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Dulz TA, Azambuja M, Lorscheider CA, Noleto RB, Moreira-Filho O, Nogaroto V, Nascimento VD, Diniz D, de Mello Affonso PRA, Vicari MR. Repetitive DNAs and chromosome evolution in Megaleporinus obtusidens and M. reinhardti (Characiformes: Anostomidae). Genetica 2024; 152:63-70. [PMID: 38587599 DOI: 10.1007/s10709-024-00206-3] [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: 01/21/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
The high dynamism of repetitive DNAs is a major driver of chromosome evolution. In particular, the accumulation of repetitive DNA sequences has been reported as part of the differentiation of sex-specific chromosomes. In turn, the fish species of the genus Megaleporinus are a monophyletic clade in which the presence of differentiated ZZ/ZW sex chromosomes represents a synapomorphic condition, thus serving as a suitable model to evaluate the dynamic evolution of repetitive DNA classes. Therefore, transposable elements (TEs) and in tandem repeats were isolated and located on chromosomes of Megaleporinus obtusidens and M. reinhardti to infer their role in chromosome differentiation with emphasis on sex chromosome systems. Despite the conserved karyotype features of both species, the location of repetitive sequences - Rex 1, Rex 3, (TTAGGG)n, (GATA)n, (GA)n, (CA)n, and (A)n - varied both intra and interspecifically, being mainly accumulated in Z and W chromosomes. The physical mapping of repetitive sequences confirmed the remarkable dynamics of repetitive DNA classes on sex chromosomes that might have promoted chromosome diversification and reproductive isolation in Megaleporinus species.
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Affiliation(s)
- Thais Aparecida Dulz
- Graduate Program in Genetics, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Matheus Azambuja
- Graduate Program in Animal Science, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | - Carla Andrea Lorscheider
- Department of Biological Sciences, Universidade Estadual do Paraná, União da Vitória, PR, Brazil
| | - Rafael Bueno Noleto
- Department of Biological Sciences, Universidade Estadual do Paraná, União da Vitória, PR, Brazil
| | - Orlando Moreira-Filho
- Department of Genetics and Evolution, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Viviane Nogaroto
- Graduate Program in Animal Science, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | | | - Débora Diniz
- Graduate Program in Genetics, Biodiversity and Conservation, Universidade Estadual do Sudoeste da Bahia, Jequié, BA, Brazil
| | | | - Marcelo Ricardo Vicari
- Graduate Program in Genetics, Universidade Federal do Paraná, Curitiba, PR, Brazil
- Graduate Program in Animal Science, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
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2
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de Sousa E Souza JF, Guimarães EMC, Figliuolo VSP, Soares SC, de Bello Cioffi M, de Menezes Cavalcante Sassi F, Feldberg E. Chromosomal mapping of repetitive DNA and retroelement sequences and its implications for the chromosomal evolution process in Ctenoluciidae (Characiformes). BMC Ecol Evol 2024; 24:72. [PMID: 38816840 PMCID: PMC11138015 DOI: 10.1186/s12862-024-02262-x] [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: 10/03/2023] [Accepted: 05/22/2024] [Indexed: 06/01/2024] Open
Abstract
Ctenoluciidae is a Neotropical freshwater fish family composed of two genera, Ctenolucius (C. beani and C. hujeta) and Boulengerella (B. cuvieri, B. lateristriga, B. lucius, B. maculata, and B. xyrekes), which present diploid number conservation of 36 chromosomes and a strong association of telomeric sequences with ribosomal DNAs. In the present study, we performed chromosomal mapping of microsatellites and transposable elements (TEs) in Boulengerella species and Ctenolucius hujeta. We aim to understand how those sequences are distributed in these organisms' genomes and their influence on the chromosomal evolution of the group. Our results indicate that repetitive sequences may had an active role in the karyotypic diversification of this family, especially in the formation of chromosomal hotspots that are traceable in the diversification processes of Ctenoluciidae karyotypes. We demonstrate that (GATA)n sequences also accumulate in the secondary constriction formed by the 18 S rDNA site, which shows consistent size heteromorphism between males and females in all Boulengerella species, suggesting an initial process of sex chromosome differentiation.
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Grants
- 573976/2008-2 Center for Studies of Adaptation to Environmental Changes in the Amazon (INCT ADAPTA II, FAPEAM/CNPq
- 573976/2008-2 Center for Studies of Adaptation to Environmental Changes in the Amazon (INCT ADAPTA II, FAPEAM/CNPq
- 573976/2008-2 Center for Studies of Adaptation to Environmental Changes in the Amazon (INCT ADAPTA II, FAPEAM/CNPq
- 573976/2008-2 Center for Studies of Adaptation to Environmental Changes in the Amazon (INCT ADAPTA II, FAPEAM/CNPq
- 301886/2019-9 Conselho Nacional de Desenvolvimento Científico e Tecnológico , Brasil
- 301886/2019-9 Conselho Nacional de Desenvolvimento Científico e Tecnológico , Brasil
- 301886/2019-9 Conselho Nacional de Desenvolvimento Científico e Tecnológico , Brasil
- 301886/2019-9 Conselho Nacional de Desenvolvimento Científico e Tecnológico , Brasil
- 301886/2019-9 Conselho Nacional de Desenvolvimento Científico e Tecnológico , Brasil
- 301886/2019-9 Conselho Nacional de Desenvolvimento Científico e Tecnológico , Brasil
- National Institute of Amazonian Research, Brazil/PPG Genetics, Conservation and Evolutionary Biology (INPA/GCBEv)
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
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Affiliation(s)
- José Francisco de Sousa E Souza
- Conservation and Evolutionary Biology, INPA, National Amazon Research Institute, Av. André Araújo, 2936, Petrópolis, CEP: 69067-375, Caixa Postal 2223, Manaus, 69060-001, Amazonas, Brazil.
