
| | - Orlando Moreira-Filho
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Sao Carlos, São Paulo, Brazil;
| | - Marcelo Ricardo Vicari
- Universidade Estadual de Ponta Grossa, Departamento de Biologia Estrutural, Molecular e Genética, Ponta Grossa, Paraná, Brazil.,Universidade Federal do Paraná, Departamento de Genética, Curitiba, PR, Brazil;
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Moraes JN, Viana PF, Favarato RM, Pinheiro-Figliuolo VS, Feldberg E. Karyotype variability in six Amazonian species of the family Curimatidae (Characiformes) revealed by repetitive sequence mapping. Genet Mol Biol 2022; 45:e20210125. [PMID: 35766400 PMCID: PMC9240918 DOI: 10.1590/1678-4685-gmb-2021-0125] [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: 04/27/2021] [Accepted: 05/17/2022] [Indexed: 11/21/2022] Open
Abstract
Fishes of the Curimatidae family represent one of the most important freshwater
ichthyofauna groups of Central and South America, with 117 recognized species
distributed in eight genera. In this study, six species - Curimata
inornata, Curimatella dorsalis, and
Psectrogaster falcata collected from the Lower Araguaia
River, Pará, Brazil; Curimata vittata, Curimatella
meyeri, and Psectrogaster rutiloides collected
from the Catalão Lake, Amazonas, Brazil - were cytogenetically analyzed,
investigate the occurrence and distribution of repetitive DNA classes in the
karyotypes. All species had 2n=54 metacentric/submetacentric chromosomes.
Despite the conservative diploid number, we observed variations in the
karyotypic structure among species. Ribosomal DNA (rDNA) 18S and 5S were found
in single or multiple sites, with the first report of synteny in
Curimatella dorsalis, and the occurrence of several
interstitial telomeric sequences (ITSs) in species of the genera
Curimatella and Psectrogaster.
Interspecific karyotypic diversity both concerning structure and
location/position of the nucleolar organizer regions (NOR) and ribosomal DNA,
suggesting the occurrence of several non-Robertsonian rearrangements driving the
evolution of this family.
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Affiliation(s)
- Juliana Nascimento Moraes
- Instituto Nacional de Pesquisas da Amazônia (INPA), Coordenação de Biodiversidade, Laboratório de Genética Animal, Manaus, AM, Brazil
| | - Patrik Ferreira Viana
- Instituto Nacional de Pesquisas da Amazônia (INPA), Coordenação de Biodiversidade, Laboratório de Genética Animal, Manaus, AM, Brazil
| | - Ramon Marin Favarato
- Instituto Nacional de Pesquisas da Amazônia (INPA), Coordenação de Biodiversidade, Laboratório de Genética Animal, Manaus, AM, Brazil
| | - Vanessa Susan Pinheiro-Figliuolo
- Instituto Nacional de Pesquisas da Amazônia (INPA), Coordenação de Biodiversidade, Laboratório de Genética Animal, Manaus, AM, Brazil
| | - Eliana Feldberg
- Instituto Nacional de Pesquisas da Amazônia (INPA), Coordenação de Biodiversidade, Laboratório de Genética Animal, Manaus, AM, Brazil
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Vicari MR, Bruschi DP, Cabral-de-Mello DC, Nogaroto V. Telomere organization and the interstitial telomeric sites involvement in insects and vertebrates chromosome evolution. Genet Mol Biol 2022; 45:e20220071. [DOI: 10.1590/1678-4685-gmb-2022-0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 09/24/2022] [Indexed: 11/16/2022] Open
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Highly divergent karyotypes and barcoding of the East African genus Gonatoxia Karsch (Orthoptera: Phaneropterinae). Sci Rep 2021; 11:22781. [PMID: 34815452 PMCID: PMC8610994 DOI: 10.1038/s41598-021-02110-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/20/2021] [Indexed: 11/09/2022] Open
Abstract
East Africa is a hotspot of biodiversity of many orthopteran taxa, including bushcrickets. Gonatoxia Karsch, 1889 species are fully alate Phaneropterinae, which are perfectly adapted to the foliage of forests. We examined five species using combined cytogenetic and molecular data to determine the inter- and intraspecific genetic diversity. The variation in the diploid number of chromosomes in males ranged from 2n = 28 + X0 and 26 + X0 to 2n = 6 + X0. Fluorescence in situ hybridization showed from one to many 18S rDNA loci as well as interstitial sequences, especially in G. helleri. 18S rDNA loci coincided with active NOR and C-banding patterns. The isolation of populations of the species explains differences in the number of chromosomes (G. maculata), chromosomal polymorphism and chromosomal heterozygosity (G. helleri). Our molecular phylogeny based on the COI locus supported the monophyly of the genus Gonatoxia and separateness of the five examined species in accordance with their morphological features and chromosome numbers as well as the species' distribution.
