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Takagui FH, Viana P, Haerter CAG, Zuanon J, Birindelli JLO, Lui RL, Feldberg E, Margarido VP. Chromosomal analysis of two Acanthodoras species (Doradidae, Siluriformes): Insights into the oldest thorny catfish clade and its karyotype evolution. JOURNAL OF FISH BIOLOGY 2024; 105:1109-1119. [PMID: 39007200 DOI: 10.1111/jfb.15863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 05/29/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024]
Abstract
The Doradidae fishes constitute one of the most diverse groups of Neotropical freshwater environments. Acanthodoradinae is the oldest lineage and the sister group to all other thorny catfishes, and it includes only the genus Acanthodoras. The diversity of Acanthodoras remains underestimated, and the use of complementary approaches, including genetic studies, is an important step to better characterize this diversity and the relationships among the species within the genus. Therefore, we conducted a comprehensive analysis using conventional cytogenetic techniques and physical mapping of three multigene families (18S and 5S ribosomal DNA [rDNA], U2 small nuclear DNA [snDNA]) and four microsatellite motifs, namely (AC)n, (AT)n, (GA)n, and (GATA)n, in two sympatric species from the Negro River: Acanthodoras cataphractus and Acanthodoras cf. polygrammus. We found significant differences in constitutive heterochromatin (CH) content, distribution of the microsatellite (AT)n, and the number of 5S rDNA and U2 snDNA sites. These differences may result from chromosome rearrangements and repetitive DNA dispersal mechanisms. Furthermore, the characterization of the diploid number (2n) of these Acanthodoras species enables us to propose 2n = 58 chromosomes as the plesiomorphic 2n state in Doradidae based on ancestral state reconstruction. Acanthodoradinae is the oldest lineage of the thorny catfishes, and knowledge about its cytogenetic patterns is crucial for disentangling the karyotype evolution of the whole group. Thus, this study contributes to the understanding of the mechanisms behind chromosome diversification of Doradidae and highlights the importance of Acanthodoradinae in the evolutionary history of thorny catfishes.
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Affiliation(s)
- Fábio Hiroshi Takagui
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Patrik Viana
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | | | - Jansen Zuanon
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - José Luís Olivan Birindelli
- Museu de Zoologia, Departamento de Biologia Animal e Vegetal, Universidade Estadual de Londrina, Londrina, Brazil
| | - Roberto Laridondo Lui
- Laboratório de Citogenética, Centro de Ciĉncias Biológicas e da Saúde, Cascavel, Brazil
| | - Eliana Feldberg
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
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Gavazzoni M, Pavanelli CS, Graça WJ, De Oliveira EA, Moreira-Filho O, Margarido VP. Species delimitation in Psalidodon fasciatus (Cuvier, 1819) complex (Teleostei: Characidae) from three hydrographic basins. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Abstract
Psalidodon fasciatus is a complex of several fish species widely distributed in Brazilian hydrographic systems that share morphological characteristics and show a high taxonomic complexity and genetic variability. Cytogenetic and molecular analyses were carried out in populations from three Brazilian hydrographic basins, aiming to contribute to systematic and biogeographical knowledge of the group. The chromosomal markers verified the occurrence of species-specific characters and indicated the existence of six distinct operational taxonomic units (OTUs): P. fasciatus (São Francisco River basin), Psalidodon sp. 1, Psalidodon sp. 2 and Psalidodon eigenmanniorum (Uruguay River basin); and Psalidodon sp. 3 and Psalidodon sp. 4 (Paraná River basin). The chromosomal markers showed more similarities among species from the Uruguay River and São Francisco River basins. DNA barcoding analyses (assemble species by automatic partitioning, neighbour-joining, maximum likelihood and maximum parsimony) indicated the existence of at least three distinct OTUs. The chromosomal evolution rates were demonstrated to be higher than the molecular evolution rates, reinforcing the importance of using chromosomal markers to delimit OTUs in integrative taxonomy studies. These results suggest that the São Francisco River Basin population (the type locality) should be considered as true P. fasciatus, and the others, until now treated as Psalidodon aff. fasciatus, are cryptic species.