| | - Erika Milena Corrêa Guimarães
- Conservation and Evolutionary Biology, INPA, National Amazon Research Institute, Av. André Araújo, 2936, Petrópolis, CEP: 69067-375, Caixa Postal 2223, Manaus, 69060-001, Amazonas, Brazil
| | - Vanessa Susan Pinheiro Figliuolo
- Conservation and Evolutionary Biology, INPA, National Amazon Research Institute, Av. André Araújo, 2936, Petrópolis, CEP: 69067-375, Caixa Postal 2223, Manaus, 69060-001, Amazonas, Brazil
| | - Simone Cardoso Soares
- Conservation and Evolutionary Biology, INPA, National Amazon Research Institute, Av. André Araújo, 2936, Petrópolis, CEP: 69067-375, Caixa Postal 2223, Manaus, 69060-001, Amazonas, Brazil
| | - Marcelo de Bello Cioffi
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
| | | | - Eliana Feldberg
- Conservation and Evolutionary Biology, INPA, National Amazon Research Institute, Av. André Araújo, 2936, Petrópolis, CEP: 69067-375, Caixa Postal 2223, Manaus, 69060-001, Amazonas, Brazil
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3
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Khensuwan S, Supiwong W, Suwannapoom C, Buasriyot P, Jantarat S, Thongnetr W, Muanglen N, Kaewmad P, Saenjundaeng P, Seetapan K, Liehr T, Tanomtong A. A comparative cytogenetic study of Hypsibarbusmalcolmi and H.wetmorei (Cyprinidae, Poropuntiini). COMPARATIVE CYTOGENETICS 2023; 17:181-194. [PMID: 37794860 PMCID: PMC10547057 DOI: 10.3897/compcytogen.17.107703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/23/2023] [Indexed: 10/06/2023]
Abstract
Cyprininae are a highly diversified but demonstrably monophyletic lineage of cypriniform fishes. Here, the karyotype and chromosomal characteristics of Hypsibarbusmalcolmi (Smith, 1945) and H.wetmorei (Smith, 1931) were examined using conventional, nucleolus organizing regions (NORs) and molecular cytogenetic protocols. The diploid chromosome number (2n) of H.malcolmi was 50, the fundamental number (FN) was equal to 62, and the karyotype displayed 8m + 4sm + 38a with NORs located at the centromeric and telomeric positions of the short arms of chromosome pairs 1 and 2, respectively. 2n of H.wetmorei was 50, FN 78, karyotype 14m + 14sm + 22a with the NORs at the telomeric position of the short arm of chromosome pair 2. 2n and FN in males and females were identical. Fluorescence in situ hybridization using different microsatellite motifs as probes also showed substantial genomic divergence between both studied species. In H.wetmorei, (CAG)n and (CAC)n microsatellites accumulated in the telomeric regions of all chromosomes, while in H.malcolmi, they had scattered signals on all chromosomes. Besides, the (GAA)n microsatellites were distributed along all chromosomes of H.malcolmi, but there was a strong hybridization pattern in the centromeric region of a single pair in H.wetmorei. These cytogenomic difference across the genomes of these Hypsibarbus Rainboth, 1996 species are markers for specific evolutionary differentiation within these two species.
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Affiliation(s)
- Sudarat Khensuwan
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Weerayuth Supiwong
- Faculty of Interdisciplinary Studies, Khon Kaen University, Nong Khai Campus, Muang, Nong Khai 43000, Thailand
| | - Chatmongkon Suwannapoom
- Department of Fishery, School of Agriculture and Natural Resources, University of Phayao, Muang, Phayao 56000, Thailand
| | - Phichaya Buasriyot
- Faculty of Science and Technology, Rajamangala University of Technology Suvarnabhumi, Mueang Nonthaburi, Nonthaburi 11000, Thailand
| | - Sitthisak Jantarat
- Department of Science, Faculty of Science and Technology, Prince of Songkla University, Pattani 94000, Thailand
| | - Weera Thongnetr
- Division of Biology, Department of Science, Faculty of Science and Technology, Rajamangala University of Technology Krungthep, Bangkok 10120, Thailand
| | - Nawarat Muanglen
- Department of Fisheries, Faculty of Agricultural Technology, Sakon Nakhon Rajabhat University, Sakon Nakhon 47000, Thailand
| | - Puntivar Kaewmad
- Faculty of Science and Technology, Mahasarakham Rajabhat University, Muang, Maha Sarakham 44000, Thailand
| | - Pasakorn Saenjundaeng
- Faculty of Interdisciplinary Studies, Khon Kaen University, Nong Khai Campus, Muang, Nong Khai 43000, Thailand
| | - Kriengkrai Seetapan
- Department of Fishery, School of Agriculture and Natural Resources, University of Phayao, Muang, Phayao 56000, Thailand
| | - Thomas Liehr
- School of Agriculture and Natural Resources, University of Phayao, Tumbol Maeka, Muang District, Phayao Province, 56000 Thailand
| | - Alongklod Tanomtong
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
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Nirchio Tursellino M, de Bello Cioffi M, de Menezes Cavalcante Sassi F, Deon GA, Oliveira C, Kuranaka M, Valdiviezo-Rivera J, Gonzalez VH, Rossi AR. Integrating Genomic and Chromosomal Data: A Cytogenetic Study of Transancistrus santarosensis (Loricariidae: Hypostominae) with Characterization of a ZZ/ZW Sex Chromosome System. Genes (Basel) 2023; 14:1662. [PMID: 37761802 PMCID: PMC10531053 DOI: 10.3390/genes14091662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/14/2023] [Accepted: 08/19/2023] [Indexed: 09/29/2023] Open
Abstract
The plecos (Loricariidae) fish represent a great model for cytogenetic investigations due to their variety of karyotypes, including diploid and polyploid genomes, and different types of sex chromosomes. In this study we investigate Transancistrus santarosensis a rare loricariid endemic to Ecuador, integrating cytogenetic methods with specimens' molecular identification by mtDNA, to describe the the species karyotype. We aim to verify whether sex chromosomes are cytologically identifiable and if they are associated with the accumulation of repetitive sequences present in other species of the family. The analysis of the karyotype (2n = 54 chromosomes) excludes recent centric fusion and pericentromeric inversion and suggests the presence of a ZZ/ZW sex chromosome system at an early stage of differentiation: the W chromosome is degenerated but is not characterized by the presence of differential sex-specific repetitive DNAs. Data indicate that although T. santarosensis has retained the ancestral diploid number of Loricariidae, it accumulated heterochromatin and shows non-syntenic ribosomal genes localization, chromosomal traits considered apomorphic in the family.