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Ernetti JR, Gazolla CB, Recco-Pimentel SM, Luca EM, Bruschi DP. Non-random distribution of microsatellite motifs and (TTAGGG)n repeats in the monkey frog Pithecopus rusticus (Anura, Phyllomedusidae) karyotype. Genet Mol Biol 2020; 42:e20190151. [PMID: 31968045 PMCID: PMC7198017 DOI: 10.1590/1678-4685-gmb-2019-0151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/21/2019] [Indexed: 02/06/2023] Open
Abstract
The monkey frog, Pithecopus rusticus (Anura, Phyllomedusidae) is endemic to the grasslands of the Araucarias Plateau, southern Brazil. This species is known only from a small population found at the type locality. Here, we analyzed for the first time the chromosomal organization of the repetitive sequences, including seven microsatellite repeats and telomeric sequences (TTAGGG)n in the karyotype of the species by Fluorescence in situ Hybridization. The dinucleotide motifs had a pattern of distribution clearly distinct from those of the tri- and tetranucleotides. The dinucleotide motifs are abundant and widely distributed in the chromosomes, located primarily in the subterminal regions. The tri- and tetranucleotides, by contrast, tend to be clustered, with signals being observed together in the secondary constriction of the homologs of pair 9, which are associated with the nucleolus organizer region. As expected, the (TTAGGG)n probe was hybridized in all the telomeres, with hybridization signals being detected in the interstitial regions of some chromosome pairs. We demonstrated the variation in the abundance and distribution of the different microsatellite motifs and revealed their non-random distribution in the karyotype of P. rusticus. These data contribute to understand the role of repetitive sequences in the karyotype diversification and evolution of this taxon.
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Affiliation(s)
- Julia R Ernetti
- Programa de Pós-graduação em Ciências Ambientais, Área de Ciências Exatas e Ambientais, Universidade Comunitária da Região de Chapecó, Chapecó, SC, Brazil
| | - Camilla B Gazolla
- Programa de Pós-graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Shirlei M Recco-Pimentel
- Departamento de Biologia Estrutural e Funcional, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Elaine M Luca
- Programa de Pós-graduação em Ciências Ambientais, Área de Ciências Exatas e Ambientais, Universidade Comunitária da Região de Chapecó, Chapecó, SC, Brazil
- Departamento de Zootecnia e Ciências Biológicas, Universidade Federal de Santa Maria, Campus de Palmeira das Missões, Palmeira das Missões, RS, Brazil
| | - Daniel P Bruschi
- Programa de Pós-graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
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Louzada S, Lopes M, Ferreira D, Adega F, Escudeiro A, Gama-Carvalho M, Chaves R. Decoding the Role of Satellite DNA in Genome Architecture and Plasticity-An Evolutionary and Clinical Affair. Genes (Basel) 2020; 11:E72. [PMID: 31936645 PMCID: PMC7017282 DOI: 10.3390/genes11010072] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 12/29/2019] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
Repetitive DNA is a major organizational component of eukaryotic genomes, being intrinsically related with their architecture and evolution. Tandemly repeated satellite DNAs (satDNAs) can be found clustered in specific heterochromatin-rich chromosomal regions, building vital structures like functional centromeres and also dispersed within euchromatin. Interestingly, despite their association to critical chromosomal structures, satDNAs are widely variable among species due to their high turnover rates. This dynamic behavior has been associated with genome plasticity and chromosome rearrangements, leading to the reshaping of genomes. Here we present the current knowledge regarding satDNAs in the light of new genomic technologies, and the challenges in the study of these sequences. Furthermore, we discuss how these sequences, together with other repeats, influence genome architecture, impacting its evolution and association with disease.
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Affiliation(s)
- Sandra Louzada
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Mariana Lopes
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Daniela Ferreira
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Filomena Adega
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Ana Escudeiro
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Margarida Gama-Carvalho
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Raquel Chaves
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
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Paço A, Freitas R, Vieira-da-Silva A. Conversion of DNA Sequences: From a Transposable Element to a Tandem Repeat or to a Gene. Genes (Basel) 2019; 10:E1014. [PMID: 31817529 PMCID: PMC6947457 DOI: 10.3390/genes10121014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 11/18/2019] [Accepted: 11/29/2019] [Indexed: 01/24/2023] Open
Abstract
Eukaryotic genomes are rich in repetitive DNA sequences grouped in two classes regarding their genomic organization: tandem repeats and dispersed repeats. In tandem repeats, copies of a short DNA sequence are positioned one after another within the genome, while in dispersed repeats, these copies are randomly distributed. In this review we provide evidence that both tandem and dispersed repeats can have a similar organization, which leads us to suggest an update to their classification based on the sequence features, concretely regarding the presence or absence of retrotransposons/transposon specific domains. In addition, we analyze several studies that show that a repetitive element can be remodeled into repetitive non-coding or coding sequences, suggesting (1) an evolutionary relationship among DNA sequences, and (2) that the evolution of the genomes involved frequent repetitive sequence reshuffling, a process that we have designated as a "DNA remodeling mechanism". The alternative classification of the repetitive DNA sequences here proposed will provide a novel theoretical framework that recognizes the importance of DNA remodeling for the evolution and plasticity of eukaryotic genomes.
