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Luo X, Liu Y, Gong X, Ye M, Xiao Q, Zeng Z. Karyotype Description and Comparative Chromosomal Mapping of 5S rDNA in 42 Species. Genes (Basel) 2024; 15:647. [PMID: 38790276 PMCID: PMC11121585 DOI: 10.3390/genes15050647] [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: 02/29/2024] [Revised: 04/29/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
This study was conducted to evaluate the 5S rDNA site number, position, and origin of signal pattern diversity in 42 plant species using fluorescence in situ hybridization. The species were selected based on the discovery of karyotype rearrangement, or because 5S rDNA had not yet been explored the species. The chromosome number varied from 14 to 160, and the chromosome length ranged from 0.63 to 6.88 μm, with 21 species having small chromosomes (<3 μm). The chromosome numbers of three species and the 5S rDNA loci of nineteen species are reported for the first time. Six 5S rDNA signal pattern types were identified. The 5S rDNA varied and was abundant in signal site numbers (2-18), positions (distal, proximal, outside of chromosome arms), and even in signal intensity. Variation in the numbers and locations of 5S rDNA was observed in 20 species, whereas an extensive stable number and location of 5S rDNA was found in 22 species. The potential origin of the signal pattern diversity was proposed and discussed. These data characterized the variability of 5S rDNA within the karyotypes of the 42 species that exhibited chromosomal rearrangements and provided anchor points for genetic physical maps.
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Affiliation(s)
- Xiaomei Luo
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; (X.G.); (M.Y.)
| | - Yunke Liu
- Chengdu Academy of Agriculture and Forestry Sciences, Nongke Road 200, Wenjiang District, Chengdu 611130, China; (Y.L.); (Q.X.); (Z.Z.)
| | - Xiao Gong
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; (X.G.); (M.Y.)
| | - Meng Ye
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; (X.G.); (M.Y.)
| | - Qiangang Xiao
- Chengdu Academy of Agriculture and Forestry Sciences, Nongke Road 200, Wenjiang District, Chengdu 611130, China; (Y.L.); (Q.X.); (Z.Z.)
| | - Zhen Zeng
- Chengdu Academy of Agriculture and Forestry Sciences, Nongke Road 200, Wenjiang District, Chengdu 611130, China; (Y.L.); (Q.X.); (Z.Z.)
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Dos Santos GE, Crepaldi C, da Silva MJ, Parise-Maltempi PP. Revealing the Satellite DNA Content in Ancistrus sp. (Siluriformes: Loricariidae) by Genomic and Bioinformatic Analysis. Cytogenet Genome Res 2024:1-8. [PMID: 38631304 DOI: 10.1159/000538926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/12/2024] [Indexed: 04/19/2024] Open
Abstract
INTRODUCTION Eukaryotic genomes are composed of simple, repetitive sequences, including satellite DNAs (satDNA), which are noncoding sequences arranged in tandem arrays. These sequences play a crucial role in genomic functions and innovations, influencing processes such as the maintenance of nuclear material, the formation of heterochromatin and the differentiation of sex chromosomes. In this genomic era, advances in next-generation sequencing and bioinformatics tools have facilitated the exhaustive cataloging of repetitive elements in genomes, particularly in non-model species. This study focuses on the satDNA content of Ancistrus sp., a diverse species of fish from the Loricariidae family. The genus Ancistrus shows significant karyotypic evolution, with extensive variability from the ancestral diploid number. METHODS By means of bioinformatic approaches, 40 satDNA families in Ancistrus sp., constituting 5.19% of the genome were identified. Analysis of the abundance and divergence landscape revealed diverse profiles, indicating recent amplification and homogenization of these satDNA sequences. RESULTS The most abundant satellite, AnSat1-142, constitutes 2.1% of the genome, while the least abundant, AnSat40-52, represents 0.0034%. The length of the monomer repeat varies from 16 to 142 base pairs, with an average length of 61 bp. These results contribute to understanding the genomic dynamics and evolution of satDNAs in Ancistrus sp. CONCLUSION The study underscores the variability of satDNAs between fish species and provides valuable information on chromosome organization and the evolution of repetitive elements in non-model organisms.
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Affiliation(s)
- Gabriel Esbrisse Dos Santos
- General and Applied Biology Department, Bioscience Institute/São Paulo State University (UNESP), Rio Claro, Brazil
| | - Carolina Crepaldi
- General and Applied Biology Department, Bioscience Institute/São Paulo State University (UNESP), Rio Claro, Brazil
| | - Marcelo João da Silva
- General and Applied Biology Department, Bioscience Institute/São Paulo State University (UNESP), Rio Claro, Brazil
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3
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de Almeida BRR, Farias Souza L, Alves TA, Cardoso AL, de Oliveira JA, Augusto Ribas TF, Dos Santos CEV, do Nascimento LAS, Sousa LM, da Cunha Sampaio MI, Martins C, Nagamachi CY, Pieczarka JC, Noronha RCR. Chromosomal organization of multigene families and meiotic analysis in species of Loricariidae (Siluriformes) from Brazilian Amazon, with description of a new cytotype for genus Spatuloricaria. Biol Open 2023; 12:bio060029. [PMID: 37819723 PMCID: PMC10651099 DOI: 10.1242/bio.060029] [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: 06/06/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023] Open
Abstract
In the Amazon, some species of Loricariidae are at risk of extinction due to habitat loss and overexploitation by the ornamental fish market. Cytogenetic data related to the karyotype and meiotic cycle can contribute to understanding the reproductive biology and help management and conservation programs of these fish. Additionally, chromosomal mapping of repetitive DNA in Loricariidae may aid comparative genomic studies in this family. However, cytogenetics analysis is limited in Amazonian locariids. In this study, chromosomal mapping of multigenic families was performed in Scobinancistrus aureatus, Scobinancistrus pariolispos and Spatuloricaria sp. Meiotic analyzes were performed in Hypancistrus zebra and Hypancistrus sp. "pão". Results showed new karyotype for Spatuloricaria sp. (2n=66, NF=82, 50m-10sm-6m). Distinct patterns of chromosomal organization of histone H1, histone H3 and snDNA U2 genes were registered in the karyotypes of the studied species, proving to be an excellent cytotaxonomic tool. Hypotheses to explain the evolutionary dynamics of these sequences in studied Loricariidae were proposed. Regarding H. zebra and H. sp. "pão", we describe the events related to synapse and transcriptional activity during the meiotic cycle, which in both species showed 26 fully synapsed bivalents, with high gene expression only during zygotene and pachytene. Both Hypancistrus species could be used may be models for evaluating changes in spermatogenesis of Loricariidae.
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Affiliation(s)
- Bruno Rafael Ribeiro de Almeida
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará. Belém 66075-750, Pará, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia do Pará. Campus Itaituba. Itaituba, 68183-300, Pará, Brazil
| | - Luciano Farias Souza
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará. Belém 66075-750, Pará, Brazil
| | - Thyana Ayres Alves
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará. Belém 66075-750, Pará, Brazil
| | - Adauto Lima Cardoso
- Laboratório Genômica Integrativa, Instituto de Biociências, Universidade Estadual Paulista. Botucatu, CEP 18618-970, São Paulo, Brazil
| | - Juliana Amorim de Oliveira
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará. Belém 66075-750, Pará, Brazil
| | - Talita Fernanda Augusto Ribas
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará. Belém 66075-750, Pará, Brazil
| | - Carlos Eduardo Vasconcelos Dos Santos
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará. Belém 66075-750, Pará, Brazil
| | | | - Leandro Melo Sousa
- Faculdade de Ciências Biológicas, Universidade Federal do Pará, Campus de Altamira. Altamira, CEP 68372-040, Pará, Brazil
| | - Maria Iracilda da Cunha Sampaio
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Universitário de Bragança.. Bragança, CEP 68600-000, Pará, Brazil
| | - Cesar Martins
- Laboratório Genômica Integrativa, Instituto de Biociências, Universidade Estadual Paulista. Botucatu, CEP 18618-970, São Paulo, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará. Belém 66075-750, Pará, Brazil
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará. Belém 66075-750, Pará, Brazil
| | - Renata Coelho Rodrigues Noronha
- Laboratório de Genética e Biologia Celular, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará. Belém 66075-750, Pará, Brazil
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Lai EC, Vogan AA. Proliferation and dissemination of killer meiotic drive loci. Curr Opin Genet Dev 2023; 82:102100. [PMID: 37625205 PMCID: PMC10900872 DOI: 10.1016/j.gde.2023.102100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/20/2023] [Accepted: 07/22/2023] [Indexed: 08/27/2023]
Abstract
Killer meiotic drive elements are selfish genetic entities that manipulate the sexual cycle to promote their own inheritance via destructive means. Two broad classes are sperm killers, typical of animals and plants, and spore killers, which are present in ascomycete fungi. Killer meiotic drive systems operate via toxins that destroy or disable meiotic products bearing the alternative allele. To avoid suicidal autotargeting, cells that bear these selfish elements must either lack the toxin target, or express an antidote. Historically, these systems were presumed to require large nonrecombining haplotypes to link multiple functional interacting loci. However, recent advances on fungal spore killers reveal that numerous systems are enacted by single genes, and similar molecular genetic studies in Drosophila pinpoint individual loci that distort gamete sex. Notably, many meiotic drivers duplicate readily, forming gene families that can have complex interactions within and between species, and providing substrates for their rapid functional diversification. Here, we summarize the known families of meiotic drivers in fungi and fruit flies, and highlight shared principles about their evolution and proliferation that promote the spread of these noxious genes.
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Affiliation(s)
- Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, 430 East 67th St, ROC-10, New York, NY 10065, USA.
| | - Aaron A Vogan
- Institute of Organismal Biology, Uppsala University, Norbyvägen 18D, Uppsala 752 36, Sweden.
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de Menezes Cavalcante Sassi F, Sember A, Deon GA, Liehr T, Padutsch N, Oyakawa OT, Vicari MR, Bertollo LAC, Moreira-Filho O, de Bello Cioffi M. Homeology of sex chromosomes in Amazonian Harttia armored catfishes supports the X-fission hypothesis for the X 1X 2Y sex chromosome system origin. Sci Rep 2023; 13:15756. [PMID: 37735233 PMCID: PMC10514344 DOI: 10.1038/s41598-023-42617-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023] Open
Abstract
The Neotropical monophyletic catfish genus Harttia represents an excellent model to study karyotype and sex chromosome evolution in teleosts. Its species split into three phylogenetic clades distributed along the Brazilian territory and they differ widely in karyotype traits, including the presence of standard or multiple sex chromosome systems in some members. Here, we investigate the chromosomal rearrangements and associated synteny blocks involved in the origin of a multiple X1X2Y sex chromosome system present in three out of six sampled Amazonian-clade species. Using 5S and 18S ribosomal DNA fluorescence in situ hybridization and whole chromosome painting with probes corresponding to X1 and X2 chromosomes of X1X2Y system from H. punctata, we confirm previous assumptions that X1X2Y sex chromosome systems of H. punctata, H. duriventris and H. villasboas represent the same linkage groups which also form the putative XY sex chromosomes of H. rondoni. The shared homeology between X1X2Y sex chromosomes suggests they might have originated once in the common ancestor of these closely related species. A joint arrangement of mapped H. punctata X1 and X2 sex chromosomes in early diverging species of different Harttia clades suggests that the X1X2Y sex chromosome system may have formed through an X chromosome fission rather than previously proposed Y-autosome fusion.