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Affiliation(s)
- Mauro Nirchio Tursellino
- Departamento de Acuicultura, Universidad Técnica de Machala, Av. Panamericana km 5.5, Vía Pasaje, Machala 070150, El Oro, Ecuador;
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-090, SP, Brazil; (M.d.B.C.); (F.d.M.C.S.); (G.A.D.)
| | | | - Geize Aparecida Deon
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-090, SP, Brazil; (M.d.B.C.); (F.d.M.C.S.); (G.A.D.)
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências Universidade Estadual Paulista-UNESP, Botucatu 18618-689, SP, Brazil; (C.O.); (M.K.)
| | - Mariana Kuranaka
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências Universidade Estadual Paulista-UNESP, Botucatu 18618-689, SP, Brazil; (C.O.); (M.K.)
| | - Jonathan Valdiviezo-Rivera
- Instituto Nacional de Biodiversidad, Rumipamba No. 341 y Av. Shyris, Parque La Carolina, Quito 170135, Pichincha, Ecuador;
| | - Víctor Hugo Gonzalez
- Departamento de Acuicultura, Universidad Técnica de Machala, Av. Panamericana km 5.5, Vía Pasaje, Machala 070150, El Oro, Ecuador;
| | - Anna Rita Rossi
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza—Università di Roma, Via Alfonso Borelli 50, 00161 Rome, Italy;
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Haerter CAG, Blanco DR, Traldi JB, Feldberg E, Margarido VP, Lui RL. Are scattered microsatellites weak chromosomal markers? Guided mapping reveals new insights into Trachelyopterus (Siluriformes: Auchenipteridae) diversity. PLoS One 2023; 18:e0285388. [PMID: 37310952 DOI: 10.1371/journal.pone.0285388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 04/22/2023] [Indexed: 06/15/2023] Open
Abstract
The scattered distribution pattern of microsatellites is a challenging problem in fish cytogenetics. This type of array hinders the identification of useful patterns and the comparison between species, often resulting in over-limited interpretations that only label it as "scattered" or "widely distributed". However, several studies have shown that the distribution pattern of microsatellites is non-random. Thus, here we tested whether a scattered microsatellite could have distinct distribution patterns on homeologous chromosomes of closely related species. The clustered sites of 18S and 5S rDNA, U2 snRNA and H3/H4 histone genes were used as a guide to compare the (GATA)n microsatellite distribution pattern on the homeologous chromosomes of six Trachelyopterus species: T. coriaceus and Trachelyopterus aff. galeatus from the Araguaia River basin; T. striatulus, T. galeatus and T. porosus from the Amazonas River basin; and Trachelyopterus aff. coriaceus from the Paraguay River basin. Most species had similar patterns of the (GATA)n microsatellite in the histone genes and 5S rDNA carriers. However, we have found a chromosomal polymorphism of the (GATA)n sequence in the 18S rDNA carriers of Trachelyopterus galeatus, which is in Hard-Weinberg equilibrium and possibly originated through amplification events; and a chromosome polymorphism in Trachelyopterus aff. galeatus, which combined with an inversion polymorphism of the U2 snRNA in the same chromosome pair resulted in six possible cytotypes, which are in Hardy-Weinberg disequilibrium. Therefore, comparing the distribution pattern on homeologous chromosomes across the species, using gene clusters as a guide to identify it, seems to be an effective way to further the analysis of scattered microsatellites in fish cytogenetics.
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Affiliation(s)
| | | | - Josiane Baccarin Traldi
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Brasil
| | | | - Vladimir Pavan Margarido
- Universidade Estadual do Oeste do Paraná, Centro de Ciências Biológicas e da Saúde, Cascavel, Paraná, Brasil
| | - Roberto Laridondo Lui
- Universidade Estadual do Oeste do Paraná, Centro de Ciências Biológicas e da Saúde, Cascavel, Paraná, Brasil
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6
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Venancio S, Noleto RB, Azambuja M, Gazolla CB, Santos BR, Nogaroto V, Vicari MR. Comparative cytogenetics among Boana species (Anura, Hylidae): focus on evolutionary variability of repetitive DNA. Genet Mol Biol 2023; 45:e20220203. [PMID: 36622243 PMCID: PMC9827724 DOI: 10.1590/1678-4685-gmb-2022-0203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 11/08/2022] [Indexed: 01/10/2023] Open
Abstract
Boana comprises a diverse genus of Neotropical treefrogs, currently rearranged into seven taxonomic species groups. Although cytogenetic studies have demonstrated diversity in its representatives, the chromosomal mapping of repetitive DNA sequences is still scarce. In this study, Boana albopunctata, Boana faber, and Boana prasina were subjected to in situ localization of different repetitive DNA units to evaluate trends of chromosomal evolution in this genus. Boana faber and B. prasina had 2n=24 chromosomes, while B. albopunctata has 2n=22 and an intra-individual variation related to the presence/absence of one B chromosome. The location of 45S rDNA sites was different in the analyzed karyotypes, corroborating with what was found in the distinct phylogenetic groups of Boana. We presented the first description of 5S rDNA in a Boana species, which showed markings resulting from transposition/translocation mechanisms. In situ localization of microsatellite loci proved to be a helpful marker for karyotype comparison in Boana, commonly with cis accumulation in the heterochromatin. On the other hand, genomic dispersion of microsatellites may be associated with hitchhiking effects during the spreading of transposable elements. The obtained results corroborated the independent diversification of these lineages of species from three distinct phylogenetic groups of Boana.