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Affiliation(s)
- Mariane Gavazzoni
- Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná , Cascavel, Paraná , Brazil
- Pós-graduação em Biologia Comparada, Centro de Ciências Biológicas, Universidade Estadual de Maringá , Maringá, Paraná , Brazil
| | - Carla S Pavanelli
- Pós-graduação em Biologia Comparada, Centro de Ciências Biológicas, Universidade Estadual de Maringá , Maringá, Paraná , Brazil
- Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Centro de Ciências Biológicas, Universidade Estadual de Maringá , Maringá, Paraná , Brazil
| | - Weferson J Graça
- Pós-graduação em Biologia Comparada, Centro de Ciências Biológicas, Universidade Estadual de Maringá , Maringá, Paraná , Brazil
- Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Centro de Ciências Biológicas, Universidade Estadual de Maringá , Maringá, Paraná , Brazil
- Departamento de Biologia, Centro de Ciências Biológicas, Universidade Estadual de Maringá , Maringá, Paraná , Brazil
| | - Ezequiel A De Oliveira
- Secretaria de Estado de Educação do Mato Grosso, São Felix do Araguaia , Mato Grosso , Brazil
| | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos , São Carlos, São Paulo , Brazil
| | - Vladimir P Margarido
- Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná , Cascavel, Paraná , Brazil
- Pós-graduação em Biologia Comparada, Centro de Ciências Biológicas, Universidade Estadual de Maringá , Maringá, Paraná , Brazil
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Barbosa P, Schemczssen-Graeff Z, Marques A, da Silva M, Favero GM, Sobreiro BP, de Almeida MC, Moreira-Filho O, Silva DMZDA, Porto-Foresti F, Foresti F, Artoni RF. Silencing of Transposable Elements Mediated by 5-mC and Compensation of the Heterochromatin Content by Presence of B Chromosomes in Astyanax scabripinnis. Cells 2021; 10:1162. [PMID: 34064768 PMCID: PMC8151356 DOI: 10.3390/cells10051162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 01/21/2023] Open
Abstract
The way in which transcriptional activity overcomes the physical DNA structure and gene regulation mechanisms involves complex processes that are not yet fully understood. Modifications in the cytosine-guanine sequence of DNA by 5-mC are preferentially located in heterochromatic regions and are related to gene silencing. Herein, we investigate evidence of epigenetic regulation related to the B chromosome model and transposable elements in A. scabripinnis. Indirect immunofluorescence using anti-5-mC to mark methylated regions was employed along with quantitative ELISA to determine the total genomic DNA methylation level. 5-mC signals were dispersed in the chromosomes of both females and males, with preferential accumulation in the B chromosome. In addition to the heterochromatic methylated regions, our results suggest that methylation is associated with transposable elements (LINE and Tc1-Mariner). Heterochromatin content was measured based on the C-band length in relation to the size of chromosome 1. The B chromosome in A. scabripinnis comprises heterochromatin located in the pericentromeric region of both arms of this isochromosome. In this context, individuals with B chromosomes should have an increased heterochromatin content when compared to individuals that do not. Although, both heterochromatin content and genome methylation showed no significant differences between sexes or in relation to the occurrence of B chromosomes. Our evidence suggests that the B chromosome can have a compensation effect on the heterochromatin content and that methylation possibly operates to silence TEs in A. scabripinnis. This represents a sui generis compensation and gene activity buffering mechanism.
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Affiliation(s)
- Patrícia Barbosa
- Post Graduate Program in Evolutionary Genetics and Molecular Biology, Department of Genetics and Evolution, Federal University of São Carlos, Rodovia Washington Luís Km 235, São Carlos 13565-905, SP, Brazil; (P.B.); (O.M.-F.)
| | - Zelinda Schemczssen-Graeff
- Post Graduate Program in Evolutionary Biology, Department of Structural, Molecular and Genetic Biology, State University of Ponta Grossa, Avenida Carlos Cavalcanti 4748, Ponta Grossa 84030-900, PR, Brazil; (Z.S.-G.); (M.d.S.); (M.C.d.A.)