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Affiliation(s)
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská, 89, Liběchov, Czech Republic
| | - Geize Aparecida Deon
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Thomas Liehr
- Institut für Humangenetik, Universitätsklinikum Jena, 07747, Jena, Germany.
| | - Niklas Padutsch
- Institut für Humangenetik, Universitätsklinikum Jena, 07747, Jena, Germany
| | | | - Marcelo Ricardo Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | - Luiz Antonio Carlos Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Orlando Moreira-Filho
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
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6
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Santos da Silva K, Glugoski L, Vicari MR, de Souza ACP, Akama A, Pieczarka JC, Nagamachi CY. Mechanisms of Karyotypic Diversification in Ancistrus (Siluriformes, Loricariidae): Inferences from Repetitive Sequence Analysis. Int J Mol Sci 2023; 24:14159. [PMID: 37762461 PMCID: PMC10532334 DOI: 10.3390/ijms241814159] [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: 07/17/2023] [Revised: 08/14/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Ancistrus is a highly diverse neotropical fish genus that exhibits extensive chromosomal variability, encompassing karyotypic morphology, diploid chromosome number (2n = 34-54), and the evolution of various types of sex chromosome systems. Robertsonian rearrangements related to unstable chromosomal sites are here described. Here, the karyotypes of two Ancistrus species were comparatively analyzed using classical cytogenetic techniques, in addition to isolation, cloning, sequencing, molecular characterization, and fluorescence in situ hybridization of repetitive sequences (i.e., 18S and 5S rDNA; U1, U2, and U5 snDNA; and telomere sequences). The species analyzed here have different karyotypes: Ancistrus sp. 1 (2n = 38, XX/XY) and Ancistrus cirrhosus (2n = 34, no heteromorphic sex chromosomes). Comparative mapping showed different organizations for the analyzed repetitive sequences: 18S and U1 sequences occurred in a single site in all populations of the analyzed species, while 5S and U2 sequences could occur in single or multiple sites. A sequencing analysis confirmed the identities of the U1, U2, and U5 snDNA sequences. Additionally, a syntenic condition for U2-U5 snDNA was found in Ancistrus. In a comparative analysis, the sequences of rDNA and U snDNA showed inter- and intraspecific chromosomal diversification. The occurrence of Robertsonian rearrangements and other dispersal mechanisms of repetitive sequences are discussed.
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Affiliation(s)
- Kevin Santos da Silva
- Cytogenetics Laboratory, Center for Advanced Biodiversity Studies Science Institute Biological, Federal University of Pará, Belém 66075-110, Brazil; (K.S.d.S.); (J.C.P.)
| | - Larissa Glugoski
- Fish Cytogenetics Laboratory, Federal University of São Carlos, São Carlos 13565-905, Brazil;
- Laboratory of Chromosome Biology: Structure and Function Department of Structural Biology, Molecular and Genetic, University of Ponta Grossa State, Ponta Grossa 84010-330, Brazil;
| | - Marcelo Ricardo Vicari
- Laboratory of Chromosome Biology: Structure and Function Department of Structural Biology, Molecular and Genetic, University of Ponta Grossa State, Ponta Grossa 84010-330, Brazil;
| | | | - Alberto Akama
- Department of Zoology, Paraense Emilio Goeldi Museum, Belém 66040-170, Brazil;
| | - Julio Cesar Pieczarka
- Cytogenetics Laboratory, Center for Advanced Biodiversity Studies Science Institute Biological, Federal University of Pará, Belém 66075-110, Brazil; (K.S.d.S.); (J.C.P.)
| | - Cleusa Yoshiko Nagamachi
- Cytogenetics Laboratory, Center for Advanced Biodiversity Studies Science Institute Biological, Federal University of Pará, Belém 66075-110, Brazil; (K.S.d.S.); (J.C.P.)
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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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Glugoski L, Deon GA, Nogaroto V, Moreira-Filho O, Vicari MR. Robertsonian Fusion Site in Rineloricaria pentamaculata (Siluriformes: Loricariidae): Involvement of 5S Ribosomal DNA and Satellite Sequences. Cytogenet Genome Res 2023; 162:657-664. [PMID: 37054691 DOI: 10.1159/000530636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 04/07/2023] [Indexed: 04/15/2023] Open
Abstract
Cytogenetic studies demonstrated that unstable chromosomal sites in armored catfishes (Loricariidae) triggered intense karyotypic diversification, mainly derived from Robertsonian rearrangements. In Loricariinae, the presence of ribosomal DNA (rDNA) clusters and their flanking repeated regions (such as microsatellites or partial transposable element sequences) was proposed to facilitate chromosomal rearrangements. Hence, this study aimed to characterize the numerical chromosomal polymorphism observed in Rineloricaria pentamaculata and evaluate the chromosomal rearrangements which originated diploid chromosome number (2n) variation, from 56 to 54. Our data indicate a centric fusion event between acrocentric chromosomes of pairs 15 and 18, bearing 5S rDNA sites on their short (p) arms. This chromosome fusion established the numerical polymorphism, decreasing the 2n from original 56 (karyomorph A) to 55 in karyomorph B and 54 in karyomorph C. Although vestiges of telomeric sequences were evidenced at the fusion point, no 5S rDNA was detected in this region. The acrocentric chromosomes involved in the origin of the fusion were enriched with (CA)n and (GA)n microsatellites. Repetitive sequences in the acrocentric chromosomes subtelomeres have facilitated the rearrangement. Our study thus reinforces the view on the important role of particular repetitive DNA classes in promoting chromosome fusions which frequently drive Rineloricaria karyotype evolution.
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Affiliation(s)
- Larissa Glugoski
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Geize A Deon
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Viviane Nogaroto
- Department of Structural Biology, Molecular and Genetics, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Orlando Moreira-Filho
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Marcelo Ricardo Vicari
- Department of Structural Biology, Molecular and Genetics, State University of Ponta Grossa, Ponta Grossa, Brazil
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Marajó L, Viana PF, Ferreira AMV, Py-Daniel LHR, Cioffi MDB, Sember A, Feldberg E. Chromosomal rearrangements and the first indication of an ♀X 1 X 1 X 2 X 2 /♂X 1 X 2 Y sex chromosome system in Rineloricaria fishes (Teleostei: Siluriformes). JOURNAL OF FISH BIOLOGY 2023; 102:443-454. [PMID: 36427042 DOI: 10.1111/jfb.15275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Rineloricaria is the most diverse genus within the freshwater fish subfamily Loricariinae, and it is widely distributed in the Neotropical region. Despite limited cytogenetic data, records from southern and south-eastern Brazil suggest a high rate of chromosomal rearrangements in this genus, mirrored in remarkable inter- and intraspecific karyotype variability. In the present work, we investigated the karyotype features of Rineloricaria teffeana, an endemic representative from northern Brazil, using both conventional and molecular cytogenetic techniques. We revealed different diploid chromosome numbers (2n) between sexes (33♂/34♀), which suggests the presence of an ♀X1 X1 X2 X2 /♂X1 X2 Y multiple sex chromosome system. The male-limited Y chromosome was the largest and the only biarmed element in the karyotype, implying Y-autosome fusion as the most probable mechanism behind its origination. C-banding revealed low amounts of constitutive heterochromatin, mostly confined to the (peri)centromeric regions of most chromosomes (including the X2 and the Y) but also occupying the distal regions of a few chromosomal pairs. The chromosomal localization of the 18S ribosomal DNA (rDNA) clusters revealed a single site on chromosome pair 4, which was adjacent to the 5S rDNA cluster. Additional 5S rDNA loci were present on the autosome pair 8, X1 chromosome, and in the presumed fusion point on the Y chromosome. The probe for telomeric repeat motif (TTAGGG)n revealed signals of variable intensities at the ends of all chromosomes except for the Y chromosome, where no detectable signals were evidenced. Male-to-female comparative genomic hybridization revealed no sex-specific or sex-biased repetitive DNA accumulations, suggesting a presumably low level of neo-Y chromosome differentiation. We provide evidence that rDNA sites might have played a role in the formation of this putative multiple sex chromosome system and that chromosome fusions originate through different mechanisms among different Rineloricaria species.
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Affiliation(s)
- Leandro Marajó
- Laboratório de Genética Animal, Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Patrik Ferreira Viana
- Laboratório de Genética Animal, Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Alex Matheus Viana Ferreira
- Laboratório de Genética Animal, Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Lúcia Helena Rapp Py-Daniel
- Coleção de Peixes, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Libechov, Czech Republic
| | - Eliana Feldberg
- Laboratório de Genética Animal, Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
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10
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Occurrence of Sex Chromosomes in Fish of the Genus Ancistrus with a New Description of Multiple Sex Chromosomes in the Ecuadorian Endemic Ancistrus clementinae (Loricariidae). Genes (Basel) 2023; 14:genes14020306. [PMID: 36833233 PMCID: PMC9956960 DOI: 10.3390/genes14020306] [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: 12/29/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Ancistrus Kner, 1854, is the most diverse genus among the Ancistrini (Loricariidae) with 70 valid species showing a wide geographic distribution and great taxonomic and systematic complexity. To date, about 40 Ancistrus taxa have been karyotyped, all from Brazil and Argentina, but the statistic is uncertain because 30 of these reports deal with samples that have not yet been identified at the species level. This study provides the first cytogenetic description of the bristlenose catfish, Ancistrus clementinae Rendahl, 1937, a species endemic to Ecuador, aiming to verify whether a sex chromosome system is identifiable in the species and, if so, which, and if its differentiation is associated with the presence of repetitive sequences reported for other species of the family. We associated the karyotype analysis with the COI molecular identification of the specimens. Karyotype analysis suggested the presence of a ♂ZZ/♀ZW1W2 sex chromosome system, never detected before in Ancistrus, with both W1W2 chromosomes enriched with heterochromatic blocks and 18S rDNA, in addition to GC-rich repeats (W2). No differences were observed between males and females in the distribution of 5S rDNA or telomeric repeats. Cytogenetic data here obtained confirm the huge karyotype diversity of Ancistrus, both in chromosome number and sex-determination systems.
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de Moraes RLR, Sassi FDMC, Marinho MMF, Ráb P, Porto JIR, Feldberg E, Cioffi MDB. Small Body, Large Chromosomes: Centric Fusions Shaped the Karyotype of the Amazonian Miniature Fish Nannostomus anduzei (Characiformes, Lebiasinidae). Genes (Basel) 2023; 14:192. [PMID: 36672933 PMCID: PMC9858914 DOI: 10.3390/genes14010192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/04/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
Miniature refers to species with extraordinarily small adult body size when adult and can be found within all major metazoan groups. It is considered that miniature species have experienced severe alteration of numerous morphological traits during evolution. For a variety of reasons, including severe labor concerns during collecting, chromosomal acquisition, and taxonomic issues, miniature fishes are neglected and understudied. Since some available studies indicate possible relationship between diploid chromosome number (2n) and body size in fishes, we aimed to study one of the smallest Neotropical fish Nannostomus anduzei (Teleostei, Characiformes, Lebiasinidae), using both conventional (Giemsa staining, C-banding) and molecular cytogenetic methods (FISH mapping of rDNAs, microsatellites, and telomeric sequences). Our research revealed that N. anduzei possesses one of the lowest diploid chromosome numbers (2n = 22) among teleost fishes, and its karyotype is entirely composed of large metacentric chromosomes. All chromosomes, except for pair number 11, showed an 18S rDNA signal in the pericentromeric region. 5S rDNA signals were detected in the pericentromeric regions of chromosome pair number 1 and 6, displaying synteny to 18S rDNA signals. Interstitial telomeric sites (ITS) were identified in the centromeric region of pairs 6 and 8, indicating that centric fusions played a significant role in karyotype evolution of studied species. Our study provides further evidence supporting the trend of diploid chromosome number reduction along with miniaturization of adult body size in fishes.