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Affiliation(s)
- Sebastião Venancio
- Universidade Federal do Paraná, Centro Politécnico, Departamento de
Genética, Programa de Pós-Graduação em Genética, Curitiba, PR, Brazil
| | - Rafael Bueno Noleto
- Universidade Estadual do Paraná, Departamento de Biologia, União da
Vitória, PR, Brazil
| | - Matheus Azambuja
- Universidade Federal do Paraná, Centro Politécnico, Departamento de
Genética, Programa de Pós-Graduação em Genética, Curitiba, PR, Brazil
| | - Camilla Borges Gazolla
- Universidade Federal do Paraná, Centro Politécnico, Departamento de
Genética, Programa de Pós-Graduação em Genética, Curitiba, PR, Brazil
| | - Bianca Rocha Santos
- Universidade Estadual do Paraná, Departamento de Biologia, União da
Vitória, PR, Brazil
| | - Viviane Nogaroto
- Universidade Estadual de Ponta Grossa, Departamento de Biologia
Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
| | - Marcelo Ricardo Vicari
- Universidade Federal do Paraná, Centro Politécnico, Departamento de
Genética, Programa de Pós-Graduação em Genética, Curitiba, PR, Brazil.,Universidade Estadual de Ponta Grossa, Departamento de Biologia
Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
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7
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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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8
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Santos da Silva K, Glugoski L, Vicari MR, de Souza ACP, Noronha RCR, Pieczarka JC, Nagamachi CY. Chromosomal Diversification in Ancistrus Species (Siluriformes: Loricariidae) Inferred From Repetitive Sequence Analysis. Front Genet 2022; 13:838462. [PMID: 35401670 PMCID: PMC8987504 DOI: 10.3389/fgene.2022.838462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/25/2022] [Indexed: 11/25/2022] Open
Abstract
The Ancistrus genus has extensive chromosomal diversity among species, including heteromorphic sex chromosomes occurrence. However, studies have been shown that chromosomal diversity may still be underestimated. Repetitive sequences represent a large part of eukaryotic genomes, associated with mechanisms of karyotypic diversification, including sex chromosomes evolution. This study analyzed the karyotype diversification of two Ancistrus species (Ancistrus sp. 1 and Ancistrus sp. 2) from the Amazon region by classical and molecular chromosomal markers. Conventional chromosome bands and fluorescence in situ hybridization using probes 18S and 5S rDNA, besides (CA)n, (CG)n, (GA)n, (CAC)n, (CAG)n, (CAT)n, (GAA)n, (GAC)n, (TAA)n, and (TTAGGG)n in tandem repeats were determined on the karyotypes. Ancistrus sp. 1 and Ancistrus sp. 2 presented karyotypes with 2n = 38 (20 m + 14sm+4st, XX/XY) and 2n = 34 (20 m + 14sm, without heteromorphic sex chromosomes), respectively. Robertsonian rearrangements can explain the diploid number difference. C-bands occurred in pericentromeric regions in some chromosomes, and a single 18S rDNA locus occurred in both species. The 5S rDNA showed variation in the number of loci between species karyotypes, suggesting the occurrence of unstable sites and rearrangements associated with these sequences in Ancistrus. The microsatellite mapping evidenced distinct patterns of organization between the two analyzed species, occurring mainly in the sex chromosomes in Ancistrus sp. 1, and in the centromeric and pericentromeric regions of chromosomes m/sm in Ancistrus sp. 2. These data shows the extensive chromosomal diversity of repetitive sequences in Ancistrus, which were involved in Robertsonian rearrangements and sex chromosomes differentiation.
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Affiliation(s)
- Kevin Santos da Silva
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Larissa Glugoski
- Laboratório de Citogenética de Peixes, Universidade Federal de São Carlos, São Carlos, Brazil
- Laboratório de Biologia Cromossômica: Estrutura e Função, Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Marcelo Ricardo Vicari
- Laboratório de Biologia Cromossômica: Estrutura e Função, Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Augusto César Paes de Souza
- Laboratório de Estudo da Ictiofauna Amazônica, Instituto Federal de Educação, Ciência e Tecnologia do Pará, Abaetetuba, Brazil
| | - Renata Coelho Rodrigues Noronha
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
- *Correspondence: Cleusa Yoshiko Nagamachi, ,
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9
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Pinheiro Figliuolo VS, Ferreira AMV, Guimarães EMC, de Sousa E Souza JF, Feldberg E, Gross MC. Cryptic Diversity in the Terminal Portion of the Chromosomes of the Dogtooth Characins, Family Cynodontidae (Ostariophysi: Characiformes). Zebrafish 2021; 18:221-230. [PMID: 33847525 DOI: 10.1089/zeb.2020.1973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The chromosomes of the dogtooth characins, fish species of the family Cynodontidae, have only a relatively small amount of heterochromatin, including the terminal portion. Curiously, in the cynodontid Cynodon gibbus, the terminal portion is rich in repetitive DNAs, including transposable retroelements and microsatellite sequences. Given this, this study investigated the composition of the terminal portion of the chromosomes of two cynodontid species (Rhaphiodon vulpinus and Hydrolycus armatus), to compile a database for the evaluation of all three cynodontid genera, and in particular, verify the possible tendency for the accumulation of repetitive DNAs in the terminal portion of the chromosomes of C. gibbus, H. armatus, and R. vulpinus. The Rex1, Rex3, and Rex6 transposable retroelements and the (CA)15, (GA)15, (GATA)8, (GACA)8, (CAT)10, and (CAC)10 microsatellite motifs are found primarily in the terminal portion of the chromosomes of the species analyzed in this study, except R. vulpinus, which has no evidence of the presence of Rex1 or Rex3 through the fluorescent in situ hybridization technique. The mapping of the repetitive sequences, principally the microsatellite motifs, indicates a marked tendency for the accumulation of these sequences in the terminal portions of the chromosomes, which may have played a fundamental role in the differentiation of the three species.