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Affiliation(s)
- Ana Paço
- MED-Mediterranean Institute for Agriculture, Environment and Development, University of Évora, 7002–554 Évora, Portugal;
| | - Renata Freitas
- IBMC-Institute for Molecular and Cell Biology, University of Porto, R. Campo Alegre 823, 4150–180 Porto, Portugal;
- I3S-Institute for Innovation and Health Research, University of Porto, Rua Alfredo Allen, 208, 4200–135 Porto, Portugal
- ICBAS-Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
| | - Ana Vieira-da-Silva
- MED-Mediterranean Institute for Agriculture, Environment and Development, University of Évora, 7002–554 Évora, Portugal;
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Escudeiro A, Adega F, Robinson TJ, Heslop-Harrison JS, Chaves R. Conservation, Divergence, and Functions of Centromeric Satellite DNA Families in the Bovidae. Genome Biol Evol 2019; 11:1152-1165. [PMID: 30888421 PMCID: PMC6475130 DOI: 10.1093/gbe/evz061] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2019] [Indexed: 12/18/2022] Open
Abstract
Repetitive satellite DNA (satDNA) sequences are abundant in eukaryote genomes, with a structural and functional role in centromeric function. We analyzed the nucleotide sequence and chromosomal location of the five known cattle (Bos taurus) satDNA families in seven species from the tribe Tragelaphini (Bovinae subfamily). One of the families (SAT1.723) was present at the chromosomes’ centromeres of the Tragelaphini species, as well in two more distantly related bovid species, Ovis aries and Capra hircus. Analysis of the interaction of SAT1.723 with centromeric proteins revealed that this satDNA sequence is involved in the centromeric activity in all the species analyzed and that it is preserved for at least 15–20 Myr across Bovidae species. The satDNA sequence similarity among the analyzed species reflected different stages of homogeneity/heterogeneity, revealing the evolutionary history of each satDNA family. The SAT1.723 monomer-flanking regions showed the presence of transposable elements, explaining the extensive shuffling of this satDNA between different genomic regions.
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Affiliation(s)
- Ana Escudeiro
- Department of Genetics and Biotechnology, CAG - Laboratory of Cytogenomics and Animal Genomics, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
| | - Filomena Adega
- Department of Genetics and Biotechnology, CAG - Laboratory of Cytogenomics and Animal Genomics, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
| | | | | | - Raquel Chaves
- Department of Genetics and Biotechnology, CAG - Laboratory of Cytogenomics and Animal Genomics, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
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Milioto V, Vlah S, Mazzoleni S, Rovatsos M, Dumas F. Chromosomal Localization of 18S-28S rDNA and (TTAGGG)n Sequences in Two South African Dormice of the Genus Graphiurus (Rodentia: Gliridae). Cytogenet Genome Res 2019; 158:145-151. [PMID: 31234172 DOI: 10.1159/000500985] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2019] [Indexed: 11/19/2022] Open
Abstract
Classical cytogenetics and mapping of 18S-28S rDNA and (TTAGGG)n sequences by fluorescence in situ hybridization (FISH) was performed on Graphiurus platyops (GPL) and Graphiurus ocularis (GOC) metaphases with the aim to characterize the genomes. In both species, inverted DAPI karyotypes showed the same diploid number, 2n = 46, and hybridization of the (TTAGGG)n probe revealed interstitial telomeric sequences (ITSs) at the centromeres of almost all bi-armed chromosomes. FISH with the rDNA probe localized nucleolus organizer regions (NORs), at the terminal ends of the p arms of the subtelocentric pairs 16 and 17 in both species and detected additional signals on GPL8 and GOC18, 19, and 22. The species have similar karyotypes, but their chromosome pairs 18-22 differ in morphology; these are acrocentric in G. platyops, as also confirmed by C-banding, and subtelocentric in G. ocularis. These differences in pairs 18-22 were also highlighted by hybridization of the telomeric probe (TTAGGG)n, which showed the small p arms in G. ocularis enriched with ITSs. FISH of rDNA probes detected multiple NOR loci in G. ocularis, underlining the intense evolutionary dynamics related to these genes. Although the Graphiurus species analyzed have similar karyotypes, the results on the repetitive sequences indicate a complex pattern of genomic reorganization and evolution occurring in these phylogenetically close species.