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Affiliation(s)
- Renata Luiza Rosa de Moraes
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, SP, Brazil
| | - Francisco de Menezes Cavalcante Sassi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, SP, Brazil
| | - Manoela Maria Ferreira Marinho
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, Cidade Universitária, Castelo Branco, João Pessoa 58051-900, PB, Brazil
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Jorge Ivan Rebelo Porto
- Laboratório de Genética Animal, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, AM, Brazil
| | - Eliana Feldberg
- Laboratório de Genética Animal, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, AM, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, SP, Brazil
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12
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Santos da Silva K, de Souza ACP, Rodrigues LRR, Pieczarka JC, Nagamachi CY. Chromosomal Diversification in Pseudacanthicus Species (Loricariidae, Hypostominae) Revealed by Comparative Mapping of Repetitive Sequences. Animals (Basel) 2022; 12:ani12192612. [PMID: 36230353 PMCID: PMC9558496 DOI: 10.3390/ani12192612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 11/19/2022] Open
Abstract
Simple Summary The fishes of the Loricariidae family have a huge genetic diversity, mainly involving variations in the number and shape of chromosomes. The recognition of the species genus Pseudacanthicus is complex due to the large diversity of forms and limited knowledge of their genetic diversity. In this study, the karyotypes of three Pseudacanthicus species were comparatively analyzed using classical and molecular methods. They presented the same diploid number, but with different compositions of repetitive DNA sequences. Such information can be useful for the recognition of distinct species, in addition to providing important insights into the real biodiversity of this important group of Neotropical fish. Abstract Pseudacanthicus is a genus of Neotropical fish with eight valid species, in addition to numerous lineages not formally identified. It occurs along the Amazon and Tocantins River basins, in Suriname and in the Guiana shield. There are no karyotypic data in the literature for species of this genus. Here, the karyotypes of three Pseudacanthicus species (P. spinosus, P. leopardus and Pseudacanthicus sp.) were comparatively analyzed by classical cytogenetics and fluorescence in situ hybridization using 18S and 5S rDNA probes, U2 snDNA and telomeric sequences. The analyzed species presented 52 chromosomes and KF = 18 m + 34 sm. Constitutive heterochromatin occurred in blocks on a few chromosomes. The 18S rDNA occurred in a single pair; interestingly, P. leopardus presented only one locus of this sequence in its diploid genome. The 5S rDNA sequence occurred in only one pair in P. leopardus, and in multiple sites in Pseudacanthicus sp. and P. spinosus. The snDNA U2 occurred in only one pair in all analyzed species. Telomeric sequences did not show interstitial sites. Although Pseudacanthicus species share the same 2n and KF, repetitive sequence analysis revealed karyotypic diversity among these species. The occurrence of DNA double-strand breaks related to fragile sites, unequal crossing over and transpositions is proposed as the mechanism of karyotypic diversification, suggesting that the conservation of the karyotypic macrostructure is only apparent in this group of fish.
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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 66075-750, Brazil
| | - Augusto César Paes de Souza
- Laboratório de Estudo da Ictiofauna Amazônica, Instituto Federal de Educação, Ciência e Tecnologia do Pará, Abaetetuba 684400-000, Brazil
| | - Luís Reginaldo Ribeiro Rodrigues
- Laboratório de Genética & Biodiversidade, Instituto de Ciências da Educação, Universidade Federal do Oeste do Pará, Santarém 68040-255, Brazil
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-750, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-750, Brazil
- Correspondence:
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13
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Schott SCQ, Glugoski L, Azambuja M, Moreira-Filho O, Vicari MR, Nogaroto V. Comparative Cytogenetic and Sequence Analysis of U Small Nuclear RNA Genes in Three Ancistrus Species (Siluriformes: Loricariidae). Zebrafish 2022; 19:200-209. [PMID: 36099209 DOI: 10.1089/zeb.2022.0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ancistrus presents a wide karyotypic diversity, resulting from numeric and structural chromosomal rearrangements. It has been proposed that some genome-specific regions containing repetitive units could organize prone-to-break DNA sites in Loricariidae, triggering chromosomal rearrangements such as Robertsonian fusions (Rb fusions), centric fissions, translocations, and inversions. The tandemly repeats of the small nuclear RNAs (snRNAs) gene families are considered good cytogenetic markers for understanding chromosomal remodeling events among closely related species, but these snRNAs have been scarcely analyzed in Ancistrus. This study presented the nucleotide sequencing and comparative in situ location of U snRNA sequences from Ancistrus aguaboensis, Ancistrus cf. multispinis, and Ancistrus sp. (2n = 50, 52, and 50, respectively), aiming to provide information about snRNA clusters in the genome and chromosome evolution in Ancistrus. U snRNA nucleotide sequences of Ancistrus presented identity to orthologous copies and folded their secondary structures correctly. In situ localization and karyotyping of the three Ancistrus species revealed clustered copies of U2 and U5 snRNA gene families to a single chromosome site, one chromosome pair bearing U1 snRNA sequence, and one main locus of U4 snRNA sequence, besides scattered signals along the chromosomes. Previous studies related the participation of the rRNA gene families in centric fusion events, contributing to chromosome rearrangements and karyotype plasticity present in Loricariidae. In this study, homeologies in U snRNA loci chromosomal locations were detected, indicating the occurrence of conserved sites of these gene families in these three Ancistrus species with 2n = 50 or 52 chromosomes.
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Affiliation(s)
| | - Larissa Glugoski
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Matheus Azambuja
- Departamento de Genética, Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Marcelo Ricardo Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
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14
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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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15
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Azambuja M, Orane Schemberger M, Nogaroto V, Moreira-Filho O, Martins C, Ricardo Vicari M. Major and minor U small nuclear RNAs genes characterization in a neotropical fish genome: Chromosomal remodeling and repeat units dispersion in Parodontidae. Gene 2022; 826:146459. [PMID: 35358649 DOI: 10.1016/j.gene.2022.146459] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/15/2022] [Accepted: 03/25/2022] [Indexed: 11/29/2022]
Abstract
In association with many proteins, small nuclear RNAs (snRNAs) organize the spliceosomes that play a significant role in processing precursor mRNAs during gene expression. According to snRNAs genic arrangements, two kinds of spliceosomes (major and minor) can be organized into eukaryotic cells. Although in situ localization of U1 and U2 snDNAs have been performed in fish karyotypes, studies with genomic characterization and functionality of U snRNAs integrated into chromosomal changes on Teleostei are still scarce. This study aimed to achieve a genomic characterization of the U snRNAs genes in Apareiodon sp. (2n = 54, ZZ/ZW), apply these data to recognize functional/defective copies, and map chromosomal changes involving snDNAs in Parodontidae species karyotype diversification. Nine snRNA multigene families (U1, U2, U4, U5, U6, U11, U12, U4atac and U6atac) arranged in putatively functional copies in the genome were analyzed. Proximal Sequence Elements (PSE) and TATA-box promoters occurrence, besides an entire transcribed region and conserved secondary structures, qualify them for spliceosome activity. In addition, several defective copies or pseudogenes were identified for the snRNAs that make up the major spliceosome. In situ localization of snDNAs in five species of Parodontidae demonstrated that U1, U2, and U4 snDNAs were involved in chromosomal location changes or units dispersion. The U snRNAs defective/pseudogenes units dispersion could be favored by the probable occurrence of active retrotransposition enzymes in the Apareiodon genome. The U2 and U4 snDNAs sites were involved in independent events in the differentiation of sex chromosomes among Parodontidae lineages. The study characterized U snRNA genes that compose major and minor spliceosomes in the Apareiodon sp. genome and proposes that their defective copies trigger chromosome differentiation and diversification events in Parodontidae.
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Affiliation(s)
- Matheus Azambuja
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. dos Santos, 100, 81531-990 Curitiba, Paraná, Brazil.
| | - Michelle Orane Schemberger
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. dos Santos, 100, 81531-990 Curitiba, Paraná, Brazil.
| | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Av. Carlos Cavalcanti, 4748, 84030-900 Ponta Grossa, Paraná, Brazil.
| | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235, 13565-905 São Carlos, São Paulo, Brazil.
| | - Cesar Martins
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Distrito de Rubião Júnior, s/n, 18618-689 Botucatu, São Paulo, Brazil.
| | - Marcelo Ricardo Vicari
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. dos Santos, 100, 81531-990 Curitiba, Paraná, Brazil; Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Av. Carlos Cavalcanti, 4748, 84030-900 Ponta Grossa, Paraná, Brazil.
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16
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Deon GA, Glugoski L, Hatanaka T, Sassi FDMC, Nogaroto V, Bertollo LAC, Liehr T, Al-Rikabi A, Moreira Filho O, Cioffi MDB, Vicari MR. Evolutionary breakpoint regions and chromosomal remodeling in Harttia (Siluriformes: Loricariidae) species diversification. Genet Mol Biol 2022; 45:e20210170. [PMID: 35604463 PMCID: PMC9126045 DOI: 10.1590/1678-4685-gmb-2021-0170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 04/03/2022] [Indexed: 11/22/2022] Open
Abstract
The Neotropical armored catfish genus Harttia presents a wide
variation of chromosomal rearrangements among its representatives. Studies
indicate that translocation and Robertsonian rearrangements have triggered the
karyotype evolution in the genus, including differentiation of sex chromosome
systems. However, few studies used powerful tools, such as comparative whole
chromosome painting, to clarify this highly diversified scenario. Here, we
isolated probes from the X1 (a 5S rDNA carrier) and the X2
(a 45S rDNA carrier) chromosomes of Harttia punctata, which
displays an
X1X1X2X2/X1X2Y
multiple sex chromosome system. Those probes were applied in other
Harttia species to evidence homeologous chromosome blocks.
The resulting data reinforce that translocation events played a role in the
origin of the X1X2Y sex chromosome system in H.
punctata. The repositioning of homologous chromosomal blocks
carrying rDNA sites among ten Harttia species has also been
demonstrated. Anchored to phylogenetic data it was possible to evidence some
events of the karyotype diversification of the studied species and to prove an
independent origin for the two types of multiple sex chromosomes,
XX/XY1Y2 and
X1X1X2X2/X1X2Y,
that occur in Harttia species. The results point to
evolutionary breakpoint regions in the genomes within or adjacent to rDNA sites
that were widely reused in Harttia chromosome remodeling.
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Affiliation(s)
- Geize Aparecida Deon
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil.,Universidade Estadual de Ponta Grossa, Departamento de Biologia Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
| | - Larissa Glugoski
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil.,Universidade Estadual de Ponta Grossa, Departamento de Biologia Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
| | - Terumi Hatanaka
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
| | | | - Viviane Nogaroto
- Universidade Estadual de Ponta Grossa, Departamento de Biologia Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
| | | | - Thomas Liehr
- University Hospital Jena, Institute of Human Genetics, Jena, Germany
| | - Ahmed Al-Rikabi
- University Hospital Jena, Institute of Human Genetics, Jena, Germany.,Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
| | - Orlando Moreira Filho
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
| | - Marcelo de Bello Cioffi
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
| | - Marcelo Ricardo Vicari
- Universidade Estadual de Ponta Grossa, Departamento de Biologia Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
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17
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Araya-Jaime CA, Silva DMZDA, da Silva LRR, do Nascimento CN, Oliveira C, Foresti F. Karyotype description and comparative chromosomal mapping of rDNA and U2 snDNA sequences in Eigenmannialimbata and E.microstoma (Teleostei, Gymnotiformes, Sternopygidae). COMPARATIVE CYTOGENETICS 2022; 16:127-142. [PMID: 36761809 PMCID: PMC9849054 DOI: 10.3897/compcytogen.v16i2.72190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 04/09/2022] [Indexed: 06/18/2023]
Abstract
The genus Eigenmannia Jordan et Evermann,1896 includes electric fishes endemic to the Neotropical region with extensive karyotype variability and occurrence of different sex chromosome systems, however, cytogenetic studies within this group are restricted to few species. Here, we describe the karyotypes of Eigenmannialimbata (Schreiner et Miranda Ribeiro, 1903) and E.microstoma (Reinhardt, 1852) and the chromosomal locations of 5S and 18S rDNAs (ribosomal RNA genes) and U2 snDNA (small nuclear RNA gene). Among them, 18S rDNA sites were situated in only one chromosomal pair in both species, and co-localized with 5S rDNA in E.microstoma. On the other hand, 5S rDNA and U2 snRNA sites were observed on several chromosomes, with variation in the number of sites between species under study. These two repetitive DNAs were observed co-localized in one chromosomal pair in E.limbata and in four pairs in E.microstoma. Our study shows a new case of association of these two types of repetitive DNA in the genome of Gymnotiformes.