| | - André Marques
- Department of Botany, Federal University of Pernambuco, Recife 50670-901, PE, Brazil;
| | - Maelin da Silva
- Post Graduate Program in Evolutionary Biology, Department of Structural, Molecular and Genetic Biology, State University of Ponta Grossa, Avenida Carlos Cavalcanti 4748, Ponta Grossa 84030-900, PR, Brazil; (Z.S.-G.); (M.d.S.); (M.C.d.A.)
| | - Giovani Marino Favero
- Department of General Biology, State University of Ponta Grossa, Avenida Carlos Cavalcanti 4748, Ponta Grossa 84030-900, PR, Brazil;
| | - Bernardo Passos Sobreiro
- Department of Medicine, State University of Ponta Grossa, Avenida Carlos Cavalcanti 4748, Ponta Grossa 84030-900, PR, Brazil;
| | - Mara Cristina de Almeida
- Post Graduate Program in Evolutionary Biology, Department of Structural, Molecular and Genetic Biology, State University of Ponta Grossa, Avenida Carlos Cavalcanti 4748, Ponta Grossa 84030-900, PR, Brazil; (Z.S.-G.); (M.d.S.); (M.C.d.A.)
| | - Orlando Moreira-Filho
- Post Graduate Program in Evolutionary Genetics and Molecular Biology, Department of Genetics and Evolution, Federal University of São Carlos, Rodovia Washington Luís Km 235, São Carlos 13565-905, SP, Brazil; (P.B.); (O.M.-F.)
| | - Duílio Mazzoni Zerbinato de Andrade Silva
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University (UNESP), Botucatu 18618-689, SP, Brazil; (D.M.Z.d.A.S.); (F.F.)
| | - Fábio Porto-Foresti
- Faculty of Sciences, Sao Paulo State University (UNESP), Bauru 01049-010, SP, Brazil;
| | - Fausto Foresti
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University (UNESP), Botucatu 18618-689, SP, Brazil; (D.M.Z.d.A.S.); (F.F.)
| | - Roberto Ferreira Artoni
- Post Graduate Program in Evolutionary Genetics and Molecular Biology, Department of Genetics and Evolution, Federal University of São Carlos, Rodovia Washington Luís Km 235, São Carlos 13565-905, SP, Brazil; (P.B.); (O.M.-F.)
- Post Graduate Program in Evolutionary Biology, Department of Structural, Molecular and Genetic Biology, State University of Ponta Grossa, Avenida Carlos Cavalcanti 4748, Ponta Grossa 84030-900, PR, Brazil; (Z.S.-G.); (M.d.S.); (M.C.d.A.)
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Goes CAG, Daniel SN, Piva LH, Yasui GS, Artoni RF, Hashimoto DT, Foresti F, Porto-Foresti F. Cytogenetic markers as a tool for characterization of hybrids of Astyanax Baird & Girard, 1854 and Hyphessobrycon Eigenmann, 1907. COMPARATIVE CYTOGENETICS 2020; 14:231-242. [PMID: 32537093 PMCID: PMC7270076 DOI: 10.3897/compcytogen.v14i2.49513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
Astyanax Baird et Girard, 1854, is one of the largest genera in the family Characidae and comprises 177 valid species. This genus has been the focus of cytogenetic studies primarily owing to the presence of B chromosomes and high karyotypic diversity among different populations. The intense genetic variability in Astyanax is one of the factors responsible for the occurrence of species complexes, which are groups (1) with certain difficulties in establishing common genetic pools or (2) belonging to different cryptic species. To evaluate cytogenetic marker inheritance and the possibility of the identification of these hybrids, this study aimed to describe cytogenetic hybrids from three strains of species of the genera Astyanax and Hyphessobrycon Eigenmann, 1908. A. lacustris Lütken, 1875, A. schubarti Britski, 1964, A. fasciatus Cuvier, 1819, and H. anisitsi Eigenmann, 1907 were used to generate three hybrid lineages. The diploid number, heterochromatin sites, and ribosomal genes (18S and 5S rDNA) of the parental strains and the hybrids were analyzed. The results indicated that the three hybrid lineages had cytogenetic markers of both parents, presenting Mendelian inheritance. However, differences in distribution of heterochromatic blocks were observed between the hybrids and the parent strains. Our results allowed the identification of the hybrid strains based on the cytogenetic markers applied, reinforcing the efficiency of cytogenetic markers as tools for identification and indicating that such events may increase the karyotypic diversity in the genera Astyanax and Hyphessobrycon.