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Frade LFDS, Almeida BRRD, Milhomem-Paixão SSR, Ready JS, Nagamachi CY, Pieczarka JC, Noronha RCR. Karyoevolution of Crenicichla heckel 1840 (Cichlidae, Perciformes): a process mediated by inversions. Biol Open 2019; 8:bio.041699. [PMID: 31036749 PMCID: PMC6550074 DOI: 10.1242/bio.041699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Crenicichla (Cichliformes, Cichlidae) present a highly conserved diploid number 2n=48 with fundamental numbers varying between 52 and 62. We analyzed four species in order to investigate the role of repetitive DNA in chromosome evolution in the genus. Crenicichla johanna, Crenicichla cf. saxatilis and Crenicichla cf. regani have 2n=48 (8 m/sm and 40st/a) and FN=56, while Crenicichla sp. ‘Xingu I’ has 2n=48 (48 st/a) and FN=48. Different patterns of constitutive heterochromatin distribution were observed including pericentric, interstitial and whole arm C bands. A single chromosome bears 18S rDNA clusters in most species, except C. johanna, where population variation exists in terms of the quantity and distribution of clusters and their association with interstitial telomeric sequences. All species showed hybridization of 5S rDNA sequences in an interstitial region on an acrocentric chromosome pair. The karyotypic differences and maintenance of the diploid number supports chromosome evolution mediated by inversions in Crenicichla. The telomeric and 18S rDNA sequence association in various chromosomes of C. johanna are proposed to represent hotspots for breakage, favoring intra-chromosomal rearrangements. The results suggest that repetitive sequences can contribute to microstructural cytogenetic diversity in Crenicichla. Summary: This paper has a great importance for understanding karyotype evolutionary dynamics in neotropical freshwater fish, focusing on repetitive DNA and the role of inversions in Crenicichla.
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Affiliation(s)
- Luan Felipe da Silva Frade
- Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Campus Guamá, Rua Augusto Corrêa, n° 01. Guamá, Belém, Pará, Brasil
| | - Bruno Rafael Ribeiro de Almeida
- Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Campus Guamá, Rua Augusto Corrêa, n° 01. Guamá, Belém, Pará, Brasil
| | - Susana Suely Rodrigues Milhomem-Paixão
- Instituto Federal de Educação, Ciência e Tecnologia de Goiás, campus Valparaıso de Goiás, BR-040, km 6, Avenida Saia Velha, S/N, Área 8, Parque Esplanada V. 72.876-601, Valparaíso de Goiás, Goiás, Brasil
| | - Jonathan Stuart Ready
- Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Campus Guamá, Rua Augusto Corrêa, n° 01. Guamá, Belém, Pará, Brasil
| | - Cleusa Yoshiko Nagamachi
- Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Campus Guamá, Rua Augusto Corrêa, n° 01. Guamá, Belém, Pará, Brasil
| | - Julio Cesar Pieczarka
- Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Campus Guamá, Rua Augusto Corrêa, n° 01. Guamá, Belém, Pará, Brasil
| | - Renata Coelho Rodrigues Noronha
- Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Campus Guamá, Rua Augusto Corrêa, n° 01. Guamá, Belém, Pará, Brasil
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12
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Escudeiro A, Ferreira D, Mendes-da-Silva A, Heslop-Harrison JS, Adega F, Chaves R. Bovine satellite DNAs – a history of the evolution of complexity and its impact in the Bovidae family. THE EUROPEAN ZOOLOGICAL JOURNAL 2019. [DOI: 10.1080/24750263.2018.1558294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- A. Escudeiro
- Department of Genetics and Biotechnology (DGB), CAG – Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - D. Ferreira
- Department of Genetics and Biotechnology (DGB), CAG – Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - A. Mendes-da-Silva
- Department of Genetics and Biotechnology (DGB), CAG – Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | | | - F. Adega
- Department of Genetics and Biotechnology (DGB), CAG – Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - R. Chaves
- Department of Genetics and Biotechnology (DGB), CAG – Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
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13
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Chaves R, Ferreira D, Mendes-da-Silva A, Meles S, Adega F. FA-SAT Is an Old Satellite DNA Frozen in Several Bilateria Genomes. Genome Biol Evol 2018; 9:3073-3087. [PMID: 29608678 PMCID: PMC5714208 DOI: 10.1093/gbe/evx212] [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] [Accepted: 10/06/2017] [Indexed: 12/17/2022] Open
Abstract
In recent years, a growing body of evidence has recognized the tandem repeat sequences, and specifically satellite DNA, as a functional class of sequences in the genomic “dark matter.” Using an original, complementary, and thus an eclectic experimental design, we show that the cat archetypal satellite DNA sequence, FA-SAT, is “frozen” conservatively in several Bilateria genomes. We found different genomic FA-SAT architectures, and the interspersion pattern was conserved. In Carnivora genomes, the FA-SAT-related sequences are also amplified, with the predominance of a specific FA-SAT variant, at the heterochromatic regions. We inspected the cat genome project to locate FA-SAT array flanking regions and revealed an intensive intermingling with transposable elements. Our results also show that FA-SAT-related sequences are transcribed and that the most abundant FA-SAT variant is not always the most transcribed. We thus conclude that the DNA sequences of FA-SAT and their transcripts are “frozen” in these genomes. Future work is needed to disclose any putative function that these sequences may play in these genomes.