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Affiliation(s)
- Cristian Andrés Araya-Jaime
- Instituto de Investigación Multidisciplinar en Ciencia y Tecnología, Universidad de La Serena, La Serena, Chile
| | | | | | | | - Claudio Oliveira
- Departamento de Biología, Universidad de La Serena, La Serena, Chile
| | - Fausto Foresti
- Departamento de Biología, Universidad de La Serena, La Serena, Chile
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18
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Takagui FH, Baumgärtner L, Viana P, Lima MCC, Bitencourt JDA, Venere PC, Lui RL, Moreira-Filho O, Feldberg E, Almeida Simões F, Birindelli JL, Giuliano-Caetano L. Karyotype Evolution of Talking Thorny Catfishes Anadoras (Doradidae, Astrodoradinae): A Process Mediated by Structural Rearrangements and Intense Reorganization of Repetitive DNAs. Cytogenet Genome Res 2022; 162:64-75. [PMID: 35500552 DOI: 10.1159/000523747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 02/17/2022] [Indexed: 11/19/2022] Open
Abstract
Anadoras is a thorny catfish genus widespread through the Amazon and Paraguay river basins. It includes 2 nominal species, A. grypus and A. weddellii, plus Anadoras sp. "araguaia," an undescribed species only recognized morphologically. Since Anadoras occupies a basal position within the Astrodoradinae phylogeny, it is crucial to identify its cytogenetic features to comprehend the mechanisms involved in the chromosomal diversification of this subfamily. Therefore, we performed a comparative cytogenetic analysis including all species of Anadoras. Furthermore, we applied a species delimitation analysis based on 600 bp of the mitochondrial cytochrome oxidase subunit 1 (CO1) gene to investigate the taxonomic status of the species. Cytogenetic markers revealed a high degree of similarity among Anadoras weddellii and Anadoras sp. "araguaia," both have 2n = 56 chromosomes (24m + 10sm + 22st/a), single NOR sites on acrocentric pair 28, and 5S rDNA sites on submetacentric pair 15. A. grypus has the most divergent chromosomal characteristics because, even though it also has 2n = 56 chromosomes, it exhibits several differences in the chromosome formula, heterochromatin distribution, and number/position of the rDNA sites. In sum, we believe that the chromosome diversification of Anadoras is due to 4 mechanisms: centric fusion, pericentric/paracentric inversions, nonreciprocal translocations, and activity of transposable elements. Additionally, our phylogenetic tree revealed well-supported clades and, by barcode species delimitation analysis, confirmed the existence of 3 molecular operational taxonomic units, including the putative new species Anadoras sp. "araguaia."
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Affiliation(s)
- Fábio Hiroshi Takagui
- Laboratory of Animal Cytogenetics, Department of General Biology, CCB, State University of Londrina, Londrina, Brazil
| | - Lucas Baumgärtner
- Cytogenetic Laboratory, Center of Biological and Health Sciences, State University of Western Paraná, Cascavel, Brazil
| | - Patrik Viana
- Laboratory of Animal Genetics, National Institute of Amazonian Research, Manaus, Brazil
| | - Moema C C Lima
- Laboratory of Genetics and Animal Ecology, Department of General Biology, CCB, State University of Londrina, Londrina, Brazil
| | - Jamille de A Bitencourt
- Cytogenetic Laboratory, Department of Biological Sciences, State University of Southwest of Bahia, Jequié, Brazil
| | - Paulo Cesar Venere
- Laboratory of Animal Cytogenetics and Genetics, Federal University of Mato Grosso, Cuiabá, Brazil
| | - Roberto Laridondo Lui
- Cytogenetic Laboratory, Center of Biological and Health Sciences, State University of Western Paraná, Cascavel, Brazil
| | - Orlando Moreira-Filho
- Laboratory of Molecular Biodiversity and Conservation, Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Eliana Feldberg
- Laboratory of Animal Genetics, National Institute of Amazonian Research, Manaus, Brazil
| | - Fernanda Almeida Simões
- Laboratory of Genetics and Animal Ecology, Department of General Biology, CCB, State University of Londrina, Londrina, Brazil
| | - José Luis Birindelli
- Museum of Zoology, Department of Animal and Plant Biology, CCB, Londrina State University, Londrina, Brazil
| | - Lucia Giuliano-Caetano
- Laboratory of Animal Cytogenetics, Department of General Biology, CCB, State University of Londrina, Londrina, Brazil
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Deon GA, Glugoski L, Sassi FDMC, Hatanaka T, Nogaroto V, Bertollo LAC, Liehr T, Al-Rikabi A, Moreira-Filho O, Cioffi MDB, Vicari MR. Chromosomal Rearrangements and Origin of the Multiple XX/XY 1Y 2 Sex Chromosome System in Harttia Species (Siluriformes: Loricariidae). Front Genet 2022; 13:877522. [PMID: 35386289 PMCID: PMC8977651 DOI: 10.3389/fgene.2022.877522] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
The Neotropical genus Harttia comprises species with extensive chromosomal remodeling and distinct sex chromosome systems (SCSs). So far, three different SCSs with male heterogamety have been characterized in the group. In some species, the presence of the XX/XY1Y2 SCS is associated with a decrease in diploid numbers and several chromosomal rearrangements, although a direct relation to sex chromosome differentiation has not been shown yet. Here, we aimed to investigate the differentiation processes that have led to the establishment of the rare XX/XY1Y2 SCS and track its evolutionary history among other Harttia species. For that, four whole chromosome painting probes derived from chromosome 1 of H. torrenticola (HTO-1), chromosomes 9 and X of H. carvalhoi (HCA-9 and HCA-X), and chromosome X from H. intermontana (HIN-X) were applied in nine Harttia species. Homeologous chromosome blocks were located in Harttia species and demonstrated that Robertsonian (Rb) fusions originated HTO-1, HCA-9, and HCA-X chromosomes, while Rb fissions explain Y1 and Y2 sex chromosomes. Specifically, in H. intermontana, HCA-X, HCA-9, and the NOR-bearing chromosome demonstrated that homeologous blocks were used in the HIN-X and metacentric pair 2 origins. Consequently, diploid numbers changed between the studied species. Overall, the data also reinforce the existence of unstable genomic sites promoting chromosomal differentiation and remodeling within the genus Harttia.
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Affiliation(s)
- Geize Aparecida Deon
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo, Brazil.,Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Paraná, Brazil
| | - Larissa Glugoski
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo, Brazil.,Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Paraná, Brazil
| | | | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo, Brazil
| | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Paraná, Brazil
| | | | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Ahmed Al-Rikabi
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo, Brazil
| | | | - Marcelo Ricardo Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Paraná, Brazil
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20
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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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21
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Vicari MR, Bruschi DP, Cabral-de-Mello DC, Nogaroto V. Telomere organization and the interstitial telomeric sites involvement in insects and vertebrates chromosome evolution. Genet Mol Biol 2022; 45:e20220071. [DOI: 10.1590/1678-4685-gmb-2022-0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 09/24/2022] [Indexed: 11/16/2022] Open
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22
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Santos da Silva K, de Souza ACP, Pety AM, Noronha RCR, Vicari MR, Pieczarka JC, Nagamachi CY. Comparative Cytogenetics Analysis Among Peckoltia Species (Siluriformes, Loricariidae): Insights on Karyotype Evolution and Biogeography in the Amazon Region. Front Genet 2021; 12:779464. [PMID: 34777486 PMCID: PMC8581261 DOI: 10.3389/fgene.2021.779464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Peckoltia is widely distributed genus in the Amazon and Orinoco basins and the Guiana Shield, containing 18 valid species, and distinct morphotypes still needing description in the scientific literature due to its great taxonomic complexity. This study performed a comparative chromosomal analysis of two undescribed Peckoltia species (Peckoltia sp. 3 Jarumã and Peckoltia sp. 4 Caripetuba) from the Brazilian Amazon using conventional chromosome bands methods and in situ localization of the repetitive DNA (5S and 18S rRNA and U1 snRNA genes and telomeric sequences). Both species presented 2n = 52 but differed in their karyotype formula, probably due to inversions or translocations. The nucleolus organizer regions (NORs) showed distal location on a probably homeologous submetacentric pair in both species, besides an extra signal in a subtelocentric chromosome in Peckoltia sp. 4 Caripetuba. Heterochromatin occurred in large blocks, with different distributions in the species. The mapping of the 18S and 5S rDNA, and U1 snDNA showed differences in locations and number of sites. No interstitial telomeric sites were detected using the (TTAGGG)n probes. Despite 2n conservationism in Peckoltia species, the results showed variation in karyotype formulas, chromosomal bands, and locations of repetitive sites, demonstrating great chromosomal diversity. A proposal for Peckoltia karyotype evolution was inferred in this study based on the diversity of location and number of chromosomal markers analyzed. A comparative analysis with other Peckoltia karyotypes described in the literature, their biogeography patterns, and molecular phylogeny led to the hypothesis that the derived karyotype was raised in the left bank of the Amazon River.
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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
| | - Augusto Cesar Paes de Souza
- Laboratório de Estudos da Ictiofauna da Amazônia, Instituto Federal de Educação Ciência e Tecnologia Do Pará, Abaetetuba, Brazil
| | - Ananda Marques Pety
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará, Belém, Brazil
| | - Renata Coelho Rodrigues Noronha
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará, Belém, 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
| | - 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
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23
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Rodrigues PP, Machado MDA, Pety AM, Silva DDS, de Souza ACP, Pieczarka JC, Nagamachi CY. Archolaemus janeae (Gymnotiformes, Teleostei): First insights into karyotype and repetitive DNA distribution in two populations of the Amazon. Ecol Evol 2021; 11:15468-15476. [PMID: 34824768 PMCID: PMC8601878 DOI: 10.1002/ece3.8092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 07/19/2021] [Accepted: 08/24/2021] [Indexed: 12/02/2022] Open
Abstract
Archolaemus, one of the five genera of Neotropical freshwater fish of the family Sternopygidae (Gymnotiformes), was long considered a monotypic genus represented by Archolaemus blax. Currently, it consists of six species, most of them occurring in the Amazon region. There are no cytogenetic data for species of this genus. In the present study, we used classical cytogenetics (conventional staining and C-banding) and molecular cytogenetics (probes of telomeric sequences and multigenic families 18S rDNA, 5S rDNA, and U2 snDNA) to study the karyotype of Archolaemus janeae from Xingu and Tapajós rivers in the state of Pará (Brazil). The results showed that the two populations have identical karyotypes with 46 chromosomes: four submetacentric and 42 acrocentric (2n = 46; 4m/sm + 42a). Constitutive heterochromatin occurs in the centromeric region of all chromosomes, in addition to small bands in the interstitial and distal regions of some pairs. The 18S rDNA occurs in the distal region of the short arm of pair 2; the 5S rDNA occurs in five chromosome pairs; and the U2 snDNA sequence occurs in chromosome pairs 3, 6, and 13. No interstitial telomeric sequence was observed. These results show karyotypic similarity between the studied populations suggesting the existence of a single species and are of great importance as a reference for future cytotaxonomic studies of the genus.