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Affiliation(s)
| | | | | | | | - Eliana Feldberg
- Laboratory of Animal Genetics, National Institute of Amazonian Research (INPA), Manaus, Brazil
| | - Maria Claudia Gross
- Institute for Natural and Life Sciences, Federal University of Latin American Integration, Foz do Iguaçu, Brazil
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Bueno GDP, Gatto KP, Gazolla CB, Leivas PT, Struett MM, Moura M, Bruschi DP. Cytogenetic characterization and mapping of the repetitive DNAs in Cycloramphus bolitoglossus (Werner, 1897): More clues for the chromosome evolution in the genus Cycloramphus (Anura, Cycloramphidae). PLoS One 2021; 16:e0245128. [PMID: 33439901 PMCID: PMC7806164 DOI: 10.1371/journal.pone.0245128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/22/2020] [Indexed: 01/13/2023] Open
Abstract
Cycloramphus bolitoglossus (Werner, 1897) is a rare species with a low population density in the Serra do Mar region of Paraná and Santa Catarina, in southern Brazil. Currently, it has been assigned to the Near Threatened (NT) category in the Brazilian List of Endangered Animal Species. Here, we described the karyotype of this species for the first time and investigated the patterns of some repetitive DNA classes in the chromosomes using molecular cytogenetic approaches. We isolated, sequenced and mapped the 5S rDNA and the satellite DNA PcP190 of C. bolitoglossus, as well as mapped the telomeric sequences and seven microsatellites motifies [(GA)15, (CA)15, (GACA)4, (GATA)8, (CAG)10, (CGC)10, and (GAA)]10. Cycloramphus bolitoglossus has 2n = 26 chromosomes and a fundamental number (FN) equal to 52, with a highly conserved karyotype compared to other genus members. Comparative cytogenetic under the phylogenetic context of genus allowed evolutionary interpretations of the morphological changes in the homologs of pairs 1, 3, and 6 along with the evolutionary history of Cycloramphus. Two subtypes of 5S rDNA type II were isolated in C. bolitoglossus genome, and several comparative analysis suggests mixed effects of concerted and birth-and-death evolution acting in this repetitive DNA. The 5S rDNA II subtype "a" and "b" was mapped on chromosome 1. However, their different position along chromosome 1 provide an excellent chromosome marker for future studies. PcP190 satellite DNA, already reported for species of the families Hylidae, Hylodidae, Leptodactylidae, and Odontophrynidae, is scattered throughout the C. bolitoglossus genome, and even non-heterochromatic regions showed hybridization signals using the PcP190 probe. Molecular analysis suggests that PcP190 satellite DNA exhibit a high-level of homogenization of this sequence in the genome of C. bolitoglossus. The PcP190 satDNA from C. bolitoglossus represents a novel sequence group, compared to other anurans, based on its hypervariable region. Overall, the present data on repetitive DNA sequences showed pseudogenization evidence and corroborated the hypothesis of the emergence of satDNA from rDNA 5S clusters. These two arguments that reinforced the importance of the birth-and-death evolutionary model to explain 5S rDNA patterns found in anuran genomes.
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Affiliation(s)
- Gislayne de Paula Bueno
- Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil
| | - Kaleb Pretto Gatto
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista, (UNESP), Rio Claro, São Paulo, Brazil
| | - Camilla Borges Gazolla
- Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil
| | - Peterson T. Leivas
- Curso de Ciências Biológicas, Universidade Positivo (UP), Curitiba, Paraná, Brazil
| | - Michelle M. Struett
- Departamento de Zoologia, Setor de Ciências Biológicas, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil
| | - Maurício Moura
- Departamento de Zoologia, Setor de Ciências Biológicas, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil
| | - Daniel Pacheco Bruschi
- Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil
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11
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Machado CRD, Domit C, Pucci MB, Gazolla CB, Glugoski L, Nogaroto V, Vicari MR. Heterochromatin and microsatellites detection in karyotypes of four sea turtle species: Interspecific chromosomal differences. Genet Mol Biol 2020; 43:e20200213. [PMID: 33270075 PMCID: PMC7734918 DOI: 10.1590/1678-4685-gmb-2020-0213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/08/2020] [Indexed: 12/27/2022] Open
Abstract
The wide variation in size and content of eukaryotic genomes is mainly attributed to the accumulation of repetitive DNA sequences, like microsatellites, which are tandemly repeated DNA sequences. Sea turtles share a diploid number (2n) of 56, however recent molecular cytogenetic data have shown that karyotype conservatism is not a rule in the group. In this study, the heterochromatin distribution and the chromosomal location of microsatellites (CA)n, (GA)n, (CAG)n, (GATA)n, (GAA)n, (CGC)n and (GACA)n in Chelonia mydas, Caretta caretta, Eretmochelys imbricata and Lepidochelys olivacea were comparatively investigated. The obtained data showed that just the (CA)n, (GA)n, (CAG)n and (GATA)n microsatellites were located on sea turtle chromosomes, preferentially in heterochromatic regions of the microchromosomes (mc). Variations in the location of heterochromatin and microsatellites sites, especially in some pericentromeric regions of macrochromosomes, corroborate to proposal of centromere repositioning occurrence in Cheloniidae species. Furthermore, the results obtained with the location of microsatellites corroborate with the temperature sex determination mechanism proposal and the absence of heteromorphic sex chromosomes in sea turtles. The findings are useful for understanding part of the karyotypic diversification observed in sea turtles, especially those that explain the diversification of Carettini from Chelonini species.