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Affiliation(s)
- Raquel Chaves
- CAG-Laboratory of Cytogenomics and Animal Genomics, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
| | - Daniela Ferreira
- CAG-Laboratory of Cytogenomics and Animal Genomics, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
| | - Ana Mendes-da-Silva
- CAG-Laboratory of Cytogenomics and Animal Genomics, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
| | - Susana Meles
- CAG-Laboratory of Cytogenomics and Animal Genomics, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
| | - Filomena Adega
- CAG-Laboratory of Cytogenomics and Animal Genomics, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
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14
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Adega F, Matoso Silva R, Kjöllerström HJ, Vercammen P, Raudsepp T, Collares-Pereira MJ, Fernandes C, do Mar Oom M, Chaves R. Comparative Chromosome Painting in Genets (Carnivora, Viverridae, Genetta), the Only Known Feliforms with a Highly Rearranged Karyotype. Cytogenet Genome Res 2018; 156:35-44. [PMID: 30086546 DOI: 10.1159/000491868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2018] [Indexed: 11/19/2022] Open
Abstract
Mammalian carnivores have been extensively studied by cross-species chromosome painting, which indicated a high degree of karyotypic conservatism in the cat-like suborder Feliformia relative to the ancestral carnivore karyotype (ACK). The first exception to this high degree of karyotypic conservation in feliforms was recently confirmed in genets, mesocarnivores belonging to the basal family Viverridae. Here, we present a comparative analysis of the chromosome rearrangements among 2 subspecies of the small-spotted genet Genetta genetta (the Iberian nominate and the Arabian grantii) and the panther genet G. maculata, the 2 most common and widespread genets, using whole-chromosome paints from the domestic cat (Felis catus). The chromosome homology maps and the presence of numerous interstitial telomeric sites in both genet species strengthen the hypothesis that a highly rearranged karyotype compared to the ACK may occur throughout Genetta. The karyotype of G. maculata appears to have undergone more rearrangements than that of G. genetta, which is an older lineage. Notably, we identified a tandem fusion distinguishing G. g. genetta and G. g.grantii. As G. g. grantii is morphologically and genetically distinctive, and tandem fusions have been associated with substantial postzygotic isolation in mammals, this cytogenetic finding flags the subspecies for future taxonomic investigations.
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15
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Bolzán AD. Interstitial telomeric sequences in vertebrate chromosomes: Origin, function, instability and evolution. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 773:51-65. [PMID: 28927537 DOI: 10.1016/j.mrrev.2017.04.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/13/2017] [Accepted: 04/17/2017] [Indexed: 12/21/2022]
Abstract
By definition, telomeric sequences are located at the very ends or terminal regions of chromosomes. However, several vertebrate species show blocks of (TTAGGG)n repeats present in non-terminal regions of chromosomes, the so-called interstitial telomeric sequences (ITSs), interstitial telomeric repeats or interstitial telomeric bands, which include those intrachromosomal telomeric-like repeats located near (pericentromeric ITSs) or within the centromere (centromeric ITSs) and those telomeric repeats located between the centromere and the telomere (i.e., truly interstitial telomeric sequences) of eukaryotic chromosomes. According with their sequence organization, localization and flanking sequences, ITSs can be classified into four types: 1) short ITSs, 2) subtelomeric ITSs, 3) fusion ITSs, and 4) heterochromatic ITSs. The first three types have been described mainly in the human genome, whereas heterochromatic ITSs have been found in several vertebrate species but not in humans. Several lines of evidence suggest that ITSs play a significant role in genome instability and evolution. This review aims to summarize our current knowledge about the origin, function, instability and evolution of these telomeric-like repeats in vertebrate chromosomes.
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Affiliation(s)
- Alejandro D Bolzán
- Laboratorio de Citogenética y Mutagénesis, Instituto Multidisciplinario de Biología Celular (IMBICE, CICPBA-UNLP-CONICET La Plata), C.C. 403, 1900 La Plata, Argentina; Facultad de Ciencias Naturales y Museo, UNLP, Calle 60 y 122, 1900 La Plata, Argentina.
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16
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Vieira-da-Silva A, Adega F, Guedes-Pinto H, Chaves R. LINE-1 distribution in six rodent genomes follow a species-specific pattern. J Genet 2016; 95:21-33. [PMID: 27019429 DOI: 10.1007/s12041-015-0595-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
L1 distribution in mammal's genomes is yet a huge riddle. However, these repetitive sequences were already found in all chromosomic regions, and in general, they seem to be nonrandomly distributed in the genome. It also seems that after insertion and when they are not deleterious, they are always involved in dynamic processes occurring on that particular chromosomic region. Furthermore, it seems that large-scale genome rearrangements and L1 activity and accumulation are somehow interconnected. In the present study, we analysed L1 genomic distribution in Tatera gambiana (Muridae, Gerbillinae), Acomys sp. (Muridae, Deomyinae), Cricetomys sp. (Nesomyidae, Cricetomyinae), Microtus arvalis (Cricetidae, Arvicolinae), Phodopus roborovskii and P. sungorus (Cricetidae, Cricetinae). All the species studied here seems to exhibit a species-specific pattern.Possible mechanisms, and processes involved in L1 distribution and preferential accumulation in certain regions are di scussed.