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Affiliation(s)
- Paula Pinto Rodrigues
- Laboratório de CitogenéticaCentro de Estudos Avançados da BiodiversidadeInstituto de Ciências BiológicasUniversidade Federal do Pará (UFPA)BelémBrazil
| | - Milla de Andrade Machado
- Laboratório de CitogenéticaCentro de Estudos Avançados da BiodiversidadeInstituto de Ciências BiológicasUniversidade Federal do Pará (UFPA)BelémBrazil
| | - Ananda Marques Pety
- Laboratório de CitogenéticaCentro de Estudos Avançados da BiodiversidadeInstituto de Ciências BiológicasUniversidade Federal do Pará (UFPA)BelémBrazil
| | | | | | - Julio Cesar Pieczarka
- Laboratório de CitogenéticaCentro de Estudos Avançados da BiodiversidadeInstituto de Ciências BiológicasUniversidade Federal do Pará (UFPA)BelémBrazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de CitogenéticaCentro de Estudos Avançados da BiodiversidadeInstituto de Ciências BiológicasUniversidade Federal do Pará (UFPA)BelémBrazil
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24
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Adding New Pieces to the Puzzle of Karyotype Evolution in Harttia (Siluriformes, Loricariidae): Investigation of Amazonian Species. BIOLOGY 2021; 10:biology10090922. [PMID: 34571799 PMCID: PMC8472603 DOI: 10.3390/biology10090922] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/21/2022]
Abstract
A remarkable morphological diversity and karyotype variability can be observed in the Neotropical armored catfish genus Harttia. These fishes offer a useful model to explore both the evolution of karyotypes and sex chromosomes, since many species possess male-heterogametic sex chromosome systems and a high rate of karyotype repatterning. Based on the karyotype organization, the chromosomal distribution of several repetitive DNA classes, and the rough estimates of genomic divergences at the intraspecific and interspecific levels via Comparative Genomic Hybridization, we identified shared diploid chromosome numbers (2n = 54) but different karyotype compositions in H. dissidens (20m + 26sm + 8a) and Harttia sp. 3 (16m + 18sm + 14st + 6a), and different 2n in H. guianensis (2n = 58; 20m + 26sm + 2st + 10a). All species further displayed similar patterns of chromosomal distribution concerning constitutive heterochromatin, 18S ribosomal DNA (rDNA) sites, and most of the surveyed microsatellite motifs. Furthermore, differences in the distribution of 5S rDNA sites and a subset of microsatellite sequences were identified. Heteromorphic sex chromosomes were lacking in H. dissidens and H. guianensis at the scale of our analysis. However, one single chromosome pair in Harttia sp. 3 males presented a remarkable accumulation of male genome-derived probe after CGH, pointing to a tentative region of early sex chromosome differentiation. Thus, our data support already previously outlined evidence that Harttia is a vital model for the investigation of teleost karyotype and sex chromosome dynamics.
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25
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Cytogenetic, morphological and molecular characterization of two cryptic species of the genus Omophoita Chevrolat, 1837 (Coleoptera: Chrysomelidae: Galerucinae). Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00715-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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26
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Souza J, Guimarães E, Pinheiro-Figliuolo V, Cioffi MB, Bertollo LAC, Feldberg E. Chromosomal Analysis of Ctenolucius hujeta Valenciennes, 1850 (Characiformes): A New Piece in the Chromosomal Evolution of the Ctenoluciidae. Cytogenet Genome Res 2021; 161:195-202. [PMID: 34126615 DOI: 10.1159/000515456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/25/2021] [Indexed: 11/19/2022] Open
Abstract
Ctenoluciidae (Characiformes), a family of freshwater fishes, comprises 2 genera, Ctenolucius and Boulengerella, with 7 recognized species. Up to now, only species of the genus Boulengerella have been subjected to cytogenetic studies. Here, we investigated the karyotype and other cytogenetic features of pike characin, Ctenolucius hujeta, using conventional (Giemsa staining, C-banding, Ag-NOR staining) and molecular (rDNA, telomeric sequences, and fiber-FISH mapping) procedures. This species has a diploid chromosome number of 2n = 36, and a karyotype composed of 12m + 20sm + 4a and FN = 68, similar to that found in Boulengerella species. However, differences regarding the number and distribution of several chromosomal markers support a distinct generic status. Colocalization of the 18S and 5S rDNA genes is an exclusive characteristic of the C. hujeta genome, with an interspersed distribution in the chromosomal fiber, an unusual phenomenon among eukaryotes. Additionally, our results support the view that Ctenoluciidae and Lebiasinidae families are closely related.
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Affiliation(s)
- José Souza
- Laboratory of Animal Genetics, National Institute of Amazonian Research (INPA), Manaus, Brazil
| | - Erika Guimarães
- Laboratory of Animal Genetics, National Institute of Amazonian Research (INPA), Manaus, Brazil
| | | | - Marcelo B Cioffi
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Luiz A C Bertollo
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Eliana Feldberg
- Laboratory of Animal Genetics, National Institute of Amazonian Research (INPA), Manaus, Brazil
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27
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Ferreira AMV, Viana PF, Zuanon J, Ezaz T, Cioffi MB, Takagui FH, Feldberg E. Cytogenetic Analysis of Panaqolus tankei Cramer & Sousa, 2016 (Siluriformes, Loricariidae), an Ornamental Fish Endemic to Xingu River, Brazil. Cytogenet Genome Res 2021; 161:187-194. [PMID: 33744896 DOI: 10.1159/000514061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 12/23/2020] [Indexed: 11/19/2022] Open
Abstract
Despite conservation of the diploid number, a huge diversity in karyotype formulae is found in the Ancistrini tribe (Loricariidae, Hypostominae). However, the lack of cytogenetic data for many groups impairs a comprehensive understanding of the chromosomal relationships and the impact of chromosomal changes on their evolutionary history. Here, we present for the first time the karyotype of Panaqolus tankei Cramer & Sousa, 2016. We focused on the chromosomal characterization, using conventional and molecular cytogenetic techniques to unravel the evolutionary trends of this tribe. P. tankei, as most species of its sister group Pterygoplichthini, also possessess a conserved diploid number of 52 chromosomes. We observed heterochromatin regions in the centromeres of many chromosomes; pairs 5 and 6 presented interstitial heterochromatin regions, whereas pairs 23 and 24 showed extensive heterochromatin regions in their q arms. In situ localization of 18S rDNA showed hybridization signals correlating with the nucleolus organizer regions, which are located in the q arms of pair 5. However, the 5S rDNA was detected in the centromeric and terminal regions of the q arms of pair 8. (TTAGGG)n hybridized only in the terminal regions of all chromosomes. Microsatellite in situ localization showed divergent patterns, (GA)15 repeated sequences were restricted to the terminal regions of some chromosomes, whereas (AC)15 and (GT)15 showed a scattered hybridization pattern throughout the genome. Intraspecific comparative genomic hybridization was performed on the chromosomes of P. tankei to verify the existence of sex-specific regions. The results revealed only a limited number of overlapping hybridization signals, coinciding with the heterochromatin in centromeric regions without any sex-specific signals in both males and females. Our study provides a karyotype description of P. tankei, highlighting extensive differences in the karyotype formula, the heterochromatin regions, and sites of 5S and 18S rDNA, as compared with data available for the genus.
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Affiliation(s)
- Alex M V Ferreira
- Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Manaus, Brazil,
| | - Patrik F Viana
- Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Manaus, Brazil
| | - Jansen Zuanon
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Manaus, Brazil
| | - Tariq Ezaz
- Institute for Applied Ecology, Faculty of Science and Technology, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Marcelo B Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Fábio H Takagui
- Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Brazil
| | - Eliana Feldberg
- Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Manaus, Brazil
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28
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Alam SMI, Sarre SD, Georges A, Ezaz T. Karyotype Characterisation of Two Australian Dragon Lizards (Squamata: Agamidae: Amphibolurinae) Reveals Subtle Chromosomal Rearrangements Between Related Species with Similar Karyotypes. Cytogenet Genome Res 2020; 160:610-624. [PMID: 33207346 DOI: 10.1159/000511344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 09/02/2020] [Indexed: 11/19/2022] Open
Abstract
Agamid lizards (Squamata: Agamidae) are karyotypically heterogeneous. Among the 101 species currently described from Australia, all are from the subfamily Amphibolurinae. This group is, with some exceptions, karyotypically conserved, and all species involving heterogametic sex show female heterogamety. Here, we describe the chromosomes of 2 additional Australian agamid lizards, Tympanocryptis lineata and Rankinia diemensis. These species are phylogenetically and cytogenetically sisters to the well-characterised Pogona vitticeps, but their sex chromosomes and other chromosomal characteristics are unknown. In this study, we applied advanced molecular cytogenetic techniques, such as fluorescence in situ hybridisation (FISH) and cross-species gene mapping, to characterise chromosomes and to identify sex chromosomes in these species. Our data suggest that both species have a conserved karyotype with P. vitticeps but with subtle rearrangements in the chromosomal landscapes. We could identify that T. lineata possesses a female heterogametic system (ZZ/ZW) with a pair of sex microchromosomes, while R. diemensis may have heterogametic sex chromosomes, but this requires further investigations. Our study shows the pattern of chromosomal rearrangements between closely related species, explaining the speciation within Australian agamid lizards of similar karyotypes.
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Affiliation(s)
- Shayer M I Alam
- Centre for Conservation Ecology and Genetics, Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia,
| | - Stephen D Sarre
- Centre for Conservation Ecology and Genetics, Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Arthur Georges
- Centre for Conservation Ecology and Genetics, Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Tariq Ezaz
- Centre for Conservation Ecology and Genetics, Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia
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29
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Highly Rearranged Karyotypes and Multiple Sex Chromosome Systems in Armored Catfishes from the Genus Harttia (Teleostei, Siluriformes). Genes (Basel) 2020; 11:genes11111366. [PMID: 33218104 PMCID: PMC7698909 DOI: 10.3390/genes11111366] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022] Open
Abstract
Harttia comprises an armored catfish genus endemic to the Neotropical region, including 27 valid species with low dispersion rates that are restricted to small distribution areas. Cytogenetics data point to a wide chromosomal diversity in this genus due to changes that occurred in isolated populations, with chromosomal fusions and fissions explaining the 2n number variation. In addition, different multiple sex chromosome systems and rDNA loci location are also found in some species. However, several Harttia species and populations remain to be investigated. In this study, Harttia intermontana and two still undescribed species, morphologically identified as Harttia sp. 1 and Harttia sp. 2, were cytogenetically analyzed. Harttia intermontana has 2n = 52 and 2n = 53 chromosomes, while Harttia sp. 1 has 2n = 56 and 2n = 57 chromosomes in females and males, respectively, thus highlighting the occurrence of an XX/XY1Y2 multiple sex chromosome system in both species. Harttia sp. 2 presents 2n = 62 chromosomes for both females and males, with fission events explaining its karyotype diversification. Chromosomal locations of the rDNA sites were also quite different among species, reinforcing that extensive rearrangements had occurred in their karyotype evolution. Comparative genomic hybridization (CGH) experiments among some Harttia species evidenced a shared content of the XY1Y2 sex chromosomes in three of them, thus pointing towards their common origin. Therefore, the comparative analysis among all Harttia species cytogenetically studied thus far allowed us to provide an evolutionary scenario related to the speciation process of this fish group.