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Affiliation(s)
- Caio Augusto Gomes Goes
- Universidade Estadual Paulista (UNESP) “Júlio de Mesquita Filho”, Faculdade de Ciências, Edmundo Carrijo Coube Avenue, Bauru, SP, BrazilUniversidade Estadual PaulistaBauruBrazil
| | - Sandro Natal Daniel
- Universidade Estadual Paulista (UNESP) “Júlio de Mesquita Filho”, Faculdade de Ciências, Edmundo Carrijo Coube Avenue, Bauru, SP, BrazilUniversidade Estadual PaulistaBauruBrazil
| | - Lucas Henrique Piva
- Centro nacional de Pesquisa e Conservação da Biota Aquática Continental (CEPTA-ICMBIO), Prefeito Euberto Nemésio Pereira Godói Highway, Pirassununga, SP, BrazilCentro nacional de Pesquisa e Conservação da Biota Aquática ContinentalPirassunungaBrazil
| | - George Shigueki Yasui
- Centro nacional de Pesquisa e Conservação da Biota Aquática Continental (CEPTA-ICMBIO), Prefeito Euberto Nemésio Pereira Godói Highway, Pirassununga, SP, BrazilCentro nacional de Pesquisa e Conservação da Biota Aquática ContinentalPirassunungaBrazil
| | - Roberto Ferreira Artoni
- Universidade Estadual de Ponta Grossa, Setor de Ciências Biológicas e da Saúde, Santos Andrade Square, Ponta Grossa, PR, BrazilUniversidade Estadual de Ponta GrossaPonta GrossaBrazil
| | - Diogo Teruo Hashimoto
- Universidade Estadual Paulista (UNESP) “Júlio de Mesquita Filho”, Centro de Aquicultura da UNESP, Prof. Paulo Donato Castelane Acess way, Jaboticabal, SP, BrazilUniversidade Estadual PaulistaJaboticabalBrazil
| | - Fausto Foresti
- Universidade Estadual Paulista (UNESP) “Júlio de Mesquita Filho”, Instituto de Biociências, Prof. Montenegro Avenue, Botucatu, SP, BrazilUniversidade Estadual PaulistaBotucatuBrazil
| | - Fábio Porto-Foresti
- Universidade Estadual Paulista (UNESP) “Júlio de Mesquita Filho”, Faculdade de Ciências, Edmundo Carrijo Coube Avenue, Bauru, SP, BrazilUniversidade Estadual PaulistaBauruBrazil
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5
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Sember A, Pelikánová Š, de Bello Cioffi M, Šlechtová V, Hatanaka T, Do Doan H, Knytl M, Ráb P. Taxonomic Diversity Not Associated with Gross Karyotype Differentiation: The Case of Bighead Carps, Genus Hypophthalmichthys (Teleostei, Cypriniformes, Xenocyprididae). Genes (Basel) 2020; 11:E479. [PMID: 32354012 PMCID: PMC7291238 DOI: 10.3390/genes11050479] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/31/2020] [Accepted: 04/24/2020] [Indexed: 11/30/2022] Open
Abstract
The bighead carps of the genus Hypophthalmichthys (H. molitrix and H. nobilis) are important aquaculture species. They were subjected to extensive multidisciplinary research, but with cytogenetics confined to conventional protocols only. Here, we employed Giemsa-/C-/CMA3- stainings and chromosomal mapping of multigene families and telomeric repeats. Both species shared (i) a diploid chromosome number 2n = 48 and the karyotype structure, (ii) low amount of constitutive heterochromatin, (iii) the absence of interstitial telomeric sites (ITSs), (iv) a single pair of 5S rDNA loci adjacent to one major rDNA cluster, and (v) a single pair of co-localized U1/U2 snDNA tandem repeats. Both species, on the other hand, differed in (i) the presence/absence of remarkable interstitial block of constitutive heterochromatin on the largest acrocentric pair 11 and (ii) the number of major (CMA3-positive) rDNA sites. Additionally, we applied here, for the first time, the conventional cytogenetics in H. harmandi, a species considered extinct in the wild and/or extensively cross-hybridized with H. molitrix. Its 2n and karyotype description match those found in the previous two species, while silver staining showed differences in distribution of major rDNA. The bighead carps thus represent another case of taxonomic diversity not associated with gross karyotype differentiation, where 2n and karyotype structure cannot help in distinguishing between genomes of closely related species. On the other hand, we demonstrated that two cytogenetic characters (distribution of constitutive heterochromatin and major rDNA) may be useful for diagnosis of pure species. The universality of these markers must be further verified by analyzing other pure populations of bighead carps.