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Affiliation(s)
- A Vieira-da-Silva
- Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trάs-os-Montes and Alto Douro (UTAD), 5001, 801 Vila Real,
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17
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Teixeira LSR, Seger KR, Targueta CP, Orrico VGD, Lourenço LB. Comparative cytogenetics of tree frogs of the Dendropsophus marmoratus (Laurenti, 1768) group: conserved karyotypes and interstitial telomeric sequences. COMPARATIVE CYTOGENETICS 2016; 10:753-767. [PMID: 28123692 PMCID: PMC5240522 DOI: 10.3897/compcytogen.v10i4.9972] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 11/04/2016] [Indexed: 06/06/2023]
Abstract
The diploid number 2n = 30 is a presumed synapomorphy of Dendropsophus Fitzinger, 1843, although a noticeable variation in the number of biarmed/telocentric chromosomes is observed in this genus. Such a variation suggests that several chromosomal rearrangements took place after the evolutionary origin of the hypothetical ancestral 30-chromosome karyotype; however, the inferred rearrangements remain unknown. Distinct numbers of telocentric chromosomes are found in the two most cytogenetically studied species groups of Dendropsophus. In contrast, all three species of the Dendropsophus marmoratus (Laurenti, 1768) group that are already karyotyped presented five pairs of telocentric chromosomes. In this study, we analyzed cytogenetically three additional species of this group to investigate if the number of telocentric chromosomes in this group is not as variable as in other Dendropsophus groups. We described the karyotypes of Dendropsophus seniculus (Cope, 1868), Dendropsophus soaresi (Caramaschi & Jim, 1983) and Dendropsophus novaisi (Bokermann, 1968) based on Giemsa staining, C-banding, silver impregnation and in situ hybridization with telomeric probes. Dendropsophus seniculus, Dendropsophus soaresi and Dendropsophus novaisi presented five pairs of telocentric chromosomes, as did the remaining species of the group previously karyotyped. Though the species of this group show a high degree of karyotypic similarity, Dendropsophus soaresi was unique in presenting large blocks of het-ITSs (heterochromatic internal telomeric sequences) in the majority of the centromeres. Although the ITSs have been interpreted as evidence of ancestral chromosomal fusions and inversions, the het-ITSs detected in the karyotype of Dendropsophus soaresi could not be explained as direct remnants of ancestral chromosomal rearrangements because no evidence of chromosomal changes emerged from the comparison of the karyotypes of all of the species of the Dendropsophus marmoratus group.
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Affiliation(s)
- Lívia S. R. Teixeira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, 13083-863 Campinas, São Paulo, Brasil
| | - Karin Regina Seger
- Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, 13083-863 Campinas, São Paulo, Brasil
| | - Cíntia Pelegrineti Targueta
- Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, 13083-863 Campinas, São Paulo, Brasil
| | - Victor G. Dill Orrico
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, 45662-900 Ilhéus, Bahia, Brasil
| | - Luciana Bolsoni Lourenço
- Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, 13083-863 Campinas, São Paulo, Brasil
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18
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Matoso Silva R, Adega F, Kjöllerström HJ, Labuschagne K, Kotze A, Fernandes C, Chaves R, do Mar Oom M. Classical and Molecular Cytogenetics of the Panther Genet Genetta maculata (Mammalia, Carnivora, Viverridae). Cytogenet Genome Res 2016; 149:274-281. [DOI: 10.1159/000450627] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2016] [Indexed: 11/19/2022] Open
Abstract
Genets (Genetta) are a genus of African mammalian carnivorans with 14 currently recognized species, although taxonomic uncertainties remain, particularly regarding the number of species within the large-spotted genet complex. This study presents the first banded karyotype and molecular cytogenetic analysis of a genetically identified panther genet, Genetta maculata, the most common and widespread taxon of the large-spotted genet complex, with a wide distribution in sub-Saharan Africa. Sampled in Gauteng Province, South Africa, it could be assigned to the subspecies G. m. letabae on geographic grounds and had a similar karyotype (2n = 52, FNa = 96) to those published for a panther genet from Ethiopia and for the West African large-spotted genet G. pardina. Notably, the specimen had a different autosomal morphology (2 acrocentric chromosomes) from that previously attributed to letabae (a single acrocentric chromosome), but the latter assignment was uncertain because the studied individuals were captive born and assigned based solely on a presumed origin in the former Transvaal Province of South Africa. Fluorescence in situ hybridization with a telomere repeat probe revealed the presence of telomeric sequences in the centromeres of most chromosomes, the so-called interstitial telomeric sites (ITSs). Since genets seem to have a unique, highly rearranged karyotype among feliforms and relatively low interspecific karyotypic variation, and considering the known instability of ITSs, we suggest that the large amount of ITSs found here might be due to evolutionarily recent extensive genomic rearrangements. This study provides cytogenetic information that contributes to our understanding of chromosomal variation and genomic rearrangements in genets, and valuable baseline data for future studies of karyotype evolution in carnivores in general and viverrids in particular.