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30
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Karyotype and leaf epidermis histology traits of Digitaria abyssinica (Hochst. Ex A. Rich.) (Poaceae). Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00630-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Dulz TA, Azambuja M, Nascimento VD, Lorscheider CA, Noleto RB, Moreira-Filho O, Nogaroto V, Diniz D, Affonso PRADM, Vicari MR. Karyotypic Diversification in Two Megaleporinus Species (Characiformes, Anostomidae) Inferred from In Situ Localization of Repetitive DNA Sequences. Zebrafish 2020; 17:333-341. [PMID: 32990531 DOI: 10.1089/zeb.2020.1918] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Anostomidae species have conserved diploid numbers (2n = 54), although comparative cytogenetic studies have demonstrated chromosomal rearrangements occurrence among them, especially in repetitive DNA rich regions. The location and distribution of ribosomal DNA (rDNA) and small nuclear RNAs (snRNAs) multigene families are highly dynamic in the genomes of several organisms. In this study, we in situ located the rDNA and snRNA sites in two populations of Megaleporinus obtusidens and a sample of Megaleporinus reinhardti to infer their chromosomal changes in the evolutionary lineages. Both species of Megaleporinus shared 2n = 54 chromosomes with the presence of ZZ/ZW sex chromosome system, but they diverged in relationship to the location of 5S and 45S rDNAs as well as the distribution of snRNAs sites. The characterization of the analyzed sequences revealed the presence of complete rDNA and snRNAs sequences as well as snRNAs containing transposable elements (TEs) and microsatellite repeats. After chromosomal mapping, the sequences encompassing TEs proved to be dispersed through autosomes and accumulated on sex chromosomes. The data demonstrate that intra- and interspecific chromosomal changes occurred involving the multigene family's sites in Megaleporinus karyotypes. Furthermore, we detected TE-like sequences in the differentiation of sex chromosome systems in M. obtusidens and M. reinhardti.
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Affiliation(s)
- Thais Aparecida Dulz
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil.,Departamento de Ciências Biológicas, Universidade Estadual do Paraná, União da Vitória, Brazil
| | - Matheus Azambuja
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | | | | | - Rafael Bueno Noleto
- Departamento de Ciências Biológicas, Universidade Estadual do Paraná, União da Vitória, Brazil
| | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Débora Diniz
- Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Brazil
| | | | - Marcelo Ricardo Vicari
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil.,Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
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The Amazonian Red Side-Necked Turtle Rhinemys rufipes (Spix, 1824) (Testudines, Chelidae) Has a GSD Sex-Determining Mechanism with an Ancient XY Sex Microchromosome System. Cells 2020; 9:cells9092088. [PMID: 32932633 PMCID: PMC7563702 DOI: 10.3390/cells9092088] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 02/06/2023] Open
Abstract
The Amazonian red side-necked turtle Rhynemis rufipes is an endemic Amazonian Chelidae species that occurs in small streams throughout Colombia and Brazil river basins. Little is known about various biological aspects of this species, including its sex determination strategies. Among chelids, the greatest karyotype diversity is found in the Neotropical species, with several 2n configurations, including cases of triploidy. Here, we investigate the karyotype of Rhinemys rufipes by applying combined conventional and molecular cytogenetic procedures. This allowed us to discover a genetic sex-determining mechanism that shares an ancestral micro XY sex chromosome system. This ancient micro XY system recruited distinct repeat motifs before it diverged from several South America and Australasian species. We propose that such a system dates back to the earliest lineages of the chelid species before the split of South America and Australasian lineages.
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Malimpensa GDC, Traldi JB, Martinez JDF, Deon G, Azambuja M, Nogaroto V, Vicari MR, Moreira-Filho O. Chromosomal Diversification in Two Species of Pimelodus (Siluriformes: Pimelodidae): Comparative Cytogenetic Mapping of Multigene Families. Zebrafish 2020; 17:278-286. [DOI: 10.1089/zeb.2020.1892] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
| | | | | | - Geize Deon
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Matheus Azambuja
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Marcelo Ricardo Vicari
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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Cavalcante MG, Nagamachi CY, Pieczarka JC, Noronha RCR. Evolutionary insights in Amazonian turtles (Testudines, Podocnemididae): co-location of 5S rDNA and U2 snRNA and wide distribution of Tc1/Mariner. Biol Open 2020; 9:bio049817. [PMID: 32229487 PMCID: PMC7197720 DOI: 10.1242/bio.049817] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/18/2020] [Indexed: 12/29/2022] Open
Abstract
Eukaryotic genomes exhibit substantial accumulation of repetitive DNA sequences. These sequences can participate in chromosomal reorganization events and undergo molecular cooption to interfere with the function and evolution of genomes. In turtles, repetitive DNA sequences appear to be accumulated at probable break points and may participate in events such as non-homologous recombination and chromosomal rearrangements. In this study, repeated sequences of 5S rDNA, U2 snRNA and Tc1/Mariner transposons were amplified from the genomes of the turtles, Podocnemis expansa and Podocnemis unifilis, and mapped by fluorescence in situ hybridization. Our data confirm the 2n=28 chromosomes for these species (the second lowest 2n in the order Testudines). We observe high conservation of the co-located 5S rDNA and U2 snRNA genes on a small chromosome pair (pair 13), and surmise that this represents the ancestral condition. Our analysis reveals a wide distribution of the Tc1/Mariner transposons and we discuss how the mobility of these transposons can act on karyotypic reorganization events (contributing to the 2n decrease of those species). Our data add new information for the order Testudines and provide important insights into the dynamics and organization of these sequences in the chelonian genomes.
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Affiliation(s)
- Manoella Gemaque Cavalcante
- Centro de Estudos Avançados da Biodiversidade, Cytogenetics Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Cleusa Yoshiko Nagamachi
- Centro de Estudos Avançados da Biodiversidade, Cytogenetics Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Julio Cesar Pieczarka
- Centro de Estudos Avançados da Biodiversidade, Cytogenetics Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Renata Coelho Rodrigues Noronha
- Centro de Estudos Avançados da Biodiversidade, Cytogenetics Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
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Sember A, de Oliveira EA, Ráb P, Bertollo LAC, de Freitas NL, Viana PF, Yano CF, Hatanaka T, Marinho MMF, de Moraes RLR, Feldberg E, Cioffi MDB. Centric Fusions behind the Karyotype Evolution of Neotropical Nannostomus Pencilfishes (Characiforme, Lebiasinidae): First Insights from a Molecular Cytogenetic Perspective. Genes (Basel) 2020; 11:genes11010091. [PMID: 31941136 PMCID: PMC7017317 DOI: 10.3390/genes11010091] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 02/07/2023] Open
Abstract
Lebiasinidae is a Neotropical freshwater family widely distributed throughout South and Central America. Due to their often very small body size, Lebiasinidae species are cytogenetically challenging and hence largely underexplored. However, the available but limited karyotype data already suggested a high interspecific variability in the diploid chromosome number (2n), which is pronounced in the speciose genus Nannostomus, a popular taxon in ornamental fish trade due to its remarkable body coloration. Aiming to more deeply examine the karyotype diversification in Nannostomus, we combined conventional cytogenetics (Giemsa-staining and C-banding) with the chromosomal mapping of tandemly repeated 5S and 18S rDNA clusters and with interspecific comparative genomic hybridization (CGH) to investigate genomes of four representative Nannostomus species: N. beckfordi, N. eques, N. marginatus, and N. unifasciatus. Our data showed a remarkable variability in 2n, ranging from 2n = 22 in N. unifasciatus (karyotype composed exclusively of metacentrics/submetacentrics) to 2n = 44 in N. beckfordi (karyotype composed entirely of acrocentrics). On the other hand, patterns of 18S and 5S rDNA distribution in the analyzed karyotypes remained rather conservative, with only two 18S and two to four 5S rDNA sites. In view of the mostly unchanged number of chromosome arms (FN = 44) in all but one species (N. eques; FN = 36), and with respect to the current phylogenetic hypothesis, we propose Robertsonian translocations to be a significant contributor to the karyotype differentiation in (at least herein studied) Nannostomus species. Interspecific comparative genome hybridization (CGH) using whole genomic DNAs mapped against the chromosome background of N. beckfordi found a moderate divergence in the repetitive DNA content among the species’ genomes. Collectively, our data suggest that the karyotype differentiation in Nannostomus has been largely driven by major structural rearrangements, accompanied by only low to moderate dynamics of repetitive DNA at the sub-chromosomal level. Possible mechanisms and factors behind the elevated tolerance to such a rate of karyotype change in Nannostomus are discussed.
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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; (A.S.); (P.R.)
| | - Ezequiel Aguiar de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
- Secretaria de Estado de Educação de Mato Grosso–SEDUC-MT, Cuiabá 78049-909, Brazil
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic; (A.S.); (P.R.)
| | - Luiz Antonio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
| | - Natália Lourenço de Freitas
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
| | - Patrik Ferreira Viana
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, Brazil; (P.F.V.); (E.F.)
| | - Cassia Fernanda Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
| | - Manoela Maria Ferreira Marinho
- Universidade Federal da Paraíba (UFPB), Departamento de Sistemática e Ecologia (DSE), Laboratório de Sistemática e Morfologia de Peixes, João Pessoa 58051-090, Brazil;
| | - Renata Luiza Rosa de Moraes
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
| | - Eliana Feldberg
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, Brazil; (P.F.V.); (E.F.)
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
- Correspondence: ; Tel.: +55-16-3351-8431; Fax: +55-16-3351-8377
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Glugoski L, Deon G, Schott S, Vicari MR, Nogaroto V, Moreira-Filho O. Comparative cytogenetic analyses in Ancistrus species (Siluriformes: Loricariidae). NEOTROPICAL ICHTHYOLOGY 2020. [DOI: 10.1590/1982-0224-2020-0013] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
ABSTRACT Ancistrus is a specious genus of armored catfishes that has been extensively used for cytogenetic studies in the last 17 years. A comparison of the extensive karyotypic plasticity within this genus is presented with new cytogenetic analysis for Ancistrus cf. multispinis and Ancistrus aguaboensis. This study aims to improve our understanding of chromosomal evolution associated with changes in the diploid number (2n) and the dispersion of ribosomal DNAs (rDNAs) within Ancistrus. Ancistrus cf. multispinis and A. aguaboensis exhibit 2n of 52 and 50 chromosomes, respectively. Given that A. cf. multispinis shares a 2n = 52 also found in Pterygoplichthyini, the sister group for Ancistrini, a Robertsonian (Rb) fusion event is proposed for the 2n reduction in A. aguaboensis. 5S rDNAs pseudogenes sites have already been associated with Rb fusion in Ancistrus and our analysis suggests that the 2n reduction in A. aguaboensis was triggered by double strand breaks (DSBs) and chromosomal rearrangements at 5S rDNA sites. The presence of evolutionary breakpoint regions (EBRs) into rDNA cluster is proposed to explain part of the Rb fusion in Ancistrus. Cytogenetic data presented extends the diversity already documented in Ancistrus to further understand the role of chromosomal rearrangements in the diversification of Ancistrini.