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Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277-21 Liběchov, Czech Republic
| | - Šárka Pelikánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277-21 Liběchov, Czech Republic
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235 cep, São Carlos 13565-905, Brazil
| | - Vendula Šlechtová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277-21 Liběchov, Czech Republic
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235 cep, São Carlos 13565-905, Brazil
| | - Hiep Do Doan
- Research Institute of Aquaculture No. 1, Dinh Bang, Tu Son, Bac Ninh 16000, Vietnam
| | - Martin Knytl
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 2-128-43 Prague, Czech Republic
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277-21 Liběchov, Czech Republic
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Pazza R, Dergam JA, Kavalco KF. Trends in Karyotype Evolution in Astyanax (Teleostei, Characiformes, Characidae): Insights From Molecular Data. Front Genet 2018; 9:131. [PMID: 29713335 PMCID: PMC5911472 DOI: 10.3389/fgene.2018.00131] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/03/2018] [Indexed: 12/05/2022] Open
Abstract
The study of patterns and evolutionary processes in neotropical fish is not always an easy task due the wide distribution of major fish groups in large and extensive river basins. Thus, it is not always possible to detect or correlate possible effects of chromosome rearrangements in the evolution of biodiversity. In the Astyanax genus, chromosome data obtained since the 1970s have shown evidence of cryptic species, karyotypic plasticity, supernumerary chromosomes, triploidies, and minor chromosomal rearrangements. In the present work, we map and discuss the main chromosomal events compatible with the molecular evolution of the genus Astyanax (Characiformes, Characidae) using mitochondrial DNA sequence data, in the search for major chromosome evolutionary trends within this taxon.
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Affiliation(s)
- Rubens Pazza
- Laboratory of Ecological and Evolutionary Genetics, Institute of Biological and Health Sciences, Federal University of Viçosa, Rio Paranaíba, Brazil
| | - Jorge A. Dergam
- Laboratory of Molecular Systematics “Beagle”, Department of Animal Biology, Federal University of Viçosa, Viçosa, Brazil
| | - Karine F. Kavalco
- Laboratory of Ecological and Evolutionary Genetics, Institute of Biological and Health Sciences, Federal University of Viçosa, Rio Paranaíba, Brazil
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Daniel SN, Penitente M, Silva DMZA, Hashimoto DT, Ferreira DC, Foresti F, Porto-Foresti F. Organization and Chromosomal Distribution of Histone Genes and Transposable Rex Elements in the Genome of Astyanax bockmanni (Teleostei, Characiformes). Cytogenet Genome Res 2015; 146:311-8. [PMID: 26618348 DOI: 10.1159/000441613] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2015] [Indexed: 11/19/2022] Open
Abstract
An important feature of eukaryotic organisms is the number of different repetitive DNA sequences in their genome, a feature not observed in prokaryotes. These sequences are considered to be important components for understanding evolutionary mechanisms and the karyotypic differentiation processes. Thus, we aimed to physically map the histone genes and transposable elements of the Rex family in 6 fish populations of Astyanax bockmanni. FISH results using a histone H1 gene probe showed fluorescent clusters in 2 chromosome pairs in all 6 samples analyzed. In contrast, FISH with a histone H3 probe showed conspicuous blocks in 4 chromosomes in 5 of the 6 populations analyzed. The sixth population revealed 7 chromosomes marked with this probe. Probes for the transposable elements Rex1 and Rex6 showed small sites dispersed on most chromosomes of the 6 populations, and the Rex3 element is located in a big block concentrated in only 1 acrocentric chromosome of 2 populations. As for the other populations, a Rex3 probe showed large blocks in more than 1 chromosome. Fish from Alambari and Campo Novo Stream have Rex3 elements dispersed along most of the chromosomes. Additionally, the conspicuous signals of Rex1, Rex3, and Rex6 were identified in the acrocentric B microchromosome of A. bockmanni found only in individuals of the Alambari River. Thus, we believe that different mechanisms drive the spread of repetitive sequences among the populations analyzed, which appear to be organized differently in the genome of A. bockmanni. The presence of transposable elements in the B chromosome also suggests that these sequences could play a role in the origin and maintenance of the supernumerary element in the genome of this species.