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19
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Paço A, Adega F, Meštrović N, Plohl M, Chaves R. The puzzling character of repetitive DNA in Phodopus genomes (Cricetidae, Rodentia). Chromosome Res 2016; 23:427-40. [PMID: 26281779 DOI: 10.1007/s10577-015-9481-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Three novel repetitive DNA sequences are described, presenting a similar heterochromatic chromosomal location in two hamster species: Phodopus roborovskii and Phodopus sungorus (Cricetidae, Rodentia). Namely, two species-specific repetitive sequences (PROsat from P. roborovskii and PSUchr1sat from P. sungorus) surrounding a third one (PsatDNA), that is shared by both hamster genomes. Fiber-FISH analyses revealed that PROsat intermingles with PsatDNA in P. roborovskii and PSUchr1sat intermingles with PsatDNA in P. sungorus. A model explaining the evolution of this intricate chromosomal distribution is proposed, which can explain better the evolution of these very derivative genomes (in comparison to the ancestral Muroidea). The most plausible evolutionary scenario seems to be the expansion of a number of repeats into other's domain, most probably resulting in its intermingling, followed by the subsequent spread of these complex repeats from a single chromosomal location to other chromosomes. Evidences of an association between repetitive sequences and the chromosome evolution process were observed, namely for PROsat. Most probably, the evolutionary breakpoints that shaped PRO and PSU chromosomes (pericentric inversions and fusions) occurred within the boundaries of PROsat blocks in the ancestor. The repeats high diversity at the heterochromatic regions of Phodopus chromosomes, together with its complex organization, suggests that these species are important models for evolutionary studies, namely in the investigation of a possible relationship between repetitive sequences and the occurrence of chromosomal rearrangements and consequently, in genome evolution.
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Affiliation(s)
- Ana Paço
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Vila Real, Portugal
| | - Filomena Adega
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Vila Real, Portugal.,University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal
| | - Nevenka Meštrović
- Department of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, HR-10002, Zagreb, Croatia
| | - Miroslav Plohl
- Department of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, HR-10002, Zagreb, Croatia
| | - Raquel Chaves
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Vila Real, Portugal. .,University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal.
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20
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Sotero-Caio CG, Volleth M, Hoffmann FG, Scott L, Wichman HA, Yang F, Baker RJ. Integration of molecular cytogenetics, dated molecular phylogeny, and model-based predictions to understand the extreme chromosome reorganization in the Neotropical genus Tonatia (Chiroptera: Phyllostomidae). BMC Evol Biol 2015; 15:220. [PMID: 26444412 PMCID: PMC4594642 DOI: 10.1186/s12862-015-0494-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/22/2015] [Indexed: 11/18/2022] Open
Abstract
Background Defining factors that contributed to the fixation of a high number of underdominant chromosomal rearrangements is a complex task because not only molecular mechanisms must be considered, but also the uniqueness of natural history attributes of each taxon. Ideally, detailed investigation of the chromosome architecture of an organism and related groups, placed within a phylogenetic context, is required. We used multiple approaches to investigate the dynamics of chromosomal evolution in lineages of bats with considerable karyotypic variation, focusing on the different facets contributing to fixation of the exceptional chromosomal changes in Tonatia saurophila. Integration of empirical data with proposed models of chromosome evolution was performed to understand the probable conditions for Tonatia’s karyotypic evolution. Results The trajectory of reorganization of chromosome blocks since the common ancestor of Glossophaginae and Phyllostominae subfamilies suggests that multiple tandem fusions, as well as disruption and fusions of conserved phyllostomid chromosomes were major drivers of karyotypic reshuffling in Tonatia. Considerable variation in the rates of chromosomal evolution between phyllostomid lineages was observed. Thirty–nine unique fusions and fission events reached fixation in Tonatia over a short period of time, followed by ~12 million years of chromosomal stasis. Physical mapping of repetitive DNA revealed an unusual accumulation of LINE-1 sequences on centromeric regions, probably associated with the chromosomal dynamics of this genus. Conclusions Multiple rearrangements have reached fixation in a wave-like fashion in phyllostomid bats. Different biological features of Tonatia support distinct models of rearrangement fixation, and it is unlikely that the fixations were a result of solely stochastic processes in small ancient populations. Increased recombination rates were probably facilitated by expansion of repetitive DNA, reinforced by aspects of taxon reproduction and ecology. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0494-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Marianne Volleth
- Department of Human Genetics, Otto-von-Guericke University, Magdeburg, Germany.