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Affiliation(s)
- Caroline Regina Dias Machado
- Universidade Federal do Paraná, Centro Politécnico, Departamento de
Genética, Programa de Pós-Graduação em Genética, Curitiba, Ponta Grossa, PR,
Brazil
| | - Camila Domit
- Universidade Federal do Paraná, Laboratório de Ecologia e
Conservação, Pontal do Paraná, PR, Brazil
| | | | - Camilla Borges Gazolla
- Universidade Federal do Paraná, Centro Politécnico, Departamento de
Genética, Programa de Pós-Graduação em Genética, Curitiba, Ponta Grossa, PR,
Brazil
| | - Larissa Glugoski
- Universidade Federal de São Carlos, Programa de Pós-Graduação em
Genética Evolutiva e Biologia Molecular, São Carlos, SP, Brazil
| | - Viviane Nogaroto
- Universidade Estadual de Ponta Grossa, Departamento de Biologia
Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
| | - Marcelo Ricardo Vicari
- Universidade Federal do Paraná, Centro Politécnico, Departamento de
Genética, Programa de Pós-Graduação em Genética, Curitiba, Ponta Grossa, PR,
Brazil
- Universidade Estadual de Ponta Grossa, Departamento de Biologia
Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
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Ditcharoen S, Sassi FDMC, Bertollo LAC, Molina WF, Liehr T, Saenjundaeng P, Tanomtong A, Supiwong W, Suwannapoom C, Cioffi MDB. Comparative chromosomal mapping of microsatellite repeats reveals divergent patterns of accumulation in 12 Siluridae (Teleostei: Siluriformes) species. Genet Mol Biol 2020; 43:e20200091. [PMID: 33156890 PMCID: PMC7654372 DOI: 10.1590/1678-4685-gmb-2020-0091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 09/03/2020] [Indexed: 01/08/2023] Open
Abstract
The freshwater family Siluridae occurs in Eurasia and is especially speciose in South and Southeast Asia, representing an important aquaculture and fishery targets. However, despite the restricted cytogenetic data, a high diploid number variation (from 2n=40 to 92) characterizes this fish group. Considering the large genomic divergence among its species, silurid genomes have experienced an enormous diversification throughout their evolutionary history. Here, we aim to investigate the chromosomal distribution of several microsatellite repeats in 12 Siluridae species and infer about their possible roles in the karyotype evolution that occurred in this group. Our results indicate divergent patterns of microsatellite distribution and accumulation among the analyzed species. Indeed, they are especially present in significant chromosome locations, such as the centromeric and telomeric regions, precisely the ones associated with several kinds of chromosomal rearrangements. Our data provide pieces of evidence that repetitive DNAs played a direct role in fostering the chromosomal differentiation and biodiversity in this fish family.
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Affiliation(s)
- Sukhonthip Ditcharoen
- Khon Kaen UniversityKhon Kaen UniversityDepartment of BiologyMuangKhon KaenThailandKhon Kaen University, Faculty of Science, Department of
Biology, Toxic Substances in Livestock and Aquatic Animals Research Group, Muang, Khon Kaen,
Thailand.
| | - Francisco de Menezes Cavalcante Sassi
- Universidade Federal de São Carlos
(UFSCar)Universidade Federal de São Carlos (UFSCar)Departamento de Genética e
EvoluçãoSão CarlosSPBrazilUniversidade Federal de São Carlos (UFSCar),
Departamento de Genética e Evolução, São Carlos, SP,
Brazil.
| | - Luiz Antonio Carlos Bertollo
- Universidade Federal de São Carlos
(UFSCar)Universidade Federal de São Carlos (UFSCar)Departamento de Genética e
EvoluçãoSão CarlosSPBrazilUniversidade Federal de São Carlos (UFSCar),
Departamento de Genética e Evolução, São Carlos, SP,
Brazil.
| | - Wagner Franco Molina
- Universidade Federal do Rio Grande do NorteUniversidade Federal do Rio Grande do NorteDepartamento de Biologia Celular e GenéticaNatalRNBrazilUniversidade Federal do Rio Grande do Norte (UFRN), Centro de
Biociências, Departamento de Biologia Celular e Genética, Natal, RN,
Brazil.
| | - Thomas Liehr
- University Hospital JenaUniversity Hospital JenaInstitute of Human GeneticsJenaGermanyUniversity Hospital Jena, Institute of Human Genetics, Jena,
Germany.
| | - Pasakorn Saenjundaeng
- Khon Kaen UniversityKhon Kaen UniversityFaculty of Applied Science and EngineeringMuangNong KhaiThailandKhon Kaen University, Faculty of Applied Science and
Engineering, Nong Khai Campus, Muang, Nong Khai, Thailand.
| | - Alongklod Tanomtong
- Khon Kaen UniversityKhon Kaen UniversityDepartment of BiologyMuangKhon KaenThailandKhon Kaen University, Faculty of Science, Department of
Biology, Toxic Substances in Livestock and Aquatic Animals Research Group, Muang, Khon Kaen,
Thailand.
| | - Weerayuth Supiwong
- Khon Kaen UniversityKhon Kaen UniversityFaculty of Applied Science and EngineeringMuangNong KhaiThailandKhon Kaen University, Faculty of Applied Science and
Engineering, Nong Khai Campus, Muang, Nong Khai, Thailand.
| | - Chatmongkon Suwannapoom
- University of PhayaoUniversity of PhayaoDepartment of FisherySchool of Agriculture and Natural ResourcesMuang PhayaoThailandUniversity of Phayao, School of Agriculture and Natural
Resources, Department of Fishery, Muang Phayao, Thailand.
| | - Marcelo de Bello Cioffi
- Universidade Federal de São Carlos
(UFSCar)Universidade Federal de São Carlos (UFSCar)Departamento de Genética e
EvoluçãoSão CarlosSPBrazilUniversidade Federal de São Carlos (UFSCar),
Departamento de Genética e Evolução, São Carlos, SP,
Brazil.
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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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Schemberger MO, Nascimento VD, Coan R, Ramos É, Nogaroto V, Ziemniczak K, Valente GT, Moreira-Filho O, Martins C, Vicari MR. DNA transposon invasion and microsatellite accumulation guide W chromosome differentiation in a Neotropical fish genome. Chromosoma 2019; 128:547-560. [DOI: 10.1007/s00412-019-00721-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/25/2019] [Accepted: 08/06/2019] [Indexed: 11/28/2022]
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15
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Traldi JB, Ziemniczak K, de Fátima Martinez J, Blanco DR, Lui RL, Schemberger MO, Nogaroto V, Moreira-Filho O, Vicari MR. Chromosome Mapping of H1 and H4 Histones in Parodontidae (Actinopterygii: Characiformes): Dispersed and/or Co-Opted Transposable Elements? Cytogenet Genome Res 2019; 158:106-113. [PMID: 31203273 DOI: 10.1159/000500987] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2019] [Indexed: 01/22/2023] Open
Abstract
The karyotypes of the family Parodontidae consist of 2n = 54 chromosomes. The main chromosomal evolutionary changes of its species are attributed to chromosome rearrangements in repetitive DNA regions in their genomes. Physical mapping of the H1 and H4 histones was performed in 7 Parodontidae species to analyze the chromosome rearrangements involved in karyotype diversification in the group. In parallel, the observation of a partial sequence of an endogenous retrovirus (ERV) retrotransposon in the H1 histone sequence was evaluated to verify molecular co-option of the transposable elements (TEs) and to assess paralogous sequence dispersion in the karyotypes. Six of the studied species had an interstitial histone gene cluster in the short arm of the autosomal pair 13. Besides this interstitial cluster, in Apareiodon davisi, a probable further site was detected in the terminal region of the long arm in the same chromosome pair. The H1/H4 clusters in Parodon cf. pongoensis were located in the smallest chromosomes (pair 20). In addition, scattered H1 signals were observed on the chromosomes in all species. The H1 sequence showed an ERV in the open reading frame (ORF), and the scattered H1 signals on the chromosomes were attributed to the ERV's location. The H4 sequence had no similarity to the TEs and displayed no dispersed signals. Furthermore, the degeneration of the inner ERV in the H1 sequence (which overlapped a stretch of the H1 ORF) was discussed regarding the likelihood of molecular co-option of this retroelement in histone gene function in Parodontidae.