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Affiliation(s)
- Sandro N Daniel
- Departamento de Cix00EA;ncias Biolx00F3;gicas, Faculdade de Cix00EA;ncias, Universidade Estadual Paulista (UNESP), Bauru, Brazil
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Silva DMZA, Utsunomia R, Pansonato-Alves JC, Oliveira C, Foresti F. Chromosomal Mapping of Repetitive DNA Sequences in Five Species of Astyanax (Characiformes, Characidae) Reveals Independent Location of U1 and U2 snRNA Sites and Association of U1 snRNA and 5S rDNA. Cytogenet Genome Res 2015; 146:144-152. [PMID: 26329975 DOI: 10.1159/000438813] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2015] [Indexed: 11/19/2022] Open
Abstract
Astyanax is a genus of Characidae fishes currently composed of 155 valid species. Previous cytogenetic studies revealed high chromosomal diversification among them, and several studies have been performed using traditional cytogenetic techniques to investigate karyotypes and chromosomal locations of 18S and 5S rDNA genes. However, only a few studies are currently available about other repetitive sequences. Here, the chromosomal location of small nuclear RNA genes, identified as U1 and U2 snRNA clusters, was established and compared to the distribution of 5S rDNA and histone clusters in 5 Astyanax species (A. paranae, A. fasciatus, A. bockmanni, A. altiparanae, and A. jordani) using FISH. The cytogenetic mapping of U1 and U2 snRNA demonstrated a conserved pattern in the number of sites per genome independent of the location in Astyanax species. The location of the U1 snRNA gene was frequently associated with 5S rDNA sequences, indicating a possible interaction between the distinct repetitive DNA families. Finally, comparisons involving the location of U1 and U2 snRNA clusters in the chromosomes of Astyanax species revealed a very diverse pattern, suggesting that many rearrangements have occurred during the diversification process of this group.