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi, MS, USA. .,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS, USA.
| | - LuAnn Scott
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA.
| | - Holly A Wichman
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA.
| | - Fengtang Yang
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.
| | - Robert J Baker
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
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21
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Paço A, Adega F, Meštrović N, Plohl M, Chaves R. Evolutionary story of a satellite DNA from Phodopus sungorus (Rodentia, Cricetidae). Genome Biol Evol 2014; 6:2944-55. [PMID: 25336681 PMCID: PMC4224359 DOI: 10.1093/gbe/evu233] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2014] [Indexed: 12/23/2022] Open
Abstract
With the goal to contribute for the understanding of satellite DNA evolution and its genomic involvement, in this work it was isolated and characterized the first satellite DNA (PSUcentSat) from Phodopus sungorus (Cricetidae). Physical mapping of this sequence in P. sungorus showed large PSUcentSat arrays located at the heterochromatic (peri)centromeric region of five autosomal pairs and Y-chromosome. The presence of orthologous PSUcentSat sequences in the genomes of other Cricetidae and Muridae rodents was also verified, presenting however, an interspersed chromosomal distribution. This distribution pattern suggests a PSUcentSat-scattered location in an ancestor of Muridae/Cricetidae families, that assumed afterwards, in the descendant genome of P. sungorus a restricted localization to few chromosomes in the (peri)centromeric region. We believe that after the divergence of the studied species, PSUcentSat was most probably highly amplified in the (peri)centromeric region of some chromosome pairs of this hamster by recombinational mechanisms. The bouquet chromosome configuration (prophase I) possibly displays an important role in this selective amplification, providing physical proximity of centromeric regions between chromosomes with similar size and/or morphology. This seems particularly evident for the acrocentric chromosomes of P. sungorus (including the Y-chromosome), all presenting large PSUcentSat arrays at the (peri)centromeric region. The conservation of this sequence in the studied genomes and its (peri)centromeric amplification in P. sungorus strongly suggests functional significance, possibly displaying this satellite family different functions in the different genomes. The verification of PSUcentSat transcriptional activity in normal proliferative cells suggests that its transcription is not stage-limited, as described for some other satellites.
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Affiliation(s)
- Ana Paço
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro (IBB/CGBUTAD), Vila Real, Portugal
| | - Filomena Adega
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro (IBB/CGBUTAD), Vila Real, Portugal Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Nevenka Meštrović
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Miroslav Plohl
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Raquel Chaves
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro (IBB/CGBUTAD), Vila Real, Portugal Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
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22
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Golczyk H, Massouh A, Greiner S. Translocations of chromosome end-segments and facultative heterochromatin promote meiotic ring formation in evening primroses. THE PLANT CELL 2014; 26:1280-93. [PMID: 24681616 PMCID: PMC4001384 DOI: 10.1105/tpc.114.122655] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Due to reciprocal chromosomal translocations, many species of Oenothera (evening primrose) form permanent multichromosomal meiotic rings. However, regular bivalent pairing is also observed. Chiasmata are restricted to chromosomal ends, which makes homologous recombination virtually undetectable. Genetic diversity is achieved by changing linkage relations of chromosomes in rings and bivalents via hybridization and reciprocal translocations. Although the structural prerequisite for this system is enigmatic, whole-arm translocations are widely assumed to be the mechanistic driving force. We demonstrate that this prerequisite is genome compartmentation into two epigenetically defined chromatin fractions. The first one facultatively condenses in cycling cells into chromocenters negative both for histone H3 dimethylated at lysine 4 and for C-banding, and forms huge condensed middle chromosome regions on prophase chromosomes. Remarkably, it decondenses in differentiating cells. The second fraction is euchromatin confined to distal chromosome segments, positive for histone H3 lysine 4 dimethylation and for histone H3 lysine 27 trimethylation. The end-segments are deprived of canonical telomeres but capped with constitutive heterochromatin. This genomic organization promotes translocation breakpoints between the two chromatin fractions, thus facilitating exchanges of end-segments. We challenge the whole-arm translocation hypothesis by demonstrating why reciprocal translocations of chromosomal end-segments should strongly promote meiotic rings and evolution toward permanent translocation heterozygosity. Reshuffled end-segments, each possessing a major crossover hot spot, can furthermore explain meiotic compatibility between genomes with different translocation histories.
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Affiliation(s)
- Hieronim Golczyk
- Department of Molecular Biology, Institute of Biotechnology, John Paul II Catholic University of Lublin, Konstantynów 1I 20-708, Poland
- Address correspondence to
| | - Amid Massouh
- Max Planck Institute of Molecular Plant Physiology, Department 3, Potsdam-Golm 14476, Germany
| | - Stephan Greiner
- Max Planck Institute of Molecular Plant Physiology, Department 3, Potsdam-Golm 14476, Germany
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