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Affiliation(s)
| | - Geize Deon
- Universidade Federal de São Carlos, Brazil
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Toma GA, de Moraes RLR, Sassi FDMC, Bertollo LAC, de Oliveira EA, Rab P, Sember A, Liehr T, Hatanaka T, Viana PF, Marinho MMF, Feldberg E, Cioffi MDB. Cytogenetics of the small-sized fish, Copeina guttata (Characiformes, Lebiasinidae): Novel insights into the karyotype differentiation of the family. PLoS One 2019; 14:e0226746. [PMID: 31856256 PMCID: PMC6922430 DOI: 10.1371/journal.pone.0226746] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/04/2019] [Indexed: 11/19/2022] Open
Abstract
Lebiasinidae is a small fish family composed by miniature to small-sized fishes with few cytogenetic data (most of them limited to descriptions of diploid chromosome numbers), thus preventing any evolutionary comparative studies at the chromosomal level. In the present study, we are providing, the first cytogenetic data for the red spotted tetra, Copeina guttata, including the standard karyotype, C-banding, repetitive DNA mapping by fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH), providing chromosomal patterns and novel insights into the karyotype differentiation of the family. Males and females share diploid chromosome number 2n = 42 and karyotype composed of 2 metacentric (m), 4 submetacentric (sm) and 36 subtelocentric to acrocentric (st-a) chromosomes. Blocks of constitutive heterochromatin were observed in the centromeric and interstitial regions of several chromosomes, in addition to a remarkably large distal block, heteromorphic in size, which fully corresponded with the 18S rDNA sites in the fourth chromosomal pair. This overlap was confirmed by 5S/18S rDNA dual-color FISH. On the other hand, 5S rDNA clusters were situated in the long and short arms of the 2nd and 15th pairs, respectively. No sex-linked karyotype differences were revealed by male/female CGH experiments. The genomic probes from other two lebiasinid species, Lebiasina melanoguttata and Pyrrhulina brevis, showed positive hybridization signals only in the NOR region in the genome of C. guttata. We demonstrated that karyotype diversification in lebiasinids was accompanied by a series of structural and numeric chromosome rearrangements of different types, including particularly fusions and fissions.
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Affiliation(s)
- Gustavo Akira Toma
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Renata Luiza Rosa de Moraes
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | - Luiz Antonio Carlos Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Ezequiel Aguiar de Oliveira
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
- Secretaria de Estado de Educação de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Petr Rab
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Terumi Hatanaka
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | | | - Eliana Feldberg
- Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
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de Souza TB, Gaeta ML, Martins C, Vanzela ALL. IGS sequences in Cestrum present AT- and GC-rich conserved domains, with strong regulatory potential for 5S rDNA. Mol Biol Rep 2019; 47:55-66. [PMID: 31571109 DOI: 10.1007/s11033-019-05104-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/24/2019] [Indexed: 11/28/2022]
Abstract
The 35S and 5S ribosomal DNA (rDNA) organized in thousands of copies in genomes, have been widely used in numerous comparative cytogenetic studies. Nevertheless, several questions related to the diversity and organization of regulatory motifs in 5S rDNA remain to be addressed. The 5S rDNA unit is composed of a conserved 120 bp length coding region and an intergenic spacer (IGS) containing potential regulatory motifs (Poly-T, AT-rich and GC-rich) differing in number, redundancy and position along the IGS. The Cestrum species (Solanaceae) have large genomes (about 10 pg/1C) and conserved 2n = 16 karyotypes. Strikingly, these genomes show high diversity of heterochromatin distribution, variability in 35S rDNA loci and the occurrence of B chromosomes. However, the 5S rDNA loci are highly conserved in the proximal region of chromosome 8. Comparison of seventy-one IGS sequences in plants revealed several conserved motifs with potential regulatory function. The AT- and GC-rich domains appeared highly conserved in Cestrum chromosomes. The 5S genic and the GC-rich IGS probe produced FISH signals in both A (pair 8) and B chromosomes. The GC-rich domain presented a strong potential for regulation because it may be associated with CpG islands organization, as well as to hairpin and loop organization. Another interesting aspect was the ability of AT- and GC-rich motifs to produce non-heterochromatic CMA/DAPI signals. While the length of the 5S rDNA IGS region varied in size between the Cestrum species, the individual sequence motifs seem to be conserved suggesting their regulatory function. The most striking feature was the conserved GC-rich domain in Cestrum, which is recognized as a signature trait of the proximal region of chromosome pair 8.
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Affiliation(s)
- Thaíssa Boldieri de Souza
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, 86057-970, Brazil
| | - Marcos Letaif Gaeta
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, 86057-970, Brazil
| | - Cesar Martins
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, CEP 18618689, Brazil
| | - André Luís Laforga Vanzela
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, 86057-970, Brazil.
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Santos EOD, Deon GA, Almeida RBD, Oliveira EAD, Nogaroto V, Silva HPD, Pavanelli CS, Cestari MM, Bertollo LAC, Moreira-Filho O, Vicari MR. Cytogenetics and DNA barcode reveal an undescribed Apareiodon species (Characiformes: Parodontidae). Genet Mol Biol 2019; 42:365-373. [PMID: 31259363 PMCID: PMC6726146 DOI: 10.1590/1678-4685-gmb-2018-0066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 08/01/2018] [Indexed: 11/22/2022] Open
Abstract
Parodontidae is a small group of fish and some species are particularly difficult
to identify due to the lack of sufficiently consistent morphological traits.
Cytogenetically, the species possess 2n = 54 chromosomes and are either
sex-homomorphic or sex-heteromorphic (regarding its chromosomes). We evaluated
data on color, tooth morphology, cytogenetics, and mitochondrial markers (COI)
in Apareiodon specimens from the Aripuanã River (Amazon basin)
and the results were compared to other congeneric taxa. Morphological results
show an overlap of body color and tooth morphology to other known
Apareiodon. The cytogenetics data showed that the 2n = 54
chromosomes, 50 m/sm + 4 st and, a ZZ/ZW sex chromosome system in
Apareiodon sp. are common to other species of the genus.
However, the number and chromosomal localization of the 45S ribosomal and
pPh2004 satellite DNA sites, in addition to W chromosome
localization of the pPh2004 appear to be exclusive cytogenetic
features in Apareiodon sp. Our phylogenetic tree revealed
well-supported clades and confirmed, by barcode species delimitation analysis, a
new Molecular Operational Taxonomic Unit (MOTU) for Apareiodon
sp. (Aripuanã River). As a whole, the above features support the occurrence of a
new species of the Apareiodon, thus far unknown for the
Parodontidae.
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Affiliation(s)
- Emanoel Oliveira Dos Santos
- Departamento de Genética, Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Geize Aparecida Deon
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | - Rafael Bonfim de Almeida
- Departamento de Genética, Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | | | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | - Hugmar Pains da Silva
- Laboratório de Citogenética e Genética Animal, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil
| | - Carla Simone Pavanelli
- Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - Marta Margarete Cestari
- Departamento de Genética, Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | | | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, SP, Brazil
| | - Marcelo Ricardo Vicari
- Departamento de Genética, Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil.,Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
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40
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Sassi FDMC, Oliveira EAD, Bertollo LAC, Nirchio M, Hatanaka T, Marinho MMF, Moreira-Filho O, Aroutiounian R, Liehr T, Al-Rikabi ABH, Cioffi MDB. Chromosomal Evolution and Evolutionary Relationships of Lebiasina Species (Characiformes, Lebiasinidae). Int J Mol Sci 2019; 20:E2944. [PMID: 31208145 PMCID: PMC6628269 DOI: 10.3390/ijms20122944] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 01/21/2023] Open
Abstract
We present the first cytogenetic data for Lebiasina bimaculata and L. melanoguttata with the aim of (1) investigating evolutionary events within Lebiasina and their relationships with other Lebiasinidae genera and (2) checking the evolutionary relationships between Lebiasinidae and Ctenoluciidae. Both species have a diploid number 2n = 36 with similar karyotypes and microsatellite distribution patterns but present contrasting C-positive heterochromatin and CMA3+ banding patterns. The remarkable interstitial series of C-positive heterochromatin occurring in L. melanoguttata is absent in L. bimaculata. Accordingly, L. bimaculata shows the ribosomal DNA sites as the only GC-rich (CMA3+) regions, while L. melanoguttata shows evidence of a clear intercalated CMA3+ banding pattern. In addition, the multiple 5S and 18S rDNA sites in L. melanogutatta contrast with single sites present in L. bimaculata. Comparative genomic hybridization (CGH) experiments also revealed a high level of genomic differentiation between both species. A polymorphic state of a conspicuous C-positive, CMA3+, and (CGG)n band was found only to occur in L. bimaculata females, and its possible relationship with a nascent sex chromosome system is discussed. Whole chromosome painting (WCP) and CGH experiments indicate that the Lebiasina species examined and Boulengerella maculata share similar chromosomal sequences, thus supporting the relatedness between them and the evolutionary relationships between the Lebiasinidae and Ctenoluciidae families.
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Affiliation(s)
| | - Ezequiel Aguiar de Oliveira
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP 13565-905, Brazil.
- Secretaria de Estado de Educação de Mato Grosso-SEDUC-MT, Cuiabá, MT 78049-909, Brazil.
| | - Luiz Antonio Carlos Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP 13565-905, Brazil.
| | - Mauro Nirchio
- Facultad de Ciencias Agropecuarias, Universidad Técnica de Machala, Machala 070151, Ecuador.
| | - Terumi Hatanaka
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP 13565-905, Brazil.
| | | | - Orlando Moreira-Filho
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP 13565-905, Brazil.
| | - Rouben Aroutiounian
- Department of Genetics and Cytology, Yerevan State University, Yerevan 0063, Armenia.
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena 07747, Germany.
| | | | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP 13565-905, Brazil.
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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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Frade LFDS, Almeida BRRD, Milhomem-Paixão SSR, Ready JS, Nagamachi CY, Pieczarka JC, Noronha RCR. Karyoevolution of Crenicichla heckel 1840 (Cichlidae, Perciformes): a process mediated by inversions. Biol Open 2019; 8:bio.041699. [PMID: 31036749 PMCID: PMC6550074 DOI: 10.1242/bio.041699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Crenicichla (Cichliformes, Cichlidae) present a highly conserved diploid number 2n=48 with fundamental numbers varying between 52 and 62. We analyzed four species in order to investigate the role of repetitive DNA in chromosome evolution in the genus. Crenicichla johanna, Crenicichla cf. saxatilis and Crenicichla cf. regani have 2n=48 (8 m/sm and 40st/a) and FN=56, while Crenicichla sp. ‘Xingu I’ has 2n=48 (48 st/a) and FN=48. Different patterns of constitutive heterochromatin distribution were observed including pericentric, interstitial and whole arm C bands. A single chromosome bears 18S rDNA clusters in most species, except C. johanna, where population variation exists in terms of the quantity and distribution of clusters and their association with interstitial telomeric sequences. All species showed hybridization of 5S rDNA sequences in an interstitial region on an acrocentric chromosome pair. The karyotypic differences and maintenance of the diploid number supports chromosome evolution mediated by inversions in Crenicichla. The telomeric and 18S rDNA sequence association in various chromosomes of C. johanna are proposed to represent hotspots for breakage, favoring intra-chromosomal rearrangements. The results suggest that repetitive sequences can contribute to microstructural cytogenetic diversity in Crenicichla. Summary: This paper has a great importance for understanding karyotype evolutionary dynamics in neotropical freshwater fish, focusing on repetitive DNA and the role of inversions in Crenicichla.