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Affiliation(s)
- Duilio M Z A Silva
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
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Medrado AS, de Mello Affonso PRA, Carneiro PLS, Vicari MR, Artoni RF, Costa MA. Allopatric divergence in Astyanax aff. fasciatus Cuvier, 1819 (Characidae, Incertae sedis) inferred from DNA mapping and chromosomes. ZOOL ANZ 2015. [DOI: 10.1016/j.jcz.2015.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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10
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Daniel SN, Penitente M, Hashimoto DT, de Andrade Silva DMZ, Foresti F, Porto-Foresti F. New insights into karyotypic relationships among populations of Astyanax bockmanni (Teleostei, Characiformes) of different watersheds. Zebrafish 2015; 12:181-8. [PMID: 25714526 DOI: 10.1089/zeb.2014.1053] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The fish constitute about 50% of all vertebrates, including a wide morphological and biological diversity, where the genus Astyanax is the most common and diverse, as described in virtually all freshwater environments. By occupying a basal position in the phylogeny of vertebrates, fish are an extremely favorable group for cytogenetic and evolutionary studies. The karyotype found in genus Astyanax diversity may involve a number of polymorphisms, which may be related to ploidy and karyotypic macrostructure, presence of B chromosomes, heterochromatin polymorphisms, and location of ribosomal genes. Nevertheless, the relationship between populations of this species is still poorly studied. Thus, the present work aimed to investigate karyotype variation, chromosomal relationships, and the behavior of 5S and 18S ribosomal genes in six populations of Astyanax bockmanni. The results confirmed the diploid number of 50 chromosomes in all the populations sampled, with the occurrence of one supernumerary chromosome in just one of them. In addition, all populations showed divergent patterns of constitutive heterochromatin and repetitive nucleolar sites. The fluorescence in situ hybridization (FISH) technique using 5S and 18S rDNA probes revealed distinct patterns of distribution for these conserved genes, while 5S rDNA genes were found located in two chromosome pairs, the 18S genes showed multiple marks dispersed in the genome characterizing an inter and intraindividual polymorphic behavior, as previously reported to occur with the utilization of the Ag-NOR technique. Thus, besides minor modifications observed in chromosome morphology, the populations of A. bockmanni analyzed revealed a preserved macrostructural feature, especially concerning to the diploid number; on the other hand, differences in microstructural characteristics indicated by the nucleolus organizer region (NOR) location, constitutive heterochromatin patterns, and distribution of ribosomal genes along the genome were clearly evident in the populations from different river basins, even located at short distances.
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Affiliation(s)
- Sandro Natal Daniel
- 1 Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista (UNESP) , Bauru, São Paulo, Brazil
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Barbosa P, de Oliveira LA, Pucci MB, Santos MH, Moreira-Filho O, Vicari MR, Nogaroto V, de Almeida MC, Artoni RF. Identification and chromosome mapping of repetitive elements in the Astyanax scabripinnis (Teleostei: Characidae) species complex. Genetica 2014; 143:55-62. [PMID: 25549800 DOI: 10.1007/s10709-014-9813-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Accepted: 12/26/2014] [Indexed: 10/24/2022]
Abstract
Most part of the eukaryotic genome is composed of repeated sequences or multiple copies of DNA, which were considered as "junk DNA", and may be associated to the heterochromatin. In this study, three populations of Astyanax aff. scabripinnis from Brazilian rivers of Guaratinguetá and Pindamonhangaba (São Paulo) and a population from Maringá (Paraná) were analyzed concerning the localization of the nucleolar organizer regions (Ag-NORs), the As51 satellite DNA, the 18S ribosomal DNA (rDNA), and the 5S rDNA. Repeated sequences were also isolated and identified by the Cot - 1 method, which indicated similarity (90%) with the LINE UnaL2 retrotransposon. The fluorescence in situ hybridization (FISH) showed the retrotransposon dispersed and more concentrated markers in centromeric and telomeric chromosomal regions. These sequences were co-localized and interspaced with 18S and 5S rDNA and As51, confirmed by fiber-FISH essay. The B chromosome found in these populations pointed to a conspicuous hybridization with LINE probe, which is also co-located in As51 sequences. The NORs were active at unique sites of a homologous pair in the three populations. There were no evidences that transposable elements and repetitive DNA had influence in the transcriptional regulation of ribosomal genes in our analyses.