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Evolutionary Insights of the ZW Sex Chromosomesin Snakes: A New Chapter Added by the AmazonianPuffing Snakes of the Genus Spilotes. Genes (Basel) 2019; 10:genes10040288. [PMID: 30970650 PMCID: PMC6523457 DOI: 10.3390/genes10040288] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/12/2019] [Accepted: 03/31/2019] [Indexed: 01/16/2023] Open
Abstract
Amazonian puffing snakes (Spilotes; Colubridae) are snakes widely distributed in the Neotropical region. However, chromosomal data are scarce in this group and, when available, are only limited to karyotype description using conventional staining. In this paper, we focused on the process of karyotype evolution and trends for sex chromosomes in two Amazonian Puffer Snakes (S. pulllatus and S. sulphureus). We performed an extensive karyotype characterization using conventional and molecular cytogenetic approaches. The karyotype of S. sulphureus (presented here for the first time) exhibits a 2n = 36, similar to that previously described in S. pullatus. Both species have highly differentiated ZZ/ZW sex chromosomes, where the W chromosome is highly heterochromatic in S. pullatus but euchromatic in S. sulphureus. Both W chromosomes are homologous between these species as revealed by cross-species comparative genomic hybridization, even with heterogeneous distributions of several repetitive sequences across their genomes, including on the Z and on the W chromosomes. Our study provides evidence that W chromosomes in these two species have shared ancestry.
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Pucci MB, Nogaroto V, Bertollo LAC, Orlando Moreira-Filho, Vicari MR. The karyotypes and evolution of ZZ/ZW sex chromosomes in the genus Characidium (Characiformes, Crenuchidae). COMPARATIVE CYTOGENETICS 2018; 12:421-438. [PMID: 30310546 PMCID: PMC6177511 DOI: 10.3897/compcytogen.v12i3.28736] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/07/2018] [Indexed: 09/29/2023]
Abstract
Available data on cytotaxonomy of the genus Characidium Reinhardt, 1867, which contains the greatest number of species in the Characidiinae (Crenuchidae), with 64 species widely distributed throughout the Neotropical region, were summarized and reviewed. Most Characidium species have uniform diploid chromosome number (2n) = 50 and karyotype with 32 metacentric (m) and 18 submetacentric (sm) chromosomes. The maintenance of the 2n and karyotypic formula in Characidium implies that their genomes did not experience large chromosomal rearrangements during species diversification. In contrast, the internal chromosomal organization shows a dynamic differentiation among their genomes. Available data indicated the role of repeated DNA sequences in the chromosomal constitution of the Characidium species, particularly, in sex chromosome differentiation. Karyotypes of the most Characidium species exhibit a heteromorphic ZZ/ZW sex chromosome system. The W chromosome is characterized by high rates of repetitive DNA accumulation, including satellite, microsatellite, and transposable elements (TEs), with a varied degree of diversification among species. In the current review, the main Characidium cytogenetic data are presented, highlighting the major features of its karyotype and sex chromosome evolution. Despite the conserved karyotypic macrostructure with prevalent 2n = 50 chromosomes in Characidium, herein we grouped the main cytogenetic information which led to chromosomal diversification in this Neotropical fish group.
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Affiliation(s)
- Marcela Baer Pucci
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235, 13565-905, São Carlos, São Paulo State, BrazilUniversidade Federal de São CarlosSão CarlosBrazil
| | - Viviane Nogaroto
- Departamanento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Av. Carlos Cavalcanti, 4748, 84030-900, Ponta Grossa, Paraná State, BrazilUniversidade Estadual de Ponta GrossaPonta GrossaBrazil
| | - Luiz Antonio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235, 13565-905, São Carlos, São Paulo State, BrazilUniversidade Federal de São CarlosSão CarlosBrazil
| | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235, 13565-905, São Carlos, São Paulo State, BrazilUniversidade Federal de São CarlosSão CarlosBrazil
| | - Marcelo Ricardo Vicari
- Departamanento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Av. Carlos Cavalcanti, 4748, 84030-900, Ponta Grossa, Paraná State, BrazilUniversidade Estadual de Ponta GrossaPonta GrossaBrazil
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Saenjundaeng P, de Bello Cioffi M, de Oliveira EA, Tanomtong A, Supiwong W, Phimphan S, Collares-Pereira MJ, Sember A, Bertollo LAC, Liehr T, Yano CF, Hatanaka T, Ráb P. Chromosomes of Asian cyprinid fishes: cytogenetic analysis of two representatives of small paleotetraploid tribe Probarbini. Mol Cytogenet 2018; 11:51. [PMID: 30202442 PMCID: PMC6123905 DOI: 10.1186/s13039-018-0399-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 08/23/2018] [Indexed: 12/01/2022] Open
Abstract
Background Polyploidy, although still poorly explored, represents an important evolutionary event in several cyprinid clades. Herein, Catlocarpio siamensis and Probarbus jullieni - representatives of the paleotetraploid tribe Probarbini, were characterized both by conventional and molecular cytogenetic methods. Results Alike most other paleotetraploid cyprinids (with 2n = 100), both species studied here shared 2n = 98 but differed in karyotypes: C. siamensis displayed 18m + 34sm + 46st/a; NF = 150, while P. jullieni exhibited 26m + 14sm + 58st/a; NF = 138. Fluorescence in situ hybridization (FISH) with rDNA probes revealed two (5S) and eight (18S) signals in C. siamensis, respectively, and six signals for both probes in P. jullieni. FISH with microsatellite motifs evidenced substantial genomic divergence between both species. The almost doubled size of the chromosome pairs #1 in C. siamensis and #14 in P. jullieni compared to the rest of corresponding karyotypes indicated chromosomal fusions. Conclusion Based on our findings, together with likely the same reduced 2n = 98 karyotypes in the remainder Probarbini species, we hypothesize that the karyotype 2n = 98 might represent a derived character, shared by all members of the Probarbini clade. Besides, we also witnessed considerable changes in the amount and distribution of certain repetitive DNA classes, suggesting complex post-polyploidization processes in this small paleotetraploid tribe.