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Affiliation(s)
- Luan Felipe da Silva Frade
- Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Campus Guamá, Rua Augusto Corrêa, n° 01. Guamá, Belém, Pará, Brasil
| | - Bruno Rafael Ribeiro de Almeida
- Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Campus Guamá, Rua Augusto Corrêa, n° 01. Guamá, Belém, Pará, Brasil
| | - Susana Suely Rodrigues Milhomem-Paixão
- Instituto Federal de Educação, Ciência e Tecnologia de Goiás, campus Valparaıso de Goiás, BR-040, km 6, Avenida Saia Velha, S/N, Área 8, Parque Esplanada V. 72.876-601, Valparaíso de Goiás, Goiás, Brasil
| | - Jonathan Stuart Ready
- Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Campus Guamá, Rua Augusto Corrêa, n° 01. Guamá, Belém, Pará, Brasil
| | - Cleusa Yoshiko Nagamachi
- Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Campus Guamá, Rua Augusto Corrêa, n° 01. Guamá, Belém, Pará, Brasil
| | - Julio Cesar Pieczarka
- Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Campus Guamá, Rua Augusto Corrêa, n° 01. Guamá, Belém, Pará, Brasil
| | - Renata Coelho Rodrigues Noronha
- Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Campus Guamá, Rua Augusto Corrêa, n° 01. Guamá, Belém, Pará, Brasil
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Benathar TCM, Nagamachi CY, Rodrigues LRR, O’Brien PCM, Ferguson-Smith MA, Yang F, Pieczarka JC. Karyotype, evolution and phylogenetic reconstruction in Micronycterinae bats with implications for the ancestral karyotype of Phyllostomidae. BMC Evol Biol 2019; 19:98. [PMID: 31064342 PMCID: PMC6505122 DOI: 10.1186/s12862-019-1421-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 04/11/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The Micronycterinae form a subfamily of leaf-nosed bats (Phyllostomidae) that contains the genera Lampronycteris Sanborn, 1949, and Micronycteris Gray, 1866 (stricto sensu), and is characterized by marked karyotypic variability and discrepancies in the phylogenetic relationships suggested by the molecular versus morphological data. In the present study, we investigated the chromosomal evolution of the Micronycterinae using classical cytogenetics and multidirectional chromosome painting with whole-chromosomes probes of Phyllostomus hastatus and Carollia brevicauda. Our goal was to perform comparative chromosome mapping between the genera of this subfamily and explore the potential for using chromosomal rearrangements as phylogenetic markers. RESULTS The Micronycterinae exhibit great inter- and intraspecific karyotype diversity, with large blocks of telomere-like sequences inserted within or adjacent to constitutive heterochromatin regions. The phylogenetic results generated from our chromosomal data revealed that the Micronycterinae hold a basal position in the phylogenetic tree of the Phyllostomidae. Molecular cytogenetic data confirmed that there is a low degree of karyotype similarity between Lampronycteris and Micronycteris specimens analyzed, indicating an absence of synapomorphic associations in Micronycterinae. CONCLUSIONS We herein confirm that karyotypic variability is present in subfamily Micronycterinae. We further report intraspecific variation and describe a new cytotype in M. megalotis. The cytogenetic data show that this group typically has large blocks of interstitial telomeric sequences that do not appear to be correlated with chromosomal rearrangement events. Phylogenetic analysis using chromosome data recovered the basal position for Micronycterinae, but did not demonstrate that it is a monophyletic lineage, due to the absence of common chromosomal synapomorphy between the genera. These findings may be related to an increase in the rate of chromosomal evolution during the time period that separates Lampronycteris from Micronycteris.
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Affiliation(s)
| | - C. Y. Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Av. Perimetral, sn. Guamá, Belém, Pará 66077 Brasil
- CNPq, Brasilia, Brazil
| | - L. R. R. Rodrigues
- Laboratório de Genética e Biodiversidade, ICED, Universidade Federal do Oeste do Pará, Belém, Brasil
| | - P. C. M. O’Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - M. A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - F. Yang
- Cytogenetics Facility, Welcome Trust Sanger Institute, Hinxton, UK
| | - J. C. Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Av. Perimetral, sn. Guamá, Belém, Pará 66077 Brasil
- CNPq, Brasilia, Brazil
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Aksenova AY, Mirkin SM. At the Beginning of the End and in the Middle of the Beginning: Structure and Maintenance of Telomeric DNA Repeats and Interstitial Telomeric Sequences. Genes (Basel) 2019; 10:genes10020118. [PMID: 30764567 PMCID: PMC6410037 DOI: 10.3390/genes10020118] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 02/07/2023] Open
Abstract
Tandem DNA repeats derived from the ancestral (TTAGGG)n run were first detected at chromosome ends of the majority of living organisms, hence the name telomeric DNA repeats. Subsequently, it has become clear that telomeric motifs are also present within chromosomes, and they were suitably called interstitial telomeric sequences (ITSs). It is well known that telomeric DNA repeats play a key role in chromosome stability, preventing end-to-end fusions and precluding the recurrent DNA loss during replication. Recent data suggest that ITSs are also important genomic elements as they confer its karyotype plasticity. In fact, ITSs appeared to be among the most unstable microsatellite sequences as they are highly length polymorphic and can trigger chromosomal fragility and gross chromosomal rearrangements. Importantly, mechanisms responsible for their instability appear to be similar to the mechanisms that maintain the length of genuine telomeres. This review compares the mechanisms of maintenance and dynamic properties of telomeric repeats and ITSs and discusses the implications of these dynamics on genome stability.
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Affiliation(s)
- Anna Y Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02421, USA.
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45
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Wellband K, Mérot C, Linnansaari T, Elliott JAK, Curry RA, Bernatchez L. Chromosomal fusion and life history-associated genomic variation contribute to within-river local adaptation of Atlantic salmon. Mol Ecol 2018; 28:1439-1459. [PMID: 30506831 DOI: 10.1111/mec.14965] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 12/30/2022]
Abstract
Chromosomal inversions have been implicated in facilitating adaptation in the face of high levels of gene flow, but whether chromosomal fusions also have similar potential remains poorly understood. Atlantic salmon are usually characterized by population structure at multiple spatial scales; however, this is not the case for tributaries of the Miramichi River in North America. To resolve genetic relationships between populations in this system and the potential for known chromosomal fusions to contribute to adaptation, we genotyped 728 juvenile salmon using a 50 K SNP array. Consistent with previous work, we report extremely weak overall population structuring (Global FST = 0.004) and failed to support hierarchical structure between the river's two main branches. We provide the first genomic characterization of a previously described polymorphic fusion between chromosomes 8 and 29. Fusion genomic characteristics included high LD, reduced heterozygosity in the fused homokaryotes, and strong divergence between the fused and the unfused rearrangement. Population structure based on fusion karyotype was five times stronger than neutral variation (FST = 0.019), and the frequency of the fusion was associated with summer precipitation supporting a hypothesis that this rearrangement may contribute local adaptation despite weak neutral differentiation. Additionally, both outlier variation among populations and a polygenic framework for characterizing adaptive variation in relation to climate identified a 250-Kb region of chromosome 9, including the gene six6 that has previously been linked to age-at-maturity and run-timing for this species. Overall, our results indicate that adaptive processes, independent of major river branching, are more important than neutral processes for structuring these populations.
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Affiliation(s)
- Kyle Wellband
- Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
| | - Tommi Linnansaari
- Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - J A K Elliott
- Cooke Aquaculture Inc, Oak Bay, New Brunswick, Canada
| | - R Allen Curry
- Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
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46
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Rosolen LAM, Vicari MR, Almeida MC. Accumulation of Transposable Elements in Autosomes and Giant Sex Chromosomes of Omophoita (Chrysomelidae: Alticinae). Cytogenet Genome Res 2018; 156:215-222. [PMID: 30504708 DOI: 10.1159/000495199] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2018] [Indexed: 12/28/2022] Open
Abstract
Coleoptera is the most diverse order among insects, and comparative molecular cytogenetic studies in this group are lacking. The species of Omophoita (Oedionychina) possess a karyotype of 2n = 22 = 10II+X+Y. They are interesting models for evolutionary cytogenetic studies due to giant sex chromosomes which are asynaptic during meiosis. Transposable elements (TEs) confer plasticity and mobility to genomes and are considered hotspots for DNA double-strand breaks and chromosomal rearrangements. The objective of the present study was to verify the role of TEs in the karyotype and in the size expansion of the giant sex chromosomes in Omophoita. Thus, different TEs were characterized in the Omophoita genome and localized in the chromosomes by fluorescence in situ hybridization (FISH). The DNA sequencing data revealed identity with TE families Tc1/Mariner and RTE/L1-56_XT. FISH showed signals of all TEs in the karyotypes and a high accumulation in the sex chromosomes of the 3 Omophoita species analyzed. These data suggest that the genome size expansion and the origin of the giant sex chromosomes of Omophoita are due to an intensive genomic invasion of TEs, as those characterized here as Tc1/Mariner-Ooc and RTE-Ooc. Differences in the chromosomal location of the TEs among the 3 species indicate that they have participated in the karyotype differentiation in Omophoita.
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47
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Bueno V, Konerat JT, Zawadzki CH, Venere PC, Blanco DR, Margarido VP. Divergent Chromosome Evolution in Hypostominae Tribes (Siluriformes: Loricariidae): Correlation of Chromosomal Data with Morphological and Molecular Phylogenies. Zebrafish 2018; 15:492-503. [DOI: 10.1089/zeb.2018.1612] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Vanessa Bueno
- Coordenação do Curso de Ciências Biológicas, Universidade Tecnológica Federal do Paraná, Santa Helena, Brazil
| | - Jocicléia Thums Konerat
- Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná, Cascavel, Brazil
| | | | - Paulo Cesar Venere
- Laboratório de Citogenética e Genética Animal, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, Brazil
| | - Daniel Rodrigues Blanco
- Coordenação do Curso de Ciências Biológicas, Universidade Tecnológica Federal do Paraná, Santa Helena, Brazil
| | - Vladimir Pavan Margarido
- Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná, Cascavel, Brazil
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48
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Prizon AC, Bruschi DP, Gazolla CB, Borin-Carvalho LA, Portela-Castro ALDB. Chromosome Spreading of the Retrotransposable Rex-3 Element and Microsatellite Repeats in Karyotypes of the Ancistrus Populations. Zebrafish 2018; 15:504-514. [DOI: 10.1089/zeb.2018.1620] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Ana Camila Prizon
- Department of Biotechnology, Genetics and Cellular Biology, Universidade Estadual de Maringá, Maringá, Brazil
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49
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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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50
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Cavalcante MG, Bastos CEMC, Nagamachi CY, Pieczarka JC, Vicari MR, Noronha RCR. Physical mapping of repetitive DNA suggests 2n reduction in Amazon turtles Podocnemis (Testudines: Podocnemididae). PLoS One 2018; 13:e0197536. [PMID: 29813087 PMCID: PMC5973585 DOI: 10.1371/journal.pone.0197536] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/03/2018] [Indexed: 01/27/2023] Open
Abstract
Cytogenetic studies show that there is great karyotypic diversity in order Testudines (2n = 26-68), and that this may be mainly attributed to the presence/absence of microchromosomes. Members of the Podocnemididae family have the smallest diploid numbers of this order (2n = 26-28), which may be a derived condition of the group. Diverse studies suggest that repetitive-DNA-rich sites generally act as hotspots for double-strand breaks and chromosomal reorganization. In this context, we used fluorescent in situ hybridization (FISH) to map telomeric sequences (TTAGGG)n, 45S rDNA, and the genes encoding histones H1 and H3 in two species of genus Podocnemis. We also observed conservation of the 45S rDNA and H1 histone sequences (probable case of conserved synteny), but multiple conserved and non-conserved clusters of H3 genes, which colocalized with the interstitial telomeric sequences in the Podocnemis genome. Our results suggest that fusions have occurred between macro and microchromosomes or between microchromosomes, leading to the observed reduction in diploid number in the family Podocnemididae.
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Affiliation(s)
- Manoella Gemaque Cavalcante
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brasil
| | - Carlos Eduardo Matos Carvalho Bastos
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brasil
| | - Cleusa Yoshiko Nagamachi
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brasil
| | - Julio Cesar Pieczarka
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brasil
| | - Marcelo Ricardo Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brasil
| | - Renata Coelho Rodrigues Noronha
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brasil
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