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Affiliation(s)
- Patrícia Barbosa
- Programa de Pós Graduação em Biologia Evolutiva, Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Avenida Carlos Cavalcanti 4748, Ponta Grossa, PR, 84030-900, Brazil
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12
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Silva DMZDA, Pansonato-Alves JC, Utsunomia R, Araya-Jaime C, Ruiz-Ruano FJ, Daniel SN, Hashimoto DT, Oliveira C, Camacho JPM, Porto-Foresti F, Foresti F. Delimiting the origin of a B chromosome by FISH mapping, chromosome painting and DNA sequence analysis in Astyanax paranae (Teleostei, Characiformes). PLoS One 2014; 9:e94896. [PMID: 24736529 PMCID: PMC3988084 DOI: 10.1371/journal.pone.0094896] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 03/19/2014] [Indexed: 12/19/2022] Open
Abstract
Supernumerary (B) chromosomes have been shown to contain a wide variety of repetitive sequences. For this reason, fluorescent in situ hybridisation (FISH) is a useful tool for ascertaining the origin of these genomic elements, especially when combined with painting from microdissected B chromosomes. In order to investigate the origin of B chromosomes in the fish species Astyanax paranae, these two approaches were used along with PCR amplification of specific DNA sequences obtained from the B chromosomes and its comparison with those residing in the A chromosomes. Remarkably, chromosome painting with the one-arm metacentric B chromosome probe showed hybridization signals on entire B chromosome, while FISH mapping revealed the presence of H1 histone and 18S rDNA genes symmetrically placed in both arms of the B chromosome. These results support the hypothesis that the B chromosome of A. paranae is an isochromosome. Additionally, the chromosome pairs Nos. 2 or 23 are considered the possible B chromosome ancestors since both contain syntenic H1 and 18S rRNA sequences. The analysis of DNA sequence fragments of the histone and rRNA genes obtained from the microdissected B chromosomes showed high similarity with those obtained from 0B individuals, which supports the intraspecific origin of B chromosomes in A. paranae. Finally, the population hereby analysed showed a female-biased B chromosome presence suggesting that B chromosomes in this species could influence sex determinism.
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Affiliation(s)
- Duílio M. Z. de A. Silva
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil
| | - José Carlos Pansonato-Alves
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil
| | - Ricardo Utsunomia
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil
| | - Cristian Araya-Jaime
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil
| | | | - Sandro Natal Daniel
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, Campus de Bauru, Bauru, São Paulo, Brazil
| | - Diogo Teruo Hashimoto
- CAUNESP, Universidade Estadual Paulista, Campus Jaboticabal, Jaboticabal, São Paulo, Brazil
| | - Cláudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil
| | | | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, Campus de Bauru, Bauru, São Paulo, Brazil
| | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil
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13
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Chromosomal organization of repetitive DNA sequences in Astyanax bockmanni (Teleostei, Characiformes): dispersive location, association and co-localization in the genome. Genetica 2013; 141:329-36. [DOI: 10.1007/s10709-013-9732-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 08/21/2013] [Indexed: 10/26/2022]
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Pansonato-Alves J, Hilsdorf A, Utsunomia R, Silva D, Oliveira C, Foresti F. Chromosomal Mapping of Repetitive DNA and Cytochrome C Oxidase I Sequence Analysis Reveal Differentiation among Sympatric Samples ofAstyanaxfasciatus(Characiformes, Characidae). Cytogenet Genome Res 2013; 141:133-42. [DOI: 10.1159/000354885] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Molecular cytogenetic characterization of the Amazon River dolphin Inia geoffrensis. Genetica 2012; 140:307-15. [PMID: 23010983 DOI: 10.1007/s10709-012-9680-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 09/08/2012] [Indexed: 10/27/2022]
Abstract
Classical and molecular cytogenetic (18S rDNA, telomeric sequence, and LINE-1 retrotransposon probes) studies were carried out to contribute to an understanding of the organization of repeated DNA elements in the Amazon River dolphin (boto, Inia geoffrensis). Twenty-seven specimens were examined, each presenting 2n = 44 chromosomes, the karyotype formula 12m + 14sm + 6st + 10t + XX/XY, and fundamental number (FN) = 74. C-positive heterochromatin was observed in terminal and interstitial positions, with the occurrence of polymorphism. Interstitial telomeric sequences were not observed. The nucleolar organizer region (NOR) was located at a single site on a smallest autosomal pair. LINE-1 was preferentially distributed in the euchromatin regions, with the greatest accumulation on the X chromosome. Although the karyotype structure in cetaceans is considered to be conserved, the boto karyotype demonstrated significant variations in its formula, heterochromatin distribution, and the location of the NOR compared to other cetacean species. These results contribute to knowledge of the chromosome organization in boto and to a better understanding of karyoevolution in cetaceans.
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