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Affiliation(s)
- Pasakorn Saenjundaeng
- 1Toxic Substances in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Muang District, Khon Kaen, Thailand
| | - Marcelo de Bello Cioffi
- 2Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Ezequiel Aguiar de Oliveira
- 2Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP Brazil.,Secretaria de Estado de Educação de Mato Grosso - SEDUC-MT, Cuiabá, MT Brazil
| | - Alongklod Tanomtong
- 1Toxic Substances in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Muang District, Khon Kaen, Thailand
| | - Weerayuth Supiwong
- 4Faculty of Applied Science and Engineering, Khon Kaen University, Nong Kai Campus, Muang, Nong Kai Thailand
| | - Sumalee Phimphan
- 1Toxic Substances in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Muang District, Khon Kaen, Thailand
| | - Maria João Collares-Pereira
- 5Faculdade de Ciencias, Centre for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Campo Grande, PT-1749-016 Lisbon, Portugal
| | - Alexandr Sember
- 6Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | | | - Thomas Liehr
- 7Institute of Human Genetics, Jena University Hospital, Am Klinikum 1, D-07747 Jena, Germany
| | - Cassia Fernanda Yano
- 2Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Terumi Hatanaka
- 2Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Petr Ráb
- 6Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
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Pucci MB, Nogaroto V, Moreira-Filho O, Vicari MR. Dispersion of transposable elements and multigene families: Microstructural variation in Characidium (Characiformes: Crenuchidae) genomes. Genet Mol Biol 2018; 41:585-592. [PMID: 30043833 PMCID: PMC6136364 DOI: 10.1590/1678-4685-gmb-2017-0121] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 11/29/2017] [Indexed: 12/16/2022] Open
Abstract
Eukaryotic genomes consist of several repetitive DNAs, including dispersed DNA
sequences that move between chromosome sites, tandem repeats of DNA sequences,
and multigene families. In this study, repeated sequences isolated from the
genome of Characidium gomesi were analyzed and mapped to
chromosomes in Characidium zebra and specimens from two
populations of C. gomesi. The sequences were transposable
elements (TEs) named retroelement of Xiphophorus (Rex);
multigene families of U2 small nuclear RNA (U2 snRNA); and
histones H1, H3, and H4. Sequence analyses revealed that U2
snRNA contains a major portion corresponding to the Tx1-type
non-LTR retrotransposon Keno, the preferential insertion sites
of which are U2 snRNA sequences. All histone sequences were
found to be associated with TEs. In situ localization revealed
that these DNA sequences are dispersed throughout the autosomes of the species,
but they are not involved in differentiation of the specific region of the W sex
chromosome in C. gomesi. We discuss mechanisms of TE invasion
into multigene families that lead to microstructural variation in
Characidium genomes.
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Affiliation(s)
- Marcela Baer Pucci
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa Ponta Grossa, PR, Brazil
| | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Marcelo Ricardo Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa Ponta Grossa, PR, Brazil
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Malimpensa GC, Traldi JB, Toyama D, Henrique-Silva F, Vicari MR, Moreira-Filho O. Chromosomal Mapping of Repeat DNA in Bergiaria westermanni (Pimelodidae, Siluriformes): Localization of 45S rDNA in B Chromosomes. Cytogenet Genome Res 2018; 154:99-106. [PMID: 29635248 DOI: 10.1159/000487652] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2017] [Indexed: 12/19/2022] Open
Abstract
The occurrence of repetitive DNA in autosomes and B chromosomes of Bergiaria westermanni was examined using conventional and molecular cytogenetic techniques. This species exhibited 2n = 56 chromosomes, with intra- and interindividual variation in the number of heterochromatic B chromosomes (from 0 to 4). The 5S rDNA was localized in pairs 1 and 5, and histone probes (H1, H3, and H4) and U2 small nuclear RNA were syntenic with 5S rDNA in pair 5. Histone sequences were also located in chromosome pair 14. The (GATA)n sequence was dispersed throughout the autosomes and B chromosomes, with clusters (microsatellite accumulation) in some chromosome regions. The telomeric probe revealed no signs of chromosomal rearrangements in the genome of B. westermanni. The 45S rDNA sites were detected in the terminal region of pair 27; these sites corresponded to a GC-rich heterochromatin block. In addition, 3 of the 4 B chromosomes also contained 45S rDNA copies. Silver nitrate staining in interphase nuclei provided indirect evidence of the expression of these rRNA genes in B chromosomes, indicating the probable origin of these elements. This report shows plasticity in the chromosomal localization of repeat DNA in B. westermanni and features a discussion of genomic diversification.
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Affiliation(s)
- Geovana C Malimpensa
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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do Nascimento VD, Coelho KA, Nogaroto V, de Almeida RB, Ziemniczak K, Centofante L, Pavanelli CS, Torres RA, Moreira-Filho O, Vicari MR. Do multiple karyomorphs and population genetics of freshwater darter characines (Apareiodon affinis) indicate chromosomal speciation? ZOOL ANZ 2018. [DOI: 10.1016/j.jcz.2017.12.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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