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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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The Adenine/Thymine Deleterious Selection Model for GC Content Evolution at the Third Codon Position of the Histone Genes in Drosophila. Genes (Basel) 2021; 12:genes12050721. [PMID: 34065869 PMCID: PMC8150595 DOI: 10.3390/genes12050721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 12/02/2022] Open
Abstract
The evolution of the GC (guanine cytosine) content at the third codon position of the histone genes (H1, H2A, H2B, H3, H4, H2AvD, H3.3A, H3.3B, and H4r) in 12 or more Drosophila species is reviewed. For explaining the evolution of the GC content at the third codon position of the genes, a model assuming selection with a deleterious effect for adenine/thymine and a size effect is presented. The applicability of the model to whole-genome genes is also discussed.
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Insights into the karyotype evolution and speciation of the beetle Euchroma gigantea (Coleoptera: Buprestidae). Chromosome Res 2018. [PMID: 29524007 DOI: 10.1007/s10577-018-9576-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Euchroma Dejean, 1833 (Buprestidae: Coleoptera) is a monotypic genus comprising the species Euchroma gigantea, with populations presenting a degree of karyotypic variation/polymorphism rarely found within a single taxonomic (specific) unit, as well as drastically incompatible meiotic configurations in populations from extremes of the species range. To better understand the complex karyotypic evolution of E. gigantea, the karyotypes of specimens from five populations in Brazil were investigated using molecular cytogenetics and phylogenetic approaches. Herein, we used FISH with histone genes as well as sequencing of the COI to determine differential distribution of markers and relationships among populations. The analyses revealed new karyotypes, with variability for chromosome number and morphology of multiple sex chromosome mechanisms, occurrence of B chromosome variants (punctiform and large ones), and high dispersion of histone genes in different karyotypes. These data indicate that chromosomal polymorphism in E. gigantea is greater than previously reported, and that the species can be a valuable model for cytogenetic studies. The COI phylogenetic and haplotype analyses highlighted the formation of three groups with chromosomally polymorphic individuals. Finally, we compared the different karyotypes and proposed a model for the chromosomal evolution of this species. The species E. gigantea includes at least three cytogenetically polymorphic lineages. Moreover, in each of these lineages, different chromosomal rearrangements have been fixed. Dispersion of repetitive sequences may have favored the high frequency of these rearrangements, which could be related to both adaptation of the species to different habitats and the speciation process.
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Siviero F, Rezende-Teixeira P, Andrade AD, Santelli RV, Machado-Santelli GM. The histone genes cluster in Rhynchosciara americana and its transcription profile in salivary glands during larval development. Genet Mol Biol 2016; 39:580-588. [PMID: 27727361 PMCID: PMC5127150 DOI: 10.1590/1678-4685-gmb-2015-0306] [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: 11/24/2015] [Accepted: 02/16/2016] [Indexed: 11/22/2022] Open
Abstract
In this work we report the characterization of the Rhynchosciara americana histone genes cluster nucleotide sequence. It spans 5,131 bp and contains the four core histones and the linker histone H1. Putative control elements were detected. We also determined the copy number of the tandem repeat unit through quantitative PCR, as well as the unequivocal chromosome location of this unique locus in chromosome A band 13. The data were compared with histone clusters from the genus Drosophila, which are the closest known homologues.
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Affiliation(s)
- Fábio Siviero
- Departamento de Biologia Celular e Desenvolvimento, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Paula Rezende-Teixeira
- Departamento de Biologia Celular e Desenvolvimento, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Alexandre de Andrade
- Departamento de Biologia Celular e Desenvolvimento, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Roberto Vicente Santelli
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Glaucia Maria Machado-Santelli
- Departamento de Biologia Celular e Desenvolvimento, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil
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Nakashima Y, Higashiyama A, Ushimaru A, Nagoda N, Matsuo Y. Evolution of GC content in the histone gene repeating units from Drosophila lutescens, D. takahashii and D. pseudoobscura. Genes Genet Syst 2016; 91:27-36. [PMID: 27021916 DOI: 10.1266/ggs.15-00018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A subset of histone genes (H1, H2A, H2B and H4), which are encoded along with H3 within repeating units, were analyzed in Drosophila lutescens, D. takahashii and D. pseudoobscura to investigate the evolutionary mechanisms influencing this multigene family and its GC content. Nucleotide divergence among species was more marked in the less functional regions. A strong inverse relationship was observed between the extent of evolutionary divergence and GC content within the repeating units; this finding indicated that the functional constraint on a region must be associated with both divergence and GC content. The GC content at 3(rd) codon positions in the histone genes from D. lutescens and D. takahashii was higher than that from D. melanogaster, while that from D. pseudoobscura was similar. These evolutionary patterns were similar to those of H3 gene regions. Based on these findings, we propose that the evolutionary mechanisms governing nucleotide content at 3(rd) codon positions tend to eliminate A and T nucleotides more frequently than G and C nucleotides. These changes might be the consequence of negative selection and would result in GC-rich 3(rd) codon positions. In addition, interspecific differences in GC content, which exhibited the same pattern for all histone genes, could be explained by different selection efficiencies that result from changes in population size.
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Affiliation(s)
- Yuko Nakashima
- Laboratory of Adaptive Evolution, Institute of Socio-Arts and Sciences, Tokushima University
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Daniel SN, Penitente M, Silva DMZA, Hashimoto DT, Ferreira DC, Foresti F, Porto-Foresti F. Organization and Chromosomal Distribution of Histone Genes and Transposable Rex Elements in the Genome of Astyanax bockmanni (Teleostei, Characiformes). Cytogenet Genome Res 2015; 146:311-8. [PMID: 26618348 DOI: 10.1159/000441613] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2015] [Indexed: 11/19/2022] Open
Abstract
An important feature of eukaryotic organisms is the number of different repetitive DNA sequences in their genome, a feature not observed in prokaryotes. These sequences are considered to be important components for understanding evolutionary mechanisms and the karyotypic differentiation processes. Thus, we aimed to physically map the histone genes and transposable elements of the Rex family in 6 fish populations of Astyanax bockmanni. FISH results using a histone H1 gene probe showed fluorescent clusters in 2 chromosome pairs in all 6 samples analyzed. In contrast, FISH with a histone H3 probe showed conspicuous blocks in 4 chromosomes in 5 of the 6 populations analyzed. The sixth population revealed 7 chromosomes marked with this probe. Probes for the transposable elements Rex1 and Rex6 showed small sites dispersed on most chromosomes of the 6 populations, and the Rex3 element is located in a big block concentrated in only 1 acrocentric chromosome of 2 populations. As for the other populations, a Rex3 probe showed large blocks in more than 1 chromosome. Fish from Alambari and Campo Novo Stream have Rex3 elements dispersed along most of the chromosomes. Additionally, the conspicuous signals of Rex1, Rex3, and Rex6 were identified in the acrocentric B microchromosome of A. bockmanni found only in individuals of the Alambari River. Thus, we believe that different mechanisms drive the spread of repetitive sequences among the populations analyzed, which appear to be organized differently in the genome of A. bockmanni. The presence of transposable elements in the B chromosome also suggests that these sequences could play a role in the origin and maintenance of the supernumerary element in the genome of this species.
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Affiliation(s)
- Sandro N Daniel
- Departamento de Cix00EA;ncias Biolx00F3;gicas, Faculdade de Cix00EA;ncias, Universidade Estadual Paulista (UNESP), Bauru, Brazil
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Gusso Goll L, Matiello RR, Artoni RF, Vicari MR, Nogaroto V, de Barros AV, Almeida MC. High-Resolution Physical Chromosome Mapping of Multigene Families in Lagria villosa (Tenebrionidae): Occurrence of Interspersed Ribosomal Genes in Coleoptera. Cytogenet Genome Res 2015; 146:64-70. [PMID: 25997861 DOI: 10.1159/000382047] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2015] [Indexed: 11/19/2022] Open
Abstract
The organization and mapping of multigene families can produce useful genetic markers, and its use may elucidate the mechanisms of karyotype variation and genomic organization in different groups of eukaryotes. To date, few species of Coleoptera have been analyzed using FISH for the location of multigene families. The purpose of this study was to use high-resolution chromosome mapping to establish the genomic organization of the 18S rDNA, 5S rDNA and histone H3 gene families in Lagria villosa. FISH was performed using 18S rDNA, 5S rDNA and histone H3 probes prepared via PCR labeling. Fiber-FISH for 18S and 5S rDNA indicated that both ribosomal elements are colocalized in the short arm of chromosome 4. Additionally, FISH, using the histone H3 probe, revealed that this sequence is found in only one autosomal pair and did not colocalize with rDNA. Fiber-FISH with 5S and 18S probes, used to improve the mapping resolution of these regions, showed that both genes are closely interspersed with varying amounts of both DNA classes.
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Affiliation(s)
- Leonardo Gusso Goll
- Departamento de Biologia Estrutural, Molecular e Genx00E9;tica, Px00F3;s-Graduax00E7;x00E3;o em Cix00EA;ncias Biolx00F3;gicas, Biologia Evolutiva, Setor de Cix00EA;ncias Biolx00F3;gicas e da Sax00FA;de, Ponta Grossa, Brazil
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Utsunomia R, Pansonato-Alves JC, Scacchetti PC, Oliveira C, Foresti F. Scattered organization of the histone multigene family and transposable elements in Synbranchus. Genet Mol Biol 2013; 37:30-6. [PMID: 24688288 PMCID: PMC3958323 DOI: 10.1590/s1415-47572014000100007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/03/2013] [Indexed: 11/21/2022] Open
Abstract
The fish species Synbranchus marmoratus is widely distributed throughout the Neotropical region and exhibits a significant karyotype differentiation. However, data concerning the organization and location of the repetitive DNA sequences in the genomes of these karyomorphs are still lacking. In this study we made a physical mapping of the H3 and H4 histone multigene family and the transposable elements Rex1 and Rex3 in the genome of three known S. marmoratus karyomorphs. The results indicated that both histone sequences seem to be linked with one another and are scattered all over the chromosomes of the complement, with a little compartmentalization in one acrocentric pair, which is different from observations in other fish groups. Likewise, the transposable elements Rex1 and Rex3 were also dispersed throughout the genome as small clusters. The data also showed that the histone sites are organized in a differentiated manner in the genomes of S. marmoratus, while the transposable elements Rex1 and Rex3 do not seem to be compartmentalized in this group.
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Affiliation(s)
- Ricardo Utsunomia
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho", Botucatu, SP, Brazil
| | - José Carlos Pansonato-Alves
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho", Botucatu, SP, Brazil
| | - Priscilla Cardim Scacchetti
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho", Botucatu, SP, Brazil
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho", Botucatu, SP, Brazil
| | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho", Botucatu, SP, Brazil
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Hashimoto D, Ferguson-Smith M, Rens W, Prado F, Foresti F, Porto-Foresti F. Cytogenetic Mapping of H1 Histone and Ribosomal RNA Genes in Hybrids between Catfish SpeciesPseudoplatystoma corruscansandPseudoplatystoma reticulatum. Cytogenet Genome Res 2013. [DOI: 10.1159/000345299] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Roehrdanz R, Heilmann L, Senechal P, Sears S, Evenson P. Histone and ribosomal RNA repetitive gene clusters of the boll weevil are linked in a tandem array. INSECT MOLECULAR BIOLOGY 2010; 19:463-471. [PMID: 20456508 DOI: 10.1111/j.1365-2583.2010.01006.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Histones are the major protein component of chromatin structure. The histone family is made up of a quintet of proteins, four core histones (H2A, H2B, H3 & H4) and the linker histones (H1). Spacers are found between the coding regions. Among insects this quintet of genes is usually clustered and the clusters are tandemly repeated. Ribosomal DNA contains a cluster of the rRNA sequences 18S, 5.8S and 28S. The rRNA genes are separated by the spacers ITS1, ITS2 and IGS. This cluster is also tandemly repeated. We found that the ribosomal RNA repeat unit of at least two species of Anthonomine weevils, Anthonomus grandis and Anthonomus texanus (Coleoptera: Curculionidae), is interspersed with a block containing the histone gene quintet. The histone genes are situated between the rRNA 18S and 28S genes in what is known as the intergenic spacer region (IGS). The complete reiterated Anthonomus grandis histone-ribosomal sequence is 16,248 bp.
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Affiliation(s)
- R Roehrdanz
- Biosciences Research Laboratory, Red River Valley Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Fargo, ND 58105, USA